A list of weird gene annotations or things that break bioinformatics assumptions
Evidence given for a 1bp length exon in Arabadopsis and different splicing models are discussed
http://www.nature.com/articles/srep18087
Another 1bp exon is discussed here https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177959
The phenomenon of recursive splicing can remove sequences progressively inside an intron, so there can exist "0bp exons" that are just the splice-site sequences pasted together.
"To identify potential zero nucleotide exon-type ratchet points, we parsed the RNA-Seq alignments to identify novel splice junctions where the reads mapped to an annotated 5' splice site and an unannotated 3' splice site, and the genomic sequence at the 3' splice site junction was AG/GT"
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529404/
A twintron is essentially an intron-within-an-intron, which could be formed by a mobile element (TE) insertion. The original idea is that the internal intron has to be spliced first before the outer one is, but several classes have been discovered. See https://en.wikipedia.org/wiki/Twintron
Satellite DNA study uncovers megabase scale introns https://www.biorxiv.org/content/early/2018/12/11/493254
An example in this paper kl-3 spans 4.3 million bp
In human, an example is Dystrophin spanning 2.3 million bp
The process of "backsplicing" circularizes RNAs. There can be alternative backsplicing too
See https://academic.oup.com/nar/article/48/4/1779/5715065
"Dscam has 24 exons; exon 4 has 12 variants, exon 6 has 48 variants, exon 9 has 33 variants, and exon 17 has two variants. The combination of exons 4, 6, and 9 leads to 19,008 possible isoforms with different extracellular domains (due to differences in Ig2, Ig3 and Ig4). With two different transmembrane domains from exon 17, the total possible protein products could reach 38,016 isoforms"
Ref https://en.wikipedia.org/wiki/DSCAM https://www.wikigenes.org/e/gene/e/35652.html
"The main distinction between frameshifts resulting from mutation and those resulting from ribosomal frameshifting is that the latter are controlled by various mechanisms found in codons...Certain codons take longer to translate, because there are not equal amounts of tRNA of that particular codon in the cytosol..." which leads to ribosomal slippage into an alternative reading frame.
Ref https://en.wikipedia.org/wiki/Translational_frameshift
https://www.sciencedirect.com/topics/neuroscience/ribosomal-frameshifting
"Ribosome hopping involves ribosomes skipping over large portions of an mRNA without translating them" Ref https://pubmed.ncbi.nlm.nih.gov/24711422/
"Eukaryotic mRNAs are typically monocistronic and translated only a single Open Reading Frame. Some viruses can reinititate translation after translation termination using an IRES" Ref https://en.wikipedia.org/wiki/Internal_ribosome_entry_site
In some cases a stop codon is not interpreted as such. When it is interpreted, it is sometimes called "Stop codon readthrough" and can encode for an amino acid. The amino acid Selenocysteine is coded for by a stop codon (https://en.wikipedia.org/wiki/Selenocysteine) and Pyrrolysine also is coded for by a stop codon (https://en.wikipedia.org/wiki/Pyrrolysine). Both of these lie outside the conventional 20 amino acid code
There are several other stop codon modifications described here https://www.nature.com/articles/nrg3963
Selenocysteine can be coded via a SECIS sequence https://en.wikipedia.org/wiki/SECIS_element and resulting products are called selenoproteins
Pyrolysine is coded through a pyIT tRNA gene that interprets the amber stop codon as pyrolysine
See also this Ensembl blog on annotating readthrough transcription which joins multiple genes http://www.ensembl.info/2019/02/11/annotating-readthrough-transcription-in-ensembl/
RNA-seq often makes extremely compelling cases for two-or-more different genes to be conjoined by splicing
Some algorithms e.g. mikado https://academic.oup.com/gigascience/article/7/8/giy093/5057872 try to avoid this calling it artifactual fusion/chimera that can be due to some tandem duplication but it does seem to be very prevalent in real data sets
The standard splice site recognition sequence is an GU in RNA (or GT in DNA) on the 5' end and AG on the 3' (remember, goes 5' to 3'). This recognition motif accounts for the large majority of splicing. If a different sequence is used it is said that a different spliceosome complex is being used "minor spliceosome"
https://en.wikipedia.org/wiki/Minor_spliceosome
Some exons harbor internal splice sites (e.g. they get split) that might be unused or underused and are so called "cryptic splice sites"
Review article https://academic.oup.com/nar/article/39/14/5837/1382796
The snaptron project from Ben Langmead analyzed huge amounts of RNA-seq public data and found many types of these cryptic splicing http://snaptron.cs.jhu.edu/
NAGNAG, GYNGYN, repeats of the splicing signal cause modified transcriptional behavior
"Another mechanism introducing small variations to protein isoforms is wobble splicing. Here, a GYN repeat at the donor splice site (5’ splice site; Y stands for C or T and N stands for A, C, G, or T) or an NAG repeat at the acceptor splice site (3’ splice site) leads to subtle length variations in the spliced transcripts and finally to alternative isoforms differing in few amino acids." ref https://onlinelibrary.wiley.com/doi/full/10.1002/bies.201900066?af=R
Intron retention (IR) is a phenomenon where intron sequence is preserved, or doesn't get spliced out, in mature RNA
It can occur in both abnormal and normal biological conditions. Transcript with IR often undergo nonsense-mediated decay.
