RetrogeneDB ID: retro_ptro_2915

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:112786529..112787482(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSPTRG00000018828
• Aliases: None
• Description: programmed cell death 2 [Source:HGNC Symbol;Acc:8762]

Sequence

>retro_ptro_2915
AGAGGGGCGGGCGGCCGGCGTGGCTGAGCGTGGCCGGGCGCGGCCGGGCTGCCGGGCCCTGGACCCTGGCCTGCGCGCTG
TGCGGCTGCCAGCTCTCCTTCCTGCTACAGGTGTACGCGCTGCTGCCCGGCCGCGCCGACGCCTTCCACCCCGGAATCTT
CCTCTTCTGCTGCTGAGAGCCGCCGTGCTGGGCCGGCCTGCGAGTTTTTACCAATCAGCTACCCAGGGAAAATGATTTTT
CCTCATATGGGCCACCTACTGAGAATCCTCTCCCAGAAACAGGACAATCAGTGTGTCTCTAACTTAAGTCTGGTGCTCAT
CTCTGCAGGGTTTGTGGCTGTTTAGGACCCAAAACGTGCTCCAGATGCCACAAAGCGTATTACTGCAGCAAGGAGCATCA
AGACCCTAGACCGGAGATTGGCACATAAGCAGGCTTGTACACAACCAGATCATTTGGACCATATAATTCCAGACCACGAC
TTCCTTTTTCCAGAATTTGCAGTTGTAGTAGAAACAGAAGATGAAGATTACACCTGAGGTTGTGGAAAAGGAAGATTACT
CAGAGATTATAGGGAGCATGGGTGACGCACTTGAAGAAGAACTGGATTCCATGGCAAAACATGAATCCAGGGAAGATAAA
TTTTTCAGAAGTTCAAAACTCAGATAGCCCTTGAACCAGAACAGATTCTCAGATATGGCAGAGATATTGCCCCCATCTGG
ATTCTAGTGAAAATATTCCTCAAGAAAAGGATATTCCAGAGAATATCCTTTGTGATGCCAAGAAAATGTTTGAATTCCAG
GTTATGCCTCAGCTCCTAAACTACCTGAAGGCTGACAGACTGGGCAAGAGCATTGACTGGGGCTTCCTGGCTGTCTTCAC
CTGGGCTGAGAGCTGCATCTTGGGTACTGGCTATACAGAATAATTTGTGTGGAAGCAGGATGTAACAGATACA

Alignment

ORF - retro_ptro_2915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.28 %
• Parental protein coverage: 92.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RGGPGRP--AWLGAAGLPGPQ-ALACELCGRPLSFLLQVYAPLPGRPDAFHRCIFLFCCREQPCCAGLRV
          RG..GR...AW.GAAGLPGP...LAC.LCG..LSFLLQVYA.LPGR.DAFH..IFLFCC.E.PC.AGLRV
Retrocopy RGAGGRRG*AWPGAAGLPGPG<TLACALCGCQLSFLLQVYALLPGRADAFHPGIFLFCC*EPPCWAGLRV

Parental  FRNQLPRKNDFYSYEPPSENPPPETGESVCLQLKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQ-TLDW
          F.NQLPR.NDF.SY.PP.ENP.PETG.SVCL.LKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQ.TLD.
Retrocopy FTNQLPRENDFSSYGPPTENPLPETGQSVCL*LKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQ>TLDR

Parental  RLGHKQACAQPDHLDHIIPDHNFLFPEFEIVIETEDE-IMPEVVEKEDYSEIIGSMGEALEEELDSMAKH
          RL.HKQAC.QPDHLDHIIPDH.FLFPEF..V.ETEDE.I.PEVVEKEDYSEIIGSMG.ALEEELDSMAKH
Retrocopy RLAHKQACTQPDHLDHIIPDHDFLFPEFAVVVETEDE>ITPEVVEKEDYSEIIGSMGDALEEELDSMAKH

Parental  ESREDK-IFQKFKTQIALEPEQILRYGRGIAPIWI-SGENIPQEKDIPD-CPCGAKRILEFQVMPQLLNY
          ESREDK.IFQKFKTQIALEPEQILRYGR.IAPIWI.S.ENIPQEKDIP....C.AK...EFQVMPQLLNY
Retrocopy ESREDK<IFQKFKTQIALEPEQILRYGRDIAPIWI<SSENIPQEKDIPENILCDAKKMFEFQVMPQLLNY

Parental  LKADRLGKSIDWGILAVFTCAESCSLGTGYTEEFVWKQDVTDT
          LKADRLGKSIDWG.LAVFT.AESC.LGTGYTE.FVWKQDVTDT
Retrocopy LKADRLGKSIDWGFLAVFTWAESCILGTGYTE*FVWKQDVTDT

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	7.29 RPM
SRP007412_cerebellum	0.00 RPM	6.35 RPM
SRP007412_heart	0.00 RPM	5.10 RPM
SRP007412_kidney	0.00 RPM	10.46 RPM
SRP007412_liver	0.00 RPM	4.68 RPM
SRP007412_testis	0.00 RPM	11.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2915 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2915 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1137

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017075	2 retrocopies	retro_amel_1329, retro_amel_1404,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915 , retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,