RetrogeneDB ID: retro_pabe_2980

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:94299847..94300600(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS5
• Ensembl ID: ENSPPYG00000018648
• Aliases: None
• Description: COP9 signalosome subunit 5 [Source:HGNC Symbol;Acc:2240]

Sequence

>retro_pabe_2980
ATGGTGACATCTAGGAGCAGTATGGTCCAAAAAACCTGGGAACTGGCCAACAACATGGAAGAAGCTCAGAGTATCCATGA
AAGCTACAAATACGACAAGAAGCAGCAGCAAGAAATCCTGCCAGCAAAGCCCTGGGTTAACAATCACTATTACTTTAAAG
TACTGCAAAATCTCAGCATTAGCTCTACTGAAGATGATGATGCATGCCAGGTCAGGGGGCAACTTGGAAATGATGGGTTT
GATGACAGGAAAGGTAGACGGTGAAACCACGATTATTATGGGCAGTTTTACTTTGCCTGTGGAGGGCACTGAAACCCAAG
AAAATGCTCAGGCTGCTGCATATGAGTACGTGGCCACATACATAGAAAATGCCAAAAAGTTTGGCTGCCTTAAAAATGCA
ATCGGTTGATATTATAGGCACCTTGGCCATGGCTGCTGGCTTTCTGGCATCATGTTAGTACTCACCTGCTCAATAAGCAG
CTCTGGGAACCATTTACAGCAGTGGTGATTGATCCAACAAGAACAATATCTGCAGGGAAGGTGAATCTTGATGCCTTTAG
GACATACCCAAAGGGCTACAAACCTCCTGATGAAGGACCTTCTGAGTACCAGACTATCCCGCTTGATAAAATAGAAGATG
TTGGTATACAATGCAAATAATATTATGCCTTAGAAGTCTTGTATTTCAAATTCTCTTTGGGTTGCAAATTGCTTGAGCTT
CTGTGGAATAAATATTGGGTGGGTACACTGAGT

Alignment

ORF - retro_pabe_2980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.45 %
• Parental protein coverage: 75.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFK-YCKISALALLKMVMHA
          M..S.S.M.QKTWELANNM.EAQSI.E.YKYDKKQQQEIL.AKPW...H.YFK.YCKISALALLKM.MHA
Retrocopy MVTSRSSMVQKTWELANNMEEAQSIHESYKYDKKQQQEILPAKPWVNNHYYFK>YCKISALALLKMMMHA

Parental  RSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHS
          RSGGNLE.MGLM.GKVDGET.IIM.SF.LPVEGTET..NAQAAAYEY.A.YIENAK..G.L.NAIG.Y..
Retrocopy RSGGNLEMMGLMTGKVDGETTIIMGSFTLPVEGTETQENAQAAAYEYVATYIENAKKFGCLKNAIG*YYR

Parental  HPGYGCWLSGI-DVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPL
          H.G.GCWLSGI..VST..LN.Q..EPF.AVVIDPTRTISAGKVNL.AFRTYPKGYKPPDEGPSEYQTIPL
Retrocopy HLGHGCWLSGI<HVSTHLLNKQLWEPFTAVVIDPTRTISAGKVNLDAFRTYPKGYKPPDEGPSEYQTIPL

Parental  NKIEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLS
          .KIED.G..CK.YYALEV.YFK.SL..KLLELLWNKYWV.TLS
Retrocopy DKIEDVGIQCK*YYALEVLYFKFSLGCKLLELLWNKYWVGTLS

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	32.57 RPM
SRP007412_cerebellum	0.00 RPM	38.06 RPM
SRP007412_heart	0.00 RPM	32.99 RPM
SRP007412_kidney	0.00 RPM	26.32 RPM
SRP007412_liver	0.00 RPM	29.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2980 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2980 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3634
Pan troglodytes	retro_ptro_2457
Gorilla gorilla	retro_ggor_2451
Callithrix jacchus	retro_cjac_2454

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004632	1 retrocopy	retro_cjac_2454,
Homo sapiens	ENSG00000121022	1 retrocopy	retro_hsap_3634,
Microcebus murinus	ENSMICG00000011042	1 retrocopy	retro_mmur_834,
Monodelphis domestica	ENSMODG00000007838	1 retrocopy	retro_mdom_1460,
Mustela putorius furo	ENSMPUG00000010175	1 retrocopy	retro_mputfur_397,
Nomascus leucogenys	ENSNLEG00000010914	1 retrocopy	retro_nleu_815,
Pongo abelii	ENSPPYG00000018648	1 retrocopy	retro_pabe_2980 ,
Pan troglodytes	ENSPTRG00000020317	2 retrocopies	retro_ptro_2457, retro_ptro_638,