Normally RNA is spliced by a specialized protein complex called a spliceosome. There is also self-splicing RNA where the splicing is done itself with RNA
The Group 1 intron type mentioned above is a "self splicing" function of RNA not requiring external spliceosome https://en.wikipedia.org/wiki/Group_I_catalytic_intron
Group 2 and group 3 with similar but different mechanisms also exist
The only types of introns known conventionally in archaea are called "bulge-helix-bulge" but recently Group 1 introns have been discovered https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky414/4999243
Many eukaryotes use the "standard genetic code" for changing codons to amino acids but frequent changes occur across the domains of life. The NCBI "genetic code" table lists several of these and contains recent additions for particular species
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG31
One article explains how alternative genetic codes work https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207430/
The 5' and 3' UTR (un-translated region) is a part of the pre-mRNA at the start and end of the gene respectively that is spliced away in the mature RNA
This blog post by Ensembl shows how they annotate UTR and 19kb 3' UTR in Grin2b http://www.ensembl.info/2018/08/17/ensembl-insights-how-are-utrs-annotated/
They have many important functionality and are often targets of miRNA binding which leads to degradation.
A poly-A tail is added to the pre-mRNA on the 3' end of the transcript to protect it from degradation. The A signal is not part of the genome https://en.wikipedia.org/wiki/Polyadenylation
A survey of poly-A using Oxford Nanopore found some transcript isoforms with 450bp ENST00000581230, with intron retention being a possible correlate of having a longer poly-A tails https://www.biorxiv.org/content/early/2018/11/09/459529.article-info
Intronic polyadenylation can also occur https://www.nature.com/articles/s41467-018-04112-z it is revealed by 3'-seq
Circularized chromosomes should be unsurprising to anyone working with plasmids and many prokaryotic genomes but for gene annotation formats which use linear coordinates, representing anything wrapping around the origin is challenging.
Many genomic viewers do not do this well. For GFF format this is done by making the end go past the end of the genome. Below, the genome is 6407 bp in length, but the CDS feature extends past this and sets Is_circular=true
##gff-version 3.2.1
# organism Enterobacteria phage f1
# Note Bacteriophage f1, complete genome.
J02448 GenBank region 1 6407 . + . ID=J02448;Name=J02448;Is_circular=true;
J02448 GenBank CDS 6006 7238 . + 0 ID=geneII;Name=II;Note=protein II;
The replication of the 2 micron plasmid found in Saccharomyces cerevisiae relies on a programmed DNA rearrangement; in any population of cells two different states of the 2 micron plasmid can be expected and these will interconvert in later generations. Reference: https://pubmed.ncbi.nlm.nih.gov/23541845/
It is possible for gene sequences to overlap possibly in alternate coding frames
https://en.wikipedia.org/wiki/Overlapping_gene
Some articles
- The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase https://www.ncbi.nlm.nih.gov/m/pubmed/30552341/
- Overlapping genes in natural and engineered genomes https://www.nature.com/articles/s41576-021-00417-w
- Uncovering de novo gene birth in yeast using deep transcriptomics https://www.nature.com/articles/s41467-021-20911-3
The gene Jingwei is a chimera of two genes, alcohol dehydrogenage and yellow emperor. Many chimeras are damaging but this has been selected for
http://www.pnas.org/content/101/46/16246
"About 70% of C. elegans mRNAs are trans-spliced to one of two 22 nucleotide spliced leaders. SL1 is used to trim off the 5' ends of pre-mRNAs and replace them with the SL1 sequence. This processing event is very closely related to cis-splicing, or intron removal."
