RetrogeneDB ID: retro_nleu_2642

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397386.1:4928272..4928738(+)
• Located in intron of: ENSNLEG00000013370

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL1
• Ensembl ID: ENSNLEG00000011822
• Aliases: None
• Description: None

Sequence

>retro_nleu_2642
GTGGTGGCTCCATGCGTGAGGCTGGTGCCATGCAGTCTCCCGGTGTTGGCATTGTCTCCCAGCCTTCTCAGTTCTGCACA
CAGCTACAAAACAAAAGAACAGTTGCCAGCACTTGGAAGAGGACTTGGATCCAAACCAAATGGAGGACAGATACTCCCTC
TACGGACAAGATACTCATGGAAGAAGTCAAGTTAGAAGAGCAGCAGAAGGAGGCTGTGGAAGAAGATGAGCAAGCATTGG
CAGATACTGAGGACTTGCAGCAGAGCAGCCAAAAATTGGTGGAGGAGGCAAATATGTATAGCATTCAGGGCTTCTGCAAG
GACTTGTCAGAGGTTGCAGATGTTTTGGAGAAGGCAACACAGTGTGTTCCAGAAGAAGGACTTAAAGACAGTAACCTCGC
CTGAAGAACCTCTATGAAACTCTCACAATGAGTGAAGTCCAGATTCAGGAAGTGTTCAGCAAGCAC

Alignment

ORF - retro_nleu_2642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.98 %
• Parental protein coverage: 72.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAQCVRLARRSLPALALSLRPSP-RLLCTATKQKNSGQNLEDDMG-QSEQKADPPATEKTLLEEKVKLE
          ..A.CVRL...SLP...L.L.PS....L.TATKQKNS.Q.LE.D...Q.....D.P.T.K.L.EE.VKLE
Retrocopy VVAPCVRLVPCSLPV--LALSPSL>SVLHTATKQKNSCQHLEEDLD>QTKWRTDTPSTDKILMEE-VKLE

Parental  EQLKETVEKYKRALADTENLRQRSQKLVEEAKLYGIQAFCKDLLEVADVLEKATQCVPKEEIKDDN-PHL
          EQ.KE.VE....ALADTE.L.Q.SQKLVEEA..Y.IQ.FCKDL.EVADVLEKATQCVP.E..KD.N.P.L
Retrocopy EQQKEAVEEDEQALADTEDLQQSSQKLVEEANMYSIQGFCKDLSEVADVLEKATQCVPEEGLKDSN<PRL

Parental  KNLYEGLVMTEVQIQKVFTKH
          KNLYE.L.M.EVQIQ.VF.KH
Retrocopy KNLYETLTMSEVQIQEVFSKH

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_2642 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014364	1 retrocopy	retro_cfam_1776,
Homo sapiens	ENSG00000109519	3 retrocopies	retro_hsap_3746, retro_hsap_3864, retro_hsap_3870,
Loxodonta africana	ENSLAFG00000002590	1 retrocopy	retro_lafr_535,
Monodelphis domestica	ENSMODG00000002955	1 retrocopy	retro_mdom_28,
Mustela putorius furo	ENSMPUG00000010471	1 retrocopy	retro_mputfur_32,
Nomascus leucogenys	ENSNLEG00000010160	1 retrocopy	retro_nleu_710,
Nomascus leucogenys	ENSNLEG00000011822	1 retrocopy	retro_nleu_2642 ,
Otolemur garnettii	ENSOGAG00000032291	1 retrocopy	retro_ogar_1765,
Procavia capensis	ENSPCAG00000011314	1 retrocopy	retro_pcap_388,
Pongo abelii	ENSPPYG00000014573	1 retrocopy	retro_pabe_3235,
Pan troglodytes	ENSPTRG00000015894	3 retrocopies	retro_ptro_2544, retro_ptro_2633, retro_ptro_2636,
Sarcophilus harrisii	ENSSHAG00000007667	1 retrocopy	retro_shar_766,