RetrogeneDB ID: retro_nleu_1517

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397297.1:8103671..8104897(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000019300
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSNLEG00000011928
• Aliases: None
• Description: None

Sequence

>retro_nleu_1517
ATGAATGTAGCAGCCAAGTACCGCATGGCCTCCCTGTATGTGGGTGACTTACATGCAGATGTCACCGAAGACCTGCTGTT
CAGGAAGTTTAGCACTGTGGGCCCTGTGCTGTCCATCCGCATTTGCAGGGACCAGGTCACCCGCCGCTCTCTGGGCTATG
CCTACGTGAACTTCTTGCAGCTGGCTGATGCCCAGAAGGCGCTGGACACAATGAACTTTGACATGATAAAAGGCAAATCC
ATCCGTCTCATGTGGTCTCAGCGCGATGCCTACTTGAGGAGATCTGGAATTGGGAACGTGTTCATCAAGAATCTGGACAA
ATCTATCGATAACAAAACCCTTTATGAACATTTTTCAGCTTTTGGAAAGATCCTTTCCTCCAAGGTGATGAGTGATGATC
AAGGCTCCAAGGGCTATGCATTTGTGCACTTTCAGAATCAGAGTGCTGCAGACAGGGCCATTGAGGAGATGAATGGAAAA
CTACTCAAGGGCTGCAAGGTGTTTGTTGGCAGATTCAAAAACCGAAAAGATCGTGAAGCTGAACTCAGAAGCAAAGCCAG
TGAATTCACCAATATTTACATCAAAAACTTTGGAGGTGACATGGATGATGAGAGACTGAAGGACGTTTTCAGCAAATATG
GCAAAACTCTGAGTGTTAAGGTGATGACAGATTCCAGTGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGATAGCCAT
GAGGCTGCCAAGAAAGCTGTTGAAGAAATGAATGGAAGGGACATAAATGGGCAGCTGATTTTCGTAGGCCGGGCGCAAAA
GAAAGTAGAGCGACAGGCTGAGTTAAAGCAAATGTTTGAGCAGCTGAAAAGGGAACGAATTCGTGGGTGCCAGGGGGTAA
AGCTCTATATTAAGAACCTTGATGACACCATTGATGATGAAAAACTACGAAACGAATTTTCTTCATTTGGATCAATTAGC
AGAGTTAAGGTAATGCAGGAAGAGGGGCAGAGCAAAGGGTTTGGCTTGATCTGCTTCTCCTCTCCTGAGGATGCTACTAA
AGCAATGACTGAGATGAATGGCCGCATCTTGGGCTCCAAACCTCTTAGCATTGCTTTGGCCCAGAGACACTAGGAAAGAA
AAACGTACCTTCCCAGCTAGTATCTGCAGCAGGTGGGGGAATGATAGTGATCTCTGCCTGAACTGACCTCAGTAAATTTC
ATATTCCACATGATGGGTGCTTAGTT

Alignment

ORF - retro_nleu_1517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.29 %
• 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 TMNFDMIKGKSIRLMWSQRDAYLRRSGIGNVFIKNLDKSIDNKTLYEHFSAFGKILSSKVMSDDQGSKGY

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

Parental  FSQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKF
          FS..GKTLSVKVM.D.SGKSKGFGFVS...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.....G..V
Retrocopy TEMNGRILGSKPLSIALAQRH*ERKTYLPS*YLQQV<GGMIVISA*TDLSKFHIPHDGCLV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1517 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

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	ENSNLEG00000003142	3 retrocopies	retro_nleu_221, retro_nleu_2412, retro_nleu_611,
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,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,