The region that is spliced out is called an outron
http://www.wormbook.org/chapters/www_transsplicingoperons/transsplicingoperons.html
Although prevalent in bacteria, operons are not common in eukaryotes. However, they are common in C. elegans specifically. "A characteristic feature of the worm genome is the existence of genes organized into operons. These polycistronic gene clusters contain two or more closely spaced genes, which are oriented in a head to tail direction. They are transcribed as a single polycistronic mRNA and separated into individual mRNAs by the process of trans-splicing"
http://www.wormbook.org/chapters/www_overviewgenestructure.2/genestructure.html
A pre-mRNA from both strands of DNA eri6 and eri7 are combined to create eri-6/7
Source http://forums.wormbase.org/index.php?topic=1225.0 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756026/
An example from drosophila, C. elegans, and rat shows a gene with a 5' exon being shared between two genes
Source http://forums.wormbase.org/index.php?topic=1225.0 https://www.fasebj.org/doi/full/10.1096/fj.00-0313rev
An example here shows 5'UTR exons shared across different olfactory receptor genes ("Some OR genes share 5'UTR exons")
https://www.biorxiv.org/content/biorxiv/early/2019/09/19/774612.full.pdf
A possible horizontal gene transfer from bacteria to eukaryotes is found in an insect that feeds on coffee beans. Changes that the gene had to undergo are covered (added poly-A tail, shine-dalgarno sequence deleted)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306691/
also https://www.cell.com/cell/fulltext/S0092-8674(19)30097-2
This phenomena of epigenetic modifications being passed down across generations garners a lot of media attention and scientific attention. The idea of it being influenced by what "one does in life" such as experiencing famine is also very interesting.
https://en.wikipedia.org/wiki/Transgenerational_epigenetic_inheritance
There are skeptics also http://www.wiringthebrain.com/2018/07/calibrating-scientific-skepticism-wider.html but the science is hopefully what speaks for itself
"The most common start codons for known Escherichia coli genes are AUG (83% of genes), GUG (14%) and UUG (3%)"
"Here, we systematically quantified translation initiation of green fluorescent protein (GFP) from all 64 codons and nanoluciferase from 12 codons on plasmids designed to interrogate a range of translation initiation conditions."
https://www.sciencedaily.com/releases/2017/02/170221080506.htm
Testing in eukaryotes has also revealed alternative starts being viable https://en.wikipedia.org/wiki/Start_codon#Eukaryotes
The standard DNA double stranded helix is called B-DNA (https://genome.cshlp.org/content/early/2018/11/06/gr.241257.118.abstract)
Other geometries are possible https://en.wikipedia.org/wiki/Nucleic_acid_double_helix#Helix_geometries
Complex structures such as four stranded quadruplex have been found that could have biological functions
See https://news.cnrs.fr/articles/unlocking-the-secrets-of-four-strand-dna
Some organisms, famously insect salivary glands, create many copies of genes through multiple phases of incomplete DNA replication https://en.wikipedia.org/wiki/Polytene_chromosome
Figure source https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768140/
"Polytene chromosomes are produced by endoreplication, in which chromosomal DNA undergoes mitotic replication, but the strands do not separate. Ten rounds of endoreplication produces 2^10 = 1,024 DNA strands, which when arranged alongside of each other produce distinctive banding patterns. Endoreplication occurs in cells of the larval salivary glands of many species of Diptera, and increases production of mRNA for Glue Protein that the larvae use to anchor themselves to the walls of (for example) culture vials." from https://www.mun.ca/biology/scarr/Polytene_Chromosomes.html
https://www.hindawi.com/journals/jna/2011/408053/tab1/
updated link on hindawi should point here http://mods.rna.albany.edu/mods/
RNA editing is a post-transcriptional modification to the mRNA to change the bases. A-to-I editing is a common one in mammals which would make the RNA, when sequenced, to have a G instead of an A. So WGS would not show a SNP but the RNA-seq would appear to have A->G.
Other editing occurs also https://en.wikipedia.org/wiki/RNA_editing
Maternal RNAs being active against the zygote (e.g. https://en.wikipedia.org/wiki/Maternal_to_zygotic_transition) and lead to complex transgenerational effects
A lncRNA VELUCT almost flies under the radar in a lung cancer screen due to being very lowly expressed such that it is "below the detection limit in total RNA from NCI-H460 cells by RT-qPCR as well as RNA-Seq", however this study confirms it as a factor in experiments
https://www.ncbi.nlm.nih.gov/pubmed/28160600?dopt=Abstract
Note that X inactivation relies on relatively lowly expressed RNA also https://twitter.com/mitchguttman/status/1454256452990734336
X chromosome inactivation is produced by a non-coding transcript called Xist is transcribed on the X that is being inactivated and actually coats the X chromosome with itself. An anti-sense transcript called Tsix regulates Xist
https://en.wikipedia.org/wiki/XIST
https://en.wikipedia.org/wiki/X-inactivation#Xist_and_Tsix_RNAs
There are many types of RNA some more weird an exotic than others, a large list https://en.wikipedia.org/wiki/List_of_RNAs
Some are named based on where they are expressed or active
Others are uniquely shaped. There are also circular RNA for example https://en.wikipedia.org/wiki/Circular_RNA
Small and long non coding RNAs often fold into important structural shapes
This is probably obvious to many people who work on proteins but while the genome has almost all genes starting with a start codon which produces methionine, this is often post translationally removed https://en.m.wikipedia.org/wiki/Methionyl_aminopeptidase
An intein is like an intron but for a protein, a segment of protein that is spliced out https://en.wikipedia.org/wiki/Intein
See section here https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#pathological-cases
Viral sequences can create a polyprotein which is fully transcribed and translated before being cleaved by a protease. In some viruses (such as coronaviruses) their translation involves ribosomal frameshifting.
Dengue, HIV, flu, etc. use this
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6040172/ https://www.sciencedirect.com/science/article/abs/pii/S0959440X15000597
Or "How a quarter of the cow genome came from snakes" http://phenomena.nationalgeographic.com/2013/01/01/how-a-quarter-of-the-cow-genome-came-from-snakes/
Source http://www.pnas.org/content/110/3/1012.full
Transposon activity can mutate DNA as it will insert itself into the genome. The genome has functions for keeping transposons inactive. However, evidence shows that the LINE1 is important for embryonic development.
https://www.ucsf.edu/news/2018/06/410781/not-junk-jumping-gene-critical-early-embryo
VDJ recombination is a process of somatic recombination (using "recombination signal sequences") that is done in immune cells. Different gene segments of class "V", class "D", and class "J" exons (sometimes to exons are referred to as "genes" themselves) are somatically rearranged into coherent genes that are then transcribed and immune diversity. Splicing at the DNA level is not precise, with terminal transferase adding random nucleotides to further diversify the sequences
https://en.wikipedia.org/wiki/V(D)J_recombination
The MHC region is a very polymorphic region of the genome on chr6. I'm not personally aware of the intricacies of MHC beyond that it is a unique contributor of some additional hg38 alternative loci/contigs
What is a tandem duplication? Why does it occur?
Factors can include
- replication slippage
- retrotransposition
- unequal crossing over (UCO).
- imperfect repair of double-strand breaks by nonhomologous end joining (NHEJ).
Ref https://academic.oup.com/mbe/article/24/5/1190/1038942
The LIF gene has many copies in Elephant but many are non-functional. One copy can be "turned back on" and play a role in cancer protection. They call this a "zombie gene"
https://www.cell.com/cell-reports/fulltext/S2211-1247(18)31145-8
https://www.sciencealert.com/lif6-pseudogene-elephant-tumour-suppression-solution-petos-paradox
It has been shown that some intron sequences can enhance expression similar to how promoter sequences work https://en.wikipedia.org/wiki/Intron-mediated_enhancement
The first intron of the UBQ10 gene in Arabidopsis exhibits IME, and "the sequences responsible for increasing mRNA accumulation are redundant and dispersed throughout the UBQ10 intron" http://www.plantcell.org/content/early/2017/04/03/tpc.17.00020.full.pdf+html
The classic peppered moth phenotype is a intron TE insertion https://wp.unil.ch/genomeeee/2016/12/16/peppered-moth-melanism-mutation-is-a-transposable-element/
Wikipedia https://en.wikipedia.org/wiki/Promoter_(genetics)#Bidirectional_(mammalian)
"Bidirectional promoters are a common feature of mammalian genomes. About 11% of human genes are bidirectionally paired."
"The two genes are often functionally related, and modification of their shared promoter region allows them to be co-regulated and thus co-expressed"
Older men can have a mosaic loss of the Y chromosome in blood samples
https://www.karger.com/Article/FullText/508564 (found from https://www.biostars.org/p/9482437/)
The latest human genome, for example, downloaded from NCBI, contains a number of Non-ACGT letters in the form of IUPAC codes https://www.bioinformatics.org/sms/iupac.html These represent ambiguous bases.
Here is the incidence of non-ACGT IUPAC letters in the entire human genome GRCh38.p10 NC_000001-24
b: 2
k: 8
m: 8
r: 26
s: 5
w: 14
y: 35
Did you expect that in your bioinformatics software? Note that the mouse genome (GRCm38.p5) as far as I could tell does not contain any non-ACGT IUPAC letters
Due to how dbSNP is creating, an rs SNP ID can occur in multiple places on the genome https://www.biostars.org/p/2323/
In response to hg38 including a colon in sequence names, which conflicts with commonly used representation of a range as chr1:1-100 for example, people analyzed meta-character frequencies in sequence names samtools/hts-specs#291
ENA
# 16927
* 1
, 231
- 122563947
. 521540419
/ 236951
\ 0
: 30181
; 72892
= 186611
@ 3713
| 949
Broad(?)
12 #
527 *
357 ,
1451132 -
1492749 .
86114 /
233731 :
2034 =
17 @
1735713 |
Reference sequences
# 203
% 203
* 525
+ 1
, 496
- 154226
. 1826561
: 1577
= 26
_ 4961932
| 1098333
Note that commas in FASTA names is being suggested as an illegal character because of the supplementary alignment tag in SAM/BAM using comma separated values
Genomes such as wheat have large chromosomes averaging 806Mbp but the BAI file format is limited to 2^29-1 ~ 536Mbp in size (this is due to the binning strategy, the max bin size is listed as 2^29)
The axolotl genome has individual chromosomes that are of size 3.14 Gbp https://genome.cshlp.org/content/29/2/317.long (2019) which is almost as big as the entire human genome
The BAM and CRAM formats can only store 2^31-1 length https://en.wikipedia.org/wiki/2,147,483,647 so bgzip/tabix SAM is used
Just some honorable mentions for largest genome
- Polychaos dubium/Amoeba dubium/Chaos chaos - ~600-1300Gbp (unsequenced, 1968 back of envelope measurement, needs confirmation) https://en.wikipedia.org/wiki/Polychaos_dubium (another ref https://bionumbers.hms.harvard.edu/bionumber.aspx?&id=117342)
- Dinoflagellates - up to 250Gbp (unsequenced, 1987 book referenced in this paper, needs confirmation, has weird chromosome "rod-like" structures) https://www.nature.com/articles/s41588-021-00841-y
- Paris japonica (canopy plant) - ~149Gbp (unsequenced) https://en.wikipedia.org/wiki/Paris_japonica
- Tmesipteris_obliqua (fern) - ~147Gbp (unsequenced) - https://en.wikipedia.org/wiki/Tmesipteris_obliqua
- Marbled lungfish - ~133Gbp (unsequenced) https://en.wikipedia.org/wiki/Marbled_lungfish
- European mistletoe - ~90Gbp (partial sequence) https://onlinelibrary.wiley.com/doi/10.1111/tpj.15558
- Australian lungfish - ~43Gbp (sequenced) https://www.smithsonianmag.com/smart-news/australian-lungfish-has-biggest-genome-ever-sequenced-180976837/
- Axolotl - ~32Gbp (sequenced) https://en.wikipedia.org/wiki/Axolotl
- Coastal redwood - ~26Gbp (sequenced) https://www.ucdavis.edu/climate/news/coast-redwood-and-sequoia-genome-sequences-completed
- Loblolly pine - ~22Gbp (sequenced) https://blogs.biomedcentral.com/on-biology/wp-content/uploads/sites/5/2014/03/genomelog030.jpg
- Wheat genome - ~17Gbp https://academic.oup.com/gigascience/article/6/11/gix097/4561661
Inspired by twitter thread https://twitter.com/PetrovADmitri/status/1506824610360168455
Also see http://www.genomesize.com/statistics.php?stats=entire#stats_top
The CG tag was invented in order to store CIGAR strings longer than 64kb, since n_cigar_opt is a uint16
- Tinman - https://en.wikipedia.org/wiki/Tinman_gene
- Sonic hedgehog (SHH) - https://en.wikipedia.org/wiki/Sonic_hedgehog
- Heart of glass (heg) - https://www.ncbi.nlm.nih.gov/pubmed/14680629
- Dracula (drc) - https://www.ncbi.nlm.nih.gov/pubmed/10985389
- Sleeping Beauty transposon - https://en.wikipedia.org/wiki/Sleeping_Beauty_transposon_system
- Skywalker protein - http://www.ebi.ac.uk/pdbe/entry/search/index?pubmed_id:27669036
- Time for coffee - http://www.plantcell.org/content/15/11/2719.abstract
