RetrogeneDB ID: retro_nleu_2676

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397395.1:1103398..1104271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XRCC6
• Ensembl ID: ENSNLEG00000015610
• Aliases: None
• Description: X-ray repair complementing defective repair in Chinese hamster cells 6 [Source:HGNC Symbol;Acc:4055]

Sequence

>retro_nleu_2676
GTTCACTTTGAGGAATCCAGCAAGCTAGAAGACCTGTTGCAGAAGGTTTGTGCCAAGGAGACCAGGAAATGAGCACTCAG
CAGGTTAAAGCTGAAGCTCAACAAAGACACAGTGