RetrogeneDB ID: retro_ptro_2093

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:136830988..136832214(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSPTRG00000000573
• Aliases: None
• Description: None

Sequence

>retro_ptro_2093
ATGAATGTAGCAGCCAAGTACCGCATGGCCTCCCTGTATGTGGGTGACTTACATGCAGATGTCACCGAGGACCTGCTGTT
CAGGAAGTTCAGCACTGTGGGGCCTGTGCTGTCCATCCGCATTTGCAGGGACCAGGTCACCCGCCGCTCTCTGGGCTATG
CCTACGTGAACTTCTTGCAGCTGGCTGATGCCCAGAAGGCGCTGGACACAATGAACTTTGACATCATAAAAGGCAAATCC
ATCCGTCTCATGTGGTCTCAGCGCGATGCCTACTTGAGGAGATCTGGAATTGGGAACGTATTCATCAAGAATCTGGACAA
ATCTATCGATAACAAAACCCTTTATGAACATTTTTCAGCTTTTGGAAAGATCCTTTCCTCCAAGGTGATGAGTGATGATC
AAGGCTCCAAGGGCTATGCATTTGTGCACTTTCAGAACCAGAGTGCTGCAGACAGGGCCATTGAGGAGATGAATGGAAAA
CTACTCAAGGGCTGCAAGGTGTTTGTTGGCAGATTCAAAAACCGAAAAGATCGTGAAGCTGAACTCAGAAGCAAAGCCAG
TGAATTCACCAACATTTACATCAAAAACTTTGGAGGTGACATGGATGATGAGAGATTGAAGGACGTTTTCAGCAAATATG
GCAAAACTCTGAGTGTTAAGGTGATGACAGATTCCAGTGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGATAGCCAT
GAGGCTGCCAAGAAAGCTGTTGAAGAAATGAATGGAAGGGACATAAATGGGCAGCTGATTTTTGTAGGCCGGGCTCAAAA
GAAAGTAGAGCGACAGGCTGAGTTAAAGCAAATGTTTGAGCAGCTGAAAAGGGAACGAATTCGTGGGTGCCAGGGGGTAA
AGCTCTATATTAAGAACCTTGATGACACCATCGATGATGAAAAACTACGAAACGAATTTTCTTCATTTGGATCAATTAGC
AGAGTTAAGGTAATGCAGGAAGAGGGGCAGAGCAAAGGGTTTGGCTTGATCTGCTTCTCCTCTCCTGAGGATGCTACTAA
AGCAATGACTGAGATGAATGGCCGCATCTTGGGCTCCAAACCTCTTAGCATTGCCTTGGCCCAGAGACACTAGGAAAGAA
AAACGTACCTTTCCAGCTAGTATCTGCAGCAGGTGGGGGAATGATAGTGATCTCTGCCTGAATTGACCTCAGTAAATTTC
ATATTCCACATGGTGGGTGCTTAGTT

Alignment

ORF - retro_ptro_2093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.4 %
• Parental protein coverage: 62.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MN.AA..Y.MASLYVGDLH.DVTE..L..KFS..GPVLSIR.CRD..TRRSLGYAYVNF.Q.ADA..ALD
Retrocopy MNVAAK-YRMASLYVGDLHADVTEDLLFRKFSTVGPVLSIRICRDQVTRRSLGYAYVNFLQLADAQKALD

Parental  TMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFD.IKGK.IR.MWSQRD..LR.S..................LY..FSAFG.ILS.KV..D..GSKGY
Retrocopy TMNFDIIKGKSIRLMWSQRDAYLRRSXXXXXXXXXXXXXXXXXXLYEHFSAFGKILSSKVMSDDQGSKGY

Parental  AFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKEL
          AFVHF..Q.AAD.AIE.MNG.LL...KVFVGRFK.RK.REAEL..KA.EFTN.YIKNFG...DDE.LK..
Retrocopy AFVHFQNQSAADRAIEEMNGKLLKGCKVFVGRFKNRKDREAELRSKASEFTNIYIKNFGGDMDDERLKDV

Parental  FSQFGKTLSVKVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKF
          FS..GKTLSVKVM.D..GKSKGFGFVS...HE.A.KAVEEMNG..I.G..IFVGRAQKKVERQAELK..F
Retrocopy FSKYGKTLSVKVMTDSSGKSKGFGFVSFDSHEAAKKAVEEMNGRDINGQLIFVGRAQKKVERQAELKQMF

Parental  EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV
          EQLK.ERI...QGV.LYIKNLDDTIDDEKLR.EFS.FGSI...KVM.E.G.SKGFG..CFSSPE.ATKA.
Retrocopy EQLKRERIRGCQGVKLYIKNLDDTIDDEKLRNEFSSFGSISRVKVMQEEGQSKGFGLICFSSPEDATKAM

Parental  TEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRV-AGMRALPANAILNQFQPAAGGYFV
          TEMNGRI.GSKPL..ALAQR..ERK..L...Y.Q.V..GM....A...L..F....GG..V
Retrocopy TEMNGRILGSKPLSIALAQRH*ERKTYLSS*YLQQV<GGMIVISA*IDLSKFHIPHGGCLV

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	0.09 RPM	36.46 RPM
SRP007412_cerebellum	0.11 RPM	42.12 RPM
SRP007412_heart	1.31 RPM	70.36 RPM
SRP007412_kidney	1.39 RPM	55.44 RPM
SRP007412_liver	0.16 RPM	63.60 RPM
SRP007412_testis	1.37 RPM	84.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2093 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2093 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_109
Gorilla gorilla	retro_ggor_2127
Pongo abelii	retro_pabe_2563
Callithrix jacchus	retro_cjac_214
Rattus norvegicus	retro_rnor_175
Canis familiaris	retro_cfam_837

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330, retro_cpor_77,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Homo sapiens	ENSG00000090621	2 retrocopies	retro_hsap_109, retro_hsap_74,
Gorilla gorilla	ENSGGOG00000004002	3 retrocopies	retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Macaca mulatta	ENSMMUG00000007497	1 retrocopy	retro_mmul_178,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys	ENSNLEG00000011928	2 retrocopies	retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus	ENSOCUG00000000562	2 retrocopies	retro_ocun_153, retro_ocun_792,
Otolemur garnettii	ENSOGAG00000004067	1 retrocopy	retro_ogar_71,
Ochotona princeps	ENSOPRG00000011984	1 retrocopy	retro_opri_1133,
Pongo abelii	ENSPPYG00000001506	2 retrocopies	retro_pabe_190, retro_pabe_2563,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093 , retro_ptro_8,
Pan troglodytes	ENSPTRG00000005104	1 retrocopy	retro_ptro_778,
Pan troglodytes	ENSPTRG00000014709	1 retrocopy	retro_ptro_16,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,