- WTF - https://www.ebi.ac.uk/interpro/entry/IPR004982 https://www.sciencedaily.com/releases/2017/06/170620093209.htm
- Mothers against decapentaplegic - https://en.wikipedia.org/wiki/Mothers_against_decapentaplegic
- Saxophone (sax) - http://www.sdbonline.org/sites/fly/gene/saxophon.htm
- Beethovan (btv) - http://www.uniprot.org/uniprot/Q0E8P6
- Superman+kryptonite - https://en.wikipedia.org/wiki/Superman_(gene)
- Supervillin (SVIL) - https://www.uniprot.org/uniprot/O95425
- Wishful thinking (wit) - https://www.wikigenes.org/e/gene/e/44096.html
- Doublesex (dsx) - https://en.wikipedia.org/wiki/Doublesex
- Fruitless (fru) - https://en.wikipedia.org/wiki/Fruitless_(gene)
- Transformer (tra) - https://en.wikipedia.org/wiki/Transformer_(gene)
- Gypsy+Flamenco - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1206375/ also described in wiki https://en.wikipedia.org/wiki/Piwi-interacting_RNA#History_and_loci
- Jockey - http://flybase.org/reports/FBgn0015952.html
- Tigger - https://www.omim.org/entry/612972
- Nanog - celtic legend https://www.sciencedaily.com/releases/2003/06/030602024530.htm (source https://twitter.com/EpgntxEinstein/status/1057359656220348417)
- Jerky (jrk) - https://www.genecards.org/cgi-bin/carddisp.pl?gene=JRK
- Hippo (Hpo) - https://www.wikigenes.org/e/gene/e/37247.html
- Dishevelled (Dsh) - https://en.wikipedia.org/wiki/Dishevelled
- Glass bottom boat (gbb) - http://www.sdbonline.org/sites/fly/dbzhnsky/60a-1.htm
- Makes catepillars floppy (mcf) - https://www.pnas.org/content/99/16/10742 (source https://twitter.com/JUNIUS_64/status/1081007886560608256)
- Eyeless http://flybase.org/reports/FBgn0005558.html
- Straightjaket (stj) - http://flybase.org/reports/FBgn0261041.html
- Huluwa http://science.sciencemag.org/content/362/6417/eaat1045 ref https://twitter.com/zhouwanding/status/1065960714978897921
- frameshifts or pseudogene? - check sequence - https://www.ncbi.nlm.nih.gov/gene/?term=24562233%5Buid%5D
- Bad response to refridgeration (brr) https://twitter.com/hitenmadhani/status/1149471071675924481?s=20
- Mindbomb (mib1) - https://www.sdbonline.org/sites/fly/hjmuller/mindbomb1.htm
- β'COP http://flybase.org/reports/FBgn0025724.html (https://twitter.com/DarrenObbard/status/1260613447198412800)
- King-tubby https://www.uniprot.org/uniprot/B0XFQ9 see also tubby https://www.uniprot.org/uniprot/P50586
- fucK https://www.uniprot.org/uniprot/?query=fuck&sort=score
- Halloween genes https://en.wikipedia.org/wiki/Halloween_genes
- VANDAL21 https://www.arabidopsis.org/servlets/TairObject?type=transposon_family&id=139
- HotDog domain - superfamily of genes/proteins https://www.wikidata.org/wiki/Q24785143 https://www.ebi.ac.uk/interpro/entry/IPR029069
- Flower/fwe - https://flybase.org/reports/FBgn0261722.html
- Brahma https://www.sdbonline.org/sites/fly/polycomb/brahma.htm
Sometimes it is not the gene, but the allele that is named
- Bad hair day http://www.informatics.jax.org/allele/MGI:3764934
- Samba, chacha, bossa nova http://www.informatics.jax.org/allele/MGI:3764934
- Yoda http://www.informatics.jax.org/allele/MGI:3797584
Ref https://twitter.com/hmdc_mgi/status/1242893531779391496
Great illustrations of interesting biology, including information about gene names https://twitter.com/vividbiology
Many of the stories behind fly gene nomenclature is available at https://web.archive.org/web/20110716201703/http://www.flynome.com/cgi-bin/search?source=browse including the famous ForRentApartments dot com gene (just kidding but lol https://web.archive.org/web/20110716202150/http://www.flynome.com/cgi-bin/search?storyID=180)
Musing article: "What is in a (gene) name?" https://web.archive.org/web/20180731060319/https://blogs.plos.org/toothandclaw/2012/06/17/whats-in-a-gene-name/