RetrogeneDB ID: retro_nleu_611

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397268.1:9016605..9018304(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC1
• Ensembl ID: ENSNLEG00000003142
• Aliases: None
• Description: None

Sequence

>retro_nleu_611
GCTTTGGACACCATGAATTTTGATTTTATAAAGGGCAAGTCAGTACGCATCACGTGGTCTCAGCCTGAACCATCACTTCG
CAGTCGAGTGGGCAACATATTCATTAAAAATCTGGACAAATCCATTGATAATAAAGCACTGTATGATACATTTTCTGATT
TTTGTAACATCGTTTCATGTAAAGTGGTTTGTGATGAAAATGGTGCCAGGGGCTATGGATTTGTACGCTTTGATATGCAC
GGAGCAGCTGAAAGAGCTCTTGAAAAAATGAATGGAATGCTCCTAAACGGTCGCAAAGTATTTGTTGGACGATTTAAGTC
TCGTAAAAAACGAGAAACTGAACTTGGAGCTAAGGTAAAAGAGTTCACCAATGTTTACAAGAATTTTGGAGGAGACATGG
ATGATGAGCGCCTTAAGGATCTCTTTGACAAGTTTGGGCCTGCCGTAAGTGTGAAAGTAATGACTGATGAAAGTGGAAAA
TCCGAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAGATGCACCGAAAGCTGTGGATTAGATTAATGGAAATGGAGCT
CAATGGAAAACGAATTTACGTTAGTCGAGCTCAGAAAAAGGTGGAACAGCAGACGGAACTTTAGCGCAAATTCGAACAGA
TGAAGCAAGATAGGATTACCAGGTACTAGGGTGTTAATCTTTATGTGAAAAATCTTGATGATGGTATTGATGATGAACGT
CTCTGGAAACATTTTCTCCATTTGGTACAATCACCAGTCCAAAGGTTATGATGGAGGGTGGTCGCAGCAAGGGTTTGGTT
TTGTATGTTTCTCCTCCCCAGAAGAAGCCACAAAAGCAGTTACAGAAACGAATGGTAGAATTGTGGTCACAAAGCCATTG
TATGTAACTTTAGCTCAGCGCAAGGGAGAGTGCCAGGCTCACTTCACTAACCAGTATATGCAGAGAATGGCAAGTGTATG
AGCTGTGCCCAACCCTGTAATCAACCCTTACCAGCTAGCGTCTCCTTCAGGTTTCTTAATGGCAGCTATCTCACAGTCTC
AGAACTGTGCTGCATACCATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGA
CCTCATCCATTCCAAAATATGCCCGGTGCTACCCACCCAGCTGCTCCTAGGCCACCATTTAGTACTATGAGACCAGCTTC
TTCACAGGTTCCACGAGTCATGTCAACACAGTGTGCTGCTAACACATCAACACGGACAATGGGTCCACATCCTGCAGCTG
CAGCTGCTGCAGCTACTCCTGCTGTCTGCACCATTCCACAGTATAAATATGGTGCGGGATTTCGCAATCCTCAGCAACAT
CTTAATGCACAGCCACAAGTTACAATGCAACAGCCTGCTGCTCATGTACAAGGTCAGGAACCTTTGACTGCTTCCATGTT
GGCATCTGCCCGTCCTCAAGAGGAAAAGCAAATGTTGGGTGAGTGGCTATTTCCTTTTATTCAAGCCACGCACCCTACTC
TTGCTAGTAAAATCACTGGCATATTGTTGGAGATTGATAATTCAGAACTTCTTCATATGCTTGAGTCTCCAGAGTCACTC
CGTTATAAGGTTGATGAAGCTGTAGCTATACTACAAGCCCATCAAGCTAAAGAGGCTTCCCAGAAAGCAGTTAGCAGCAC
CACTGGTGTTCCAACTGTT

Alignment

ORF - retro_nleu_611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.69 %
• Parental protein coverage: 89.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS
          ALDTMNFD.IKGK.VRI.WSQ..PSLR.S.VGNIFIKNLDKSIDNKALYDTFS.F.NI.SCKVVCDENG.
Retrocopy ALDTMNFDFIKGKSVRITWSQPEPSLR-SRVGNIFIKNLDKSIDNKALYDTFSDFCNIVSCKVVCDENGA

Parental  KGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERL
          .GYGFV.F....AAERA.EKMNGMLLN.RKVFVGRFKSRK.RE.ELGA..KEFTNVY.KNFG.DMDDERL
Retrocopy RGYGFVRFDMHGAAERALEKMNGMLLNGRKVFVGRFKSRKKRETELGAKVKEFTNVY-KNFGGDMDDERL

Parental  KDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHE-DAQKAVDEMNGK-ELNGKQIYVGRAQKKVERQTE
          KDLF.KFGPA.SVKVMTDESGKS.GFGFVSFERHE.DA.KAVD..NG..ELNGK.IYV.RAQKKVE.QTE
Retrocopy KDLFDKFGPAVSVKVMTDESGKSEGFGFVSFERHE<DAPKAVD*INGN>ELNGKRIYVSRAQKKVEQQTE

Parental  LKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEF-SPFGTITSAKVMMEGGRSKG-FGFVCFSSP
          L.RKFEQMKQDRITRY.GVNLYVKNLDDGIDDERL.K.F.SPFGTITS.KVMMEGGRSKG.FGFVCFSSP
Retrocopy L*RKFEQMKQDRITRY*GVNLYVKNLDDGIDDERLWKHF<SPFGTITSPKVMMEGGRSKG<FGFVCFSSP

Parental  EEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAI
          EEATKAVTE.NGRIV.TKPLYV.LAQRK.E.QAH.TNQYMQRMASV.AVPNPVINPYQ.A.PSG..MAAI
Retrocopy EEATKAVTETNGRIVVTKPLYVTLAQRKGECQAHFTNQYMQRMASV*AVPNPVINPYQLASPSGFLMAAI

Parental  PQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVA
          .Q.QN.AAY.PPSQIAQLRPSPRWTAQGARPHPFQNMPGA..PAAPRPPFSTMRPASSQVPRVMSTQ..A
Retrocopy SQSQNCAAYHPPSQIAQLRPSPRWTAQGARPHPFQNMPGATHPAAPRPPFSTMRPASSQVPRVMSTQCAA

Parental  NTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASA
          NTST.TMGP.PAAAAAAATPAV.T.PQYKY.AG.RNPQQHLNAQPQVTMQQPA.HVQGQEPLTASMLASA
Retrocopy NTSTRTMGPHPAAAAAAATPAVCTIPQYKYGAGFRNPQQHLNAQPQVTMQQPAAHVQGQEPLTASMLASA

Parental  PPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAA
          .PQE.KQMLGE.LFP.IQA.HPTLA.KITG.LLEIDNSELLHMLESPESLR.KVDEAVA.LQAHQAKEA.
Retrocopy RPQEEKQMLGEWLFPFIQATHPTLASKITGILLEIDNSELLHMLESPESLRYKVDEAVAILQAHQAKEAS

Parental  QKAVNSATGVPTV
          QKAV.S.TGVPTV
Retrocopy QKAVSSTTGVPTV

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_611 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.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
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	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,