RetrogeneDB ID: retro_nleu_1849

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397313.1:1550097..1551868(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MATR3
• Ensembl ID: ENSNLEG00000009093
• Aliases: None
• Description: None

Sequence

>retro_nleu_1849
ATGTCCAAGTCATTCCAACAGTCATCTCTCAGTAGGGACTCACAGGGTCATGGGTGTGACCTGTCTGCGGTAGGTATAGG
CCTTCCTGCTGCTGTTACCCAGTCTTTAATATGTCAGCATCTCTTGGAAGGATGAACCAGGGTACTGCACGCCTTGCTAG
TTTAATGAATCTTGGAACGAGTTCTTCATTGAATCAACAAGGAGCTCATAGTGCATGGTCTTCTGCTAGTACTTCTTTCC
GTAATTTACCGTCTATATTTAACATTGGAAGTAGAGGTCTACTCCCTTTATCTTCTCAACACCGTGGAGATGCAGACCAG
GCCAGTAACATTTTGGCCAGCTTTGGTCTGTCTGCCAGAGACTTAGATGAACTGAGTCGTTAACCAGAGGACAAGATGAC
TCCTGAGAATTTGCCCCAAATCCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACCTTGAGTTATGGTAGAG
ATGACAGATCTGCTGCATGGGAGCCACCATACAGAGTACCTAGGGATGACTTGGAAGAAAAAAAGGCACTTTAGAAGAGA
GAGTTTTGATGATCGTGGTTCTAGTCTCAACCTGGTGCTTCATTATGATCATGGAAGTCATTCTCAAGAATCTGGTTATT
ATGACAGAATGGATTATGAAGATGACAGATTACAAGATGGAGAAAGGTGTAGGGATGATTCTTTTTTGGTGAGACCTTGC
ATAACTATCATAAATTTGACAGTGAGTATGAGAGAATGGGATGTGGTCATGGTCCTGACCCCTTACAAGAGAGACTTCTC
TTTGAGAAAAAGAGGGGCACTCCTCCAAATAGCAATATTAAAGACTTTCATGGACTCTTACTGAAGGGTTATACCCATCT
GTGCTCTATATGTGATTTGCCAGTTCATTCTAATGAGGAGTTAAGTCAACATATCAATGGAGCAAGCCACAGTCGTCGAT
GCCAGCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACAGAACACACAATGGGTGATCCATTCATGTTG
CAGCAGTCTTCAAACACAGCACCAGGAATTCTGGGATCTCCACCTCCCTCATTTCATCTTGGAGGACCAGCAATTGGACC
AAGAGGAAATCTGGGTGCTGGAAATGGAAACCTGCAAAGACCTAGACACATGAAAATGGCAGCGTGGAAACTAGCAGAGT
TGTTCACATGGATTTTCAGAGAGGGAAAAACTTGAGATACCAGCTATTACAGCTGGTAGAACCATTTGGTGTCATTTCAA
ATCATCTGATTCTAAATAAAATTAATGAGGCATTTACTGAAATGGCAACCACAGAGGATGCTCAGGCTGCAGTGGATTAT
TATACAACCACACCAGCGTTAGTATTAGGCAAGGCAGTGAGAGTTCATTTATCCCAGAAGTATAAAAGAATAAAGTAACC
TGAAGGAAAGCCAGATCAGAAGTTTGATCAAAGGCAAGAGCTTGGACGTGTGATACATCTCAGCAATTTGCCCCATTCTT
GCTATTCTGATAGTGCTGTCCTCAAACTTGCTGAGCCTTATGGGAAAATAAAGAATTACATATTGATGAGGATGAAAAGT
CAGGCTTTTATTGAGATGGAGACAAGAGAAGATGAAATGGCAATGGTTGAGCACTGTTTGAAAAAAGCCCTTTAGTTTCA
GGGAAGATGTGTGAAGGCAGACCTGTCTGAGAAATATAAAAAACTGGTACTGAGGATTCCAAACAGAGGCACTGATTTAC
TGAAAAAAGAT

Alignment

ORF - retro_nleu_1849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.43 %
• Parental protein coverage: 69.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSKSFQQSSLSRDSQGHGRDLSAAGIGLLAAATQSL-SMPASLGRMNQGTARLASLMNLGMSSSLNQQGA
          MSKSFQQSSLSRDSQGHG.DLSA.GIGL.AA.TQSL..M.ASLGRMNQGTARLASLMNLG.SSSLNQQGA
Retrocopy MSKSFQQSSLSRDSQGHGCDLSAVGIGLPAAVTQSL<NMSASLGRMNQGTARLASLMNLGTSSSLNQQGA

