RetrogeneDB ID: retro_nleu_1580

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397300.1:9757721..9758332(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAF1
• Ensembl ID: ENSNLEG00000010478
• Aliases: None
• Description: None

Sequence

>retro_nleu_1580
CACGTACTGAAGGCTCTCTCTCTATCGCAGACCTCAGGCCTCAGGCCCAGCAGCCTGAGCAAGAACCAAGGTGGCAAGGA
CGAGGTCCCCCTCAGGGACAAGTGCAATTGCAAGACCCTCTTCCACTTGATTGTCATGCTCAGCGAGTCCTTTCAGGCCT
GACTATGACCTCAGCACAGCCCGCAGCCATGGGTTCAGCTGGAAGCCCAGCCTCAGCTGGGTGGTAAATGCAGTTAACTG
CAGTCTGTTCTCAGCTGCGTGGGGGGACATTAAGGTCCTAGAACACAGCTGCGGAACACAGTGGATGAGGAGATCCGCCT
GGCTTAATGGAACACCTACAGCTATAACCCAGACATGGACCCAGACCCCTTCAGGGAAGAAGATACCCTCTGGTCCTTCA
ACTAATTCCTCTACAACAAAGGGCTCAAGCAAATTGTCTTCTTCAGCCACTGCTCCATTAGCAGCTCCACCTGCACACCC
TCAGAGGCAGGCAACGAGATGGACCTGGAACTGGGGGAAGAGGAGGAAGAGAAAGAAAGCAGAGGCGGAGGCAGTGAGGG
TGGGGCCGAAGAGACCAGACCATGGAGGATGGGTTCCCAGTGATTTGTATG

Alignment

ORF - retro_nleu_1580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.71 %
• Parental protein coverage: 79.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HVLEALSPPQTSGLSPSRLSKSQGGEDEGPLSDKCSRKTLFYLIATLNESF-RPDYDFSTARSHEFSREP
          HVL.ALS..QTSGL.PS.LSK.QGG.DE.PL.DKC..KTLF.LI..L.ESF.RPDYD.STARSH.FS..P
Retrocopy HVLKALSLSQTSGLRPSSLSKNQGGKDEVPLRDKCNCKTLFHLIVMLSESF>RPDYDLSTARSHGFSWKP

Parental  SLSWVVNAVNCSLFSAVREDFKAL-KPQLWNAVDEEICLTECDIYSYNPDLDSDPFGEDGSLWSFNYFFY
          SLSWVVNAVNCSLFSA...D.K.L...QL.N.VDEEI.L.....YSYNPD.D.DPF.E...LWSFN.F.Y
Retrocopy SLSWVVNAVNCSLFSAAWGDIKVL<RTQLRNTVDEEIRLA*WNTYSYNPDMDPDPFREEDTLWSFN*FLY

Parental  NKRLKRIVFFSCRSISGSTYTPSEAGNELDMELGEEEVEEESRSGGS--GAEET-STMEEDRVPVICI
          NK.LK.IVFFS..SIS.ST.TPSEAGNE.D.ELGEEE.E.ESR.GGS..GAEET..TM.ED..PVIC.
Retrocopy NKGLKQIVFFSHCSISSSTCTPSEAGNEMDLELGEEEEEKESRGGGSEGGAEET<QTM-EDGFPVICM

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_1580 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021450	1 retrocopy	retro_cjac_2111,
Homo sapiens	ENSG00000179632	1 retrocopy	retro_hsap_2708,
Macaca mulatta	ENSMMUG00000007155	1 retrocopy	retro_mmul_1537,
Nomascus leucogenys	ENSNLEG00000010478	1 retrocopy	retro_nleu_1580 ,
Pongo abelii	ENSPPYG00000018963	1 retrocopy	retro_pabe_2259,
Pan troglodytes	ENSPTRG00000020681	1 retrocopy	retro_ptro_1829,