RetrogeneDB ID: retro_gacu_6

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupIX:19645997..19646999(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000019821
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: gtf3ab
• Ensembl ID: ENSGACG00000003107
• Aliases: None
• Description: general transcription factor IIIA, b [Source:ZFIN;Acc:ZDB-GENE-030131-7698]

Sequence

>retro_gacu_6
ATGGAGAGCAAACGGGAGCCGCTCAGACGGTACATCTGCTCGTTCGCGGGCTGCCCGGCGGCCTACAACAGGCAGTGGAA
GCTCGACGCGCACCTGTGCAAACACACCGGCGTGAAGCCGCACGCGTGCGCGCGCTGCGCCAAGTCCTTCTGCACCTCGT
ACCACCTGGCGCGCCACGCGCTCAGCCACAGCGGCGAGAAGCCCTTCCGGTGCCCCGAGGACGGCTGCGGGGAGGCCTTC
ACCACCGCCGCCAACCGCGCCCGGCACGTGGGCCGCGTGCACGCGCCCGGCCGGAAGAGGACGTACGCGTGCAGGTTCGA
GGGCTGCGCGCTCGAGTTCCGGAAGAACAAGCAGCTGAAGGCCCACGTGTGCGAGCGCCACGGCCCGCCGGCCGGCCACC
CGTGCACGCACGAGGGCTGCGCCATGCGCTTCGCCGTGCCCAGCAAGCTGAGGCGGCACGAGAAGGTGCACCGGGGGTAC
CCGTGCGCGGACGAGGGCTGCGGCTTCACCGGGAAGACGTGGACCGAGTACCTGCGGCACCGGAAGGAGCGGCACCGGCC
CGTCCTGCGGTGCGACCAGTGCGACAAGTCCTTCCGGGACTCGTGGTTCCTGCAGCAGCACCGCCGCGTCCACTCGGAGA
CGCGCGTGGTCCTCCGGTGCCCGAGGGCCGGCTGCGAGCGCTCCTTCACCACCGCCTTCAACCTGCAGAGCCACGTCGGC
TCCTTCCACGAGGAGCGCCGGCCCTTCGCCTGCGCGCACGCCGGCTGCGGGAAGACGTTCGCCATGAAGCAGAGCCTCCG
GCGCCACAGCGTCGCCCACGACCCGGACAAGAAGAAGCTGGCCAAGGCCCGGCCCAAGAGGTCGCTGGCCTCCAGGCTGA
GCGGCTACGGCGGCACGGCGGCGGGGAAGCCGGCCGAGGAGTCCGGCCCGCCCGGCCCCGTCGAGCTGGTGTCCCTCCTG
CAGGACACGTCTCTGCTGTGCGGCCCCGCCGTGGACACCCAC

Alignment

ORF - retro_gacu_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.52 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGERLQSPKMYICSFSDCKAAFSKSWKLEAHLCKHTGLKPFSCENCDQSFCTRYQLTKHELHHSGEKTHK
          M.........YICSF..C.AA....WKL.AHLCKHTG.KP..C..C..SFCT.Y.L..H.L.HSGEK...
Retrocopy MESKREPLRRYICSFAGCPAAYNRQWKLDAHLCKHTGVKPHACARCAKSFCTSYHLARHALSHSGEKPFR

Parental  CPADGCSRVFVTKGSMKNHVARAHQQQEKQ-YPCDHQGCGKGFNKRNQLKAHKCE-HLQILPFPCTISGC
          CP.DGC...F.T......HV.R.H....K..Y.C...GC...F.K..QLKAH.CE.H......PCT..GC
Retrocopy CPEDGCGEAFTTAANRARHVGRVHAPGRKRTYACRFEGCALEFRKNKQLKAHVCERHGPPAGHPCTHEGC

Parental  TKALPTHGKLKRHEKVHRGYQCEQEACPFQGNTWTEYLQHRKE-HKVKVQCGECKKLFNNAWFLHQHGLR
          ........KL.RHEKVHRGY.C..E.C.F.G.TWTEYL.HRKE.H.....C..C.K.F...WFL.QH..R
Retrocopy AMRFAVPSKLRRHEKVHRGYPCADEGCGFTGKTWTEYLRHRKERHRPVLRCDQCDKSFRDSWFLQQH-RR

Parental  VHAGEKPQQQLLCPKEGCGKRFTRPFNLESHVLGDHEGKKPFSCVYAGCGKSFAMKESLWRHGVVHDVTK
          VH........L.CP..GC...FT..FNL.SHV...HE...PF.C..AGCGK.FAMK.SL.RH.V.HD..K
Retrocopy VHS--ETRVVLRCPRAGCERSFTTAFNLQSHVGSFHEERRPFACAHAGCGKTFAMKQSLRRHSVAHDPDK

Parental  KKLKKVPKKKT
          KKL.K...K..
Retrocopy KKLAKARPKRS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_6 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_6 has 0 orthologous retrocopies within teleost group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019373	1 retrocopy	retro_cjac_3066,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866,
Felis catus	ENSFCAG00000006982	1 retrocopy	retro_fcat_426,
Gasterosteus aculeatus	ENSGACG00000003107	1 retrocopy	retro_gacu_6 ,
Gorilla gorilla	ENSGGOG00000008407	1 retrocopy	retro_ggor_2622,
Microcebus murinus	ENSMICG00000014763	1 retrocopy	retro_mmur_368,
Macaca mulatta	ENSMMUG00000009029	1 retrocopy	retro_mmul_1632,
Nomascus leucogenys	ENSNLEG00000000331	2 retrocopies	retro_nleu_1134, retro_nleu_214,
Oreochromis niloticus	ENSONIG00000014134	1 retrocopy	retro_onil_8,
Vicugna pacos	ENSVPAG00000004995	1 retrocopy	retro_vpac_456,