RetrogeneDB ID: retro_pabe_2482

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:160380811..160381436(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: WDR77
• Ensembl ID: ENSPPYG00000001033
• Aliases: None
• Description: methylosome protein 50 [Source:RefSeq peptide;Acc:NP_001125399]

Sequence

>retro_pabe_2482
CTACCCTCAGTGCTCTCGGCTGTCAGCGGCAGCAAAGACTTCAGCATCAAGGATTGGGACCTTTCTCAGCAGGTGGCACT
GAATTCATACCGATCTCATGTTGGGCAGGTCACCTGTGCTGCTGCCTCTCCCCGCAAGGACTCTGTGTTTCTTTCCTGCA
GTGAGGACAGTAGAATTTTATTCGGCGATACTCTCTGTCCCAAGCCGACGTCACAGGTGGGCTGCAGTGCCTCTGGCTGC
CTTCCCACCTCACTGGCTTGGCATCCTCAGCAAAGTGAAGTCTTCATCTTTGTGATGGGAATGGGACAGTCTCCCTTGTG
GACACCAAGAGAGGGAGAGGTGCCCTTGGCTCAGCTGTACAAGACCAATGTGTCATTGGGCTGGTGTTTTCCTCACACCA
TGTTCCCTTCCCAGCCTCTTACAGCGAAGATGGCTCATTAGCTGTGCTGGACTCCAGCCTTTCTGAGGTGTTTAGAAGCC
GAGGCCACAGTGACCTTGTGAGAGATGCTGCTTGATCCCCACTCAATCACTTTCTGCTTACCACAATGGGCTGGGACCAT
CAGGTCGTCTGCCACAAGTGCCCACAGAACCTCTCCCAGCCCCTGGACCTGAGAGCGTTGCTGAG

Alignment

ORF - retro_pabe_2482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.41 %
• Parental protein coverage: 61.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSSGTQAVSGSKDICIKVWDLAQQVVLNSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPA
          L.S...AVSGSKD..IK.WDL.QQV.LNSYR.H..QVTC.AASP.KDSVFLSCSED.RIL..DT.CPKP.
Retrocopy LPSVLSAVSGSKDFSIKDWDLSQQVALNSYRSHVGQVTCAAASPRKDSVFLSCSEDSRILFGDTLCPKPT

Parental  SQIGCSAPGYLPTSLAWHPQQSEVFVF-GDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLA
          SQ.GCSA.G.LPTSLAWHPQQSEVF.F..D.NGTVSLVDTK.....L.SAV..QCV.GLVFS.H.VPF.A
Retrocopy SQVGCSASGCLPTSLAWHPQQSEVFIF<CDGNGTVSLVDTKRGRGALGSAVQDQCVIGLVFSSHHVPFPA

Parental  SLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHH-IVPTEPLPAPGPASVT
          S.SED.SLAVLDSSLSE.FRS..H.D.VRDA..SPLNH.LLTT.GWDHQVV.H..VPTEPLPAPGP.SV.
Retrocopy SYSEDGSLAVLDSSLSEVFRSRGHSDLVRDAA*SPLNHFLLTTMGWDHQVVCH<QVPTEPLPAPGPESVA

Parental  E
          E
Retrocopy E

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	21.29 RPM
SRP007412_cerebellum	0.00 RPM	18.60 RPM
SRP007412_heart	0.00 RPM	14.90 RPM
SRP007412_kidney	0.00 RPM	28.17 RPM
SRP007412_liver	0.00 RPM	15.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2482 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2482 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2482 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2995
Pan troglodytes	retro_ptro_2026
Macaca mulatta	retro_mmul_1917

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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,