RetrogeneDB ID: retro_pabe_1945

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:45295581..45296201(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB12
• Ensembl ID: ENSPPYG00000002353
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily B, member 12 [Source:HGNC Symbol;Acc:14891]

Sequence

>retro_pabe_1945
AGGAAGCAGTATGACCACTTGGGCGATAACAGGAGCCAGGCAGTCAGGTCTGGCATCGTCACGGGGACTTCTACCACGTC
TTTGAGGCTGACATCTCCCCTGAAGACCTCTTCAACATGTTCTTTGGCAGTGGCTTCCCTTCTAGTAAAGTCCACATCTA
CAGCAATGGCTGCACGAGCTATACCTACCAGCAAAGGCAGGGCTGCAGGGAGAAGCAGAGTGACAGCAGGTTAGGGGTGT
TTGTGCAGCTGATGCCCATCCTCATCCTCATGTCAGCTCTCAGCCAGCTCATGGTCTCCAGTCCACCCTACAGTCTGAGC
CCAAGACTGTTTGTGGGCCACATCACAGGTGAGTCACTGACCACCTGAGTGTCATCTACTATGTGGCAGGCACTTTCTCC
GAGGAGTACACAGGCTCCAGCCTCCAAACAGTCAAACCAAATGTGGAAGATGATTATATCGCCAACCTCTGGAACAACTG
CTAGAAGGAGAAGCAGCAGACAAAAGGCTTGCTGTACCGGGGCCGCTACTTTGGTCACACAGATATGTACCACAAAGCAC
AGAAGATGGGGAGCCCCCTGCTGCAGCTGACTGTCACAGGAGCAGGCCTCCCTGCATGGA

Alignment

ORF - retro_pabe_1945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.42 %
• Parental protein coverage: 51.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKQYDQFGDDKSQAARHG-HGHGDFHRGFEADISPEDLFNMFFGGGFPSSNVHVYSNGRMRYTYQQRQDR
          RKQYD..GD..SQA.R.G.H.HGDF...FEADISPEDLFNMFFG.GFPSS.VH.YSNG...YTYQQRQ..
Retrocopy RKQYDHLGDNRSQAVRSG<HRHGDFYHVFEADISPEDLFNMFFGSGFPSSKVHIYSNGCTSYTYQQRQGC

Parental  RDNQGDGGLGVFVQLMPILILILVSALSQLMVSSPPYSLSPRPSVGHI-HRRVTDHLGVVYYVGDTFSEE
          R..Q.D..LGVFVQLMPILIL...SALSQLMVSSPPYSLSPR..VGHI.HR.VTDHL.V.YYV..TFSEE
Retrocopy REKQSDSRLGVFVQLMPILILM--SALSQLMVSSPPYSLSPRLFVGHI<HR*VTDHLSVIYYVAGTFSEE

Parental  YTGSSLKTVERNVEDDYIANLRNNCWKEKQQKEGLLYRARYFGDTDMYHKAQKMGT-PSCSRLSEVQASL
          YTGSSL.TV..NVEDDYIANL.NNC.KEKQQ..GLLYR.RYFG.TDMYHKAQKMG..P.CS.LS..QASL
Retrocopy YTGSSLQTVKPNVEDDYIANLWNNC*KEKQQTKGLLYRGRYFGHTDMYHKAQKMGS>PCCS*LSQEQASL

Parental  HG
          HG
Retrocopy HG

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	12.99 RPM
SRP007412_cerebellum	0.00 RPM	14.84 RPM
SRP007412_heart	0.00 RPM	7.16 RPM
SRP007412_kidney	0.00 RPM	17.00 RPM
SRP007412_liver	0.00 RPM	10.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1945 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1945 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2273
Pan troglodytes	retro_ptro_1608
Gorilla gorilla	retro_ggor_1691
Callithrix jacchus	retro_cjac_1200

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007303	1 retrocopy	retro_cjac_1200,
Dasypus novemcinctus	ENSDNOG00000009977	1 retrocopy	retro_dnov_866,
Homo sapiens	ENSG00000148719	1 retrocopy	retro_hsap_2273,
Gorilla gorilla	ENSGGOG00000000683	1 retrocopy	retro_ggor_1691,
Macropus eugenii	ENSMEUG00000002024	2 retrocopies	retro_meug_1115, retro_meug_1511,
Pongo abelii	ENSPPYG00000002353	1 retrocopy	retro_pabe_1945 ,
Pongo abelii	ENSPPYG00000014956	3 retrocopies	retro_pabe_1304, retro_pabe_982, retro_pabe_983,
Pan troglodytes	ENSPTRG00000002613	1 retrocopy	retro_ptro_1608,