RetrogeneDB ID: retro_ocun_535

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:135445120..135445655(+)
• Located in intron of: ENSOCUG00000015080

Retrocopy information

• Ensembl ID: ENSOCUG00000010903
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WDR77
• Ensembl ID: ENSOCUG00000007801
• Aliases: None
• Description: WD repeat domain 77 [Source:HGNC Symbol;Acc:29652]

Sequence

>retro_ocun_535
GCTCACGCGGGGCAGGTCACCTGTGTTGCTGCCTCTCCCCATAAGGACTCCGTGTTTCTTTCGTGCAGTGAGGACAATAG
AATTTTACTGTGGGATACCCGCTGTCCCAAGCCAGCATCACAGATGGGCTGCAGTGTCTCTGGCTACATTGCTACTTCGC
TGGCTTGGCATCCTCAGCAAAGTGAAGTCTTTGTCTTTGGTGATGAGAATGGGACTGTCTCTCGTGTGGACACCAAGAGC
GCGGGCTTTGCGCTCAGTTCAGCTGTGCACTCGCAGTGTGTCACTGGGCTGGTGTTCTCGCCCCACACTGCGCCCTTCCT
GGCCTCTCTCAGTGAAGACTGCTCGCTTGCTGTGCCGGACTCCAGCCTTTCCGAGGTGTTTAGGAGCCGGGCTCACAGAG
ACTTTGTTGAGAGATGCTACTTGGTCCCCGCTCAATCACTCCCTCCTTACCACAGTGGGCTGGGACCAGCAAGTCATCCA
CCATGCTGTGCCCACAGAGCCTCTCCCAGCCCCAGGACCTGAGAGTGTGGCCAAG

Alignment

ORF - retro_ocun_535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.89 %
• Parental protein coverage: 52.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AHAGQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQMGCNASGYLATSLAWHPQQSEVFVFAGDE
          AHAGQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQMGC..SGY.ATSLAWHPQQSEVFVF.GDE
Retrocopy AHAGQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQMGCSVSGYIATSLAWHPQQSEVFVF-GDE

Parental  NGTVSLVDTKSAGCALSSAVHSQCVTGLVFSPHSAPFLASLSEDCSLAVLDSSLSEVFRSRAHRDFV-RD
          NGTVS.VDTKSAG.ALSSAVHSQCVTGLVFSPH.APFLASLSEDCSLAV.DSSLSEVFRSRAHRDFV.RD
Retrocopy NGTVSRVDTKSAGFALSSAVHSQCVTGLVFSPHTAPFLASLSEDCSLAVPDSSLSEVFRSRAHRDFV>RD

Parental  ATWSPLNHSLLTTVGWDHQVIHHAVPTEPLPAPGPESVAE
          ATWSPLNHSLLTTVGWD.QVIHHAVPTEPLPAPGPESVA.
Retrocopy ATWSPLNHSLLTTVGWDQQVIHHAVPTEPLPAPGPESVAK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.99 RPM	38.52 RPM
SRP017611_kidney	0.41 RPM	29.39 RPM
SRP017611_liver	0.23 RPM	8.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_535 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_535 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014102	1 retrocopy	retro_btau_1342,
Choloepus hoffmanni	ENSCHOG00000013829	1 retrocopy	retro_chof_2618,
Callithrix jacchus	ENSCJAG00000013344	2 retrocopies	retro_cjac_1166, retro_cjac_3063,
Dasypus novemcinctus	ENSDNOG00000006521	1 retrocopy	retro_dnov_695,
Homo sapiens	ENSG00000116455	1 retrocopy	retro_hsap_2995,
Gorilla gorilla	ENSGGOG00000005208	1 retrocopy	retro_ggor_2076,
Macaca mulatta	ENSMMUG00000003311	1 retrocopy	retro_mmul_1917,
Mus musculus	ENSMUSG00000000561	1 retrocopy	retro_mmus_1120,
Nomascus leucogenys	ENSNLEG00000003918	1 retrocopy	retro_nleu_746,
Oryctolagus cuniculus	ENSOCUG00000007801	1 retrocopy	retro_ocun_535 ,
Pongo abelii	ENSPPYG00000001033	1 retrocopy	retro_pabe_2482,
Pan troglodytes	ENSPTRG00000001098	1 retrocopy	retro_ptro_2026,
Tupaia belangeri	ENSTBEG00000010325	1 retrocopy	retro_tbel_2253,