Parental  HSALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDADQASNILASFGLSARDLDELSRYPEDKITPENLP
          HSA.SSASTS..NL.SIFNIGSRG.LPLSSQHRGDADQASNILASFGLSARDLDELSR.PEDK.TPENLP
Retrocopy HSAWSSASTSFRNLPSIFNIGSRGLLPLSSQHRGDADQASNILASFGLSARDLDELSR*PEDKMTPENLP

Parental  QILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDD-WEEKRHFRRDSFDDRGPSLNPVLDYDHGSRS
          QILLQLKRRRTEEGPTLSYGRD.RSA..EPPYRVPRDD.W..KRHFRR.SFDDRG.SLN.VL.YDHGS.S
Retrocopy QILLQLKRRRTEEGPTLSYGRDDRSAAWEPPYRVPRDD>WKKKRHFRRESFDDRGSSLNLVLHYDHGSHS

Parental  QESGYYDRMDYEDDRLRDGERCRDDSF-FGETSHNYHKFDSEYERMG--RGPGPLQERSLFEKKRGAPPS
          QESGYYDRMDYEDDRL.DGERCRDDSF.FGET.HNYHKFDSEYERMG...GP.PLQER.LFEKKRG.PP.
Retrocopy QESGYYDRMDYEDDRLQDGERCRDDSF<FGETLHNYHKFDSEYERMGCGHGPDPLQERLLFEKKRGTPPN

Parental  SNIEDFHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFML
          SNI.DFHGLL.KGY.HLCSICDLPVHSN.E.SQHINGASHSRRCQLLLEIYPEWNPDNDT.HTMGDPFML
Retrocopy SNIKDFHGLLLKGYTHLCSICDLPVHSNEELSQHINGASHSRRCQLLLEIYPEWNPDNDTEHTMGDPFML

Parental  QQSTNPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHM-QKGRVETSRVVHIMDFQRGKNLRYQ
          QQS.N.APGILG.PPPSFHLGGPA.GPRGNLGAGNGNLQ.PRHM...G.VETSRVVH.MDFQRGKNLRYQ
Retrocopy QQSSNTAPGILGSPPPSFHLGGPAIGPRGNLGAGNGNLQRPRHM<ENGSVETSRVVH-MDFQRGKNLRYQ

Parental  LLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKP
          LLQLVEPFGVISNHLILNKINEAF.EMATTEDAQAAVDYYTTTPALV.GK.VRVHLSQKYKRIK.PEGKP
Retrocopy LLQLVEPFGVISNHLILNKINEAFTEMATTEDAQAAVDYYTTTPALVLGKAVRVHLSQKYKRIK*PEGKP

Parental  DQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLK
          DQKFDQ.QELGRVIHLSNLPHS.YSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETRED.MAMV.HCLK
Retrocopy DQKFDQRQELGRVIHLSNLPHSCYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDEMAMVEHCLK

Parental  KALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKD
          KAL.FQGRCVK.DLSEKYKKLVLRIPNRG.DLLKKD
Retrocopy KAL*FQGRCVKADLSEKYKKLVLRIPNRGTDLLKKD

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_1849 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006888	1 retrocopy	retro_cjac_3950,
Homo sapiens	ENSG00000015479	1 retrocopy	retro_hsap_199,
Gorilla gorilla	ENSGGOG00000007308	2 retrocopies	retro_ggor_276, retro_ggor_421,
Nomascus leucogenys	ENSNLEG00000009093	1 retrocopy	retro_nleu_1849 ,
Oryctolagus cuniculus	ENSOCUG00000026311	1 retrocopy	retro_ocun_652,
Otolemur garnettii	ENSOGAG00000010607	1 retrocopy	retro_ogar_3417,
Pongo abelii	ENSPPYG00000015835	2 retrocopies	retro_pabe_1722, retro_pabe_438,
Pan troglodytes	ENSPTRG00000017294	1 retrocopy	retro_ptro_181,
Rattus norvegicus	ENSRNOG00000019875	2 retrocopies	retro_rnor_1124, retro_rnor_475,