RetrogeneDB ID: retro_pabe_15

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:46128857..46130000(+)
• Located in intron of: ENSPPYG00000011488

Retrocopy information

• Ensembl ID: ENSPPYG00000011493
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000011492
• Aliases: None
• Description: None

Sequence

>retro_pabe_15
ATGGCCGCATCCACTATGTCCATCTGCTCCAGCGACCTGAGCTACAGCAGCCGCGTCTGCCTTCCTGGTTCCTGTGACAC
TTGCTCTGACTCCTGGCAGGTGGACGACTGCCCAGAGAGCTGCTGTGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCCC
CAGCCCCCTGCCTGACCCTCGTCTGCACCCCAGTGAGCTGTGTGTCCAGCCCCTGCTGCCAGGTGACCTGTGAGCCCAAC
CCCTGCCAATCAGGCTGCACCAGCTCCTGCACGCCCTCATTCTGCCAGCAGTCTAGCTGCCAGCCGGCTTGCTGCGCCTC
CTCCCCCTGCCAGCAGTCTTGCTGCGTGCCCGTCTACTGCAAGACTGTCTGCTGCAAGCCTGTGTGCTGTGTGCCCATCT
GCAGTGGGGCTTCTTCATGCTGCCAGCAGTCTAGCTGCCAGCCAGCTTGCTGCACCTCCTCCCCCTGCCAGCAGGCCTGC
TGTGTGCCCATCTGCTGCAAGCCTGTCTGCTCTGGGATTTCCTCTTCGTGCTGCCAGCAGTCTAGCTGTGTGAGCTGTGT
GTCCAGCCCCTGCTGCCAGGCGGTCTGTGAGCCCAGCCCCTGCCAATCAGGCTGCACCAGCTCCTGCACACCCTCGTGCT
GCCAGCAGTCTAGCTGCCAGCCAGCTTGCTGCACCTCCTCCCCCTGCCAGCAGTCCTGCTGCATGCCTGTCTGCTGCAAG
CCCGTCTGCTATGCGCCCACCTGCTCTGATGATTCCTGTTCATGCTGCCAGCAGTCTAGCTGCCAGCCAGCTTGCTGCAC
CTCCTCCCAAAGCCAACAGGGCTGCTGCGTGCCCGTCTGCTGTAAGCCTGTGTGCTGTGTGCCCGTCTGCTCTGGGGCTT
CCACTTCATGCTGCCAGCAGTCTAGCTGCCAGCCAGCTTGCTGCACCACCTCTTGCTGCAGACCCTCCTCCTCTGTGTCC
CTCCTCTGCCGCCCCGTGTGCAGGCCCGCCTGCTGCGTGCCCGTCTCCTCCTGCTGCGCCCCCACCTCCTCCTGCCAGGC
CACCTGCTGCCGCCCGGCGTCCTGTGTGTCTCTCCTTTGCCGCCCCGCAAGCTCCCGCCCAGCCTGCTGTGGCCCCACCT
CAATCCAGAAGTCCAGCTGCTGA

Alignment

ORF - retro_pabe_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.89 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVCSSNLSYGSRVCLAGSCDSYSDSWQVDDCPESCCEPPCCTPSCCAPAPCLTLVCTPVSCVSSPCCQAT
          S.CSS.LSY.SRVCL.GSCD..SDSWQVDDCPESCCEPPCC.PSCCAPAPCLTLVCTPVSCVSSPCCQ.T
Retrocopy SICSSDLSYSSRVCLPGSCDTCSDSWQVDDCPESCCEPPCCAPSCCAPAPCLTLVCTPVSCVSSPCCQVT

Parental  CEPSPQSGCTSSCTPSCCQQSSCQQACCTSSPCQQSCCVPVCCKPVCCVPVCCKPVCCVPICSEDSSSCC
          CEP.P...C.S.CT.SC...S.CQQ..C....C..S.C...CC.PV.C..VCCKPVCCVPICS...SSCC
Retrocopy CEPNP---CQSGCTSSCTP-SFCQQSSCQPACCASSPCQQSCCVPVYCKTVCCKPVCCVPICS-GASSCC

Parental  QQSSCQPACCASSSCQQSCCVPVCCKPVC--YVPSCSEDSSS-CCQQSSCQPACCTSSPCQHTC---CVP
          QQSSCQPACC.SS.CQQ.CCVP.CCKPVC.....SC...SS...C..S.C..A.C..SPCQ..C...C.P
Retrocopy QQSSCQPACCTSSPCQQACCVPICCKPVCSGISSSCCQQSSCVSCVSSPCCQAVCEPSPCQSGCTSSCTP

Parental  ACCVPICCKPVCCVPTCSKDSSSCCQQSSCQPTCCASSSCQQSCCVPVCCKPVCCVPVCSGASTSCCQQS
          .CC....C.P.CC..T.S....SCC....C.P.C.A......SC....CC....C.P.C...S.S..QQ.
Retrocopy SCCQQSSCQPACC--TSSPCQQSCCMPVCCKPVCYAPTCSDDSCS---CCQQSSCQPACCTSSQS--QQG

Parental  SCQPACYTTSCCRP---SSSVSLLCRPICRPACCMPVSSCCAHASSCQASC---CRPASCV
          .C.P.C....CC.P.....S.S......C.PACC....SCC...SS....C...CRPA.CV
Retrocopy CCVPVCCKPVCCVPVCSGASTSCCQQSSCQPACC--TTSCCRPSSSVSLLCRPVCRPACCV

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.06 RPM	0.03 RPM
SRP007412_kidney	0.27 RPM	0.07 RPM
SRP007412_liver	0.09 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_15 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_15 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_15 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008415	1 retrocopy	retro_amel_1917,
Pongo abelii	ENSPPYG00000011492	3 retrocopies	retro_pabe_14, retro_pabe_15 , retro_pabe_16,
Rattus norvegicus	ENSRNOG00000001218	2 retrocopies	retro_rnor_380, retro_rnor_382,