RetrogeneDB ID: retro_pabe_2563

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:139437287..139438513(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSPPYG00000001506
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]

Sequence

>retro_pabe_2563
ATGAATGTAGCAGCCAAGTACCGCATGGCCTCCCTGTATGTGGGTGACTTACATGCAGATGTCACCGAGGACCTGCTGTT
CAGGAAGTTCAGCACTGTGGGGCCTGTGCTGTCCATCCGCATTTGCAGGGACCAGGTCACCCGCCGCTCTCTGGGCTATG
CCTACGTGAACTTCTTGCAGCTGGCTGATGCCCAGAAGGCGCTGGACACAATGAACTTTGACATCATAAAAGGCAAATCC
ATCCGTCTCATGTGGTCTCAGCGCGATGCCTACTTGAGGAGATCTGGAATTGGGAACGTGTTCATCAAGAATCTGGACAA
ATCTATCGATAACAAAACCCTTTATGAACATTTTTCAGCTTTTGGAAAGATCCTTTCCTCCAAAGTGATGAGTGATGATC
AAGGCTCCAAGGGCTATGCATTTGTGCACTTTCAGAACCAGAGTGCTGCAGACAGGGCCATTGAGGAGATGAATGGAAAA
CTACTCAAGGGCTGCAAGGTGTTTGTTGGCAGATTCAAAAACCGAAAAGATCGTGAAGCTGAACTCAGAAGCAAAGCCAG
TGAATTCACCAATATTTACATCAAAAACTTTGGCGGTGACATGGATGATGAGAGATTGAAGGACGTTTTCAGCAAATATG
GCAAAACTCTGAGTGTTAAGGTGATGACAGATTCCAGTGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGATAGCCAT
GAGGCTGCCAAGAAAGCTGTTGAAGAAATGAATGGAAGGGACATAAATGGGCAGCTGATTTTTGTAGGCCGGGCGCAAAA
GAAAGTAGAGCGACAGGCTGAGTTAAAGCAAATGTTTGAGCAGCTGAAAAGGGAACGAATTTGTGGGTGCCAGGGGGTAA
AGCTCTATATTAAGAACCTTGATGACACCATTGATGATGAAAAACTACGAAACGAGTTTTCTTCATTTGGATCAATTAGC
AGAGTTAAGGTAATGCAGGAAGAGGGACAGAGCAAAGGGTTTGGCTTGATCTGCTTCTCCTCTCCTGAGGATGCTACTAA
AGCAATGACTGAGATGAATGGCCGCATCTTGGGCTCCAAACCTCTTAGCATTGCCTTGGCCCAGAGACACTAGGAAAGAA
AAACGTACCTTCCCAGCTAGTATCTGCAGCAGGTGGAGGAATGATAGTGATCTCTGCCTGAATTGACCTCAGTAAATTTC
ATATTCCACATGATGGGTGCTTAGTT

Alignment

ORF - retro_pabe_2563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.05 %
• 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.SG.GNVFIKNLDKSIDNK.LY..FSAFG.ILS.KV..D..GSKGY
Retrocopy TMNFDIIKGKSIRLMWSQRDAYLRRSGIGNVFIKNLDKSIDNKTLYEHFSAFGKILSSKVMSDDQGSKGY

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 EQLKRERICGCQGVKLYIKNLDDTIDDEKLRNEFSSFGSISRVKVMQEEGQSKGFGLICFSSPEDATKAM

Parental  TEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRV-AGMRALPANAILNQFQPAAGGYFV
          TEMNGRI.GSKPL..ALAQR..ERK..L...Y.Q.V..GM....A...L..F.....G..V
Retrocopy TEMNGRILGSKPLSIALAQRH*ERKTYLPS*YLQQV<GGMIVISA*IDLSKFHIPHDGCLV

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	0.06 RPM	41.19 RPM
SRP007412_cerebellum	0.00 RPM	37.70 RPM
SRP007412_heart	0.39 RPM	108.43 RPM
SRP007412_kidney	0.73 RPM	63.77 RPM
SRP007412_liver	0.21 RPM	73.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2563 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2563 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_109
Pan troglodytes	retro_ptro_2093
Gorilla gorilla	retro_ggor_2127
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 20 parental genes, and 44 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 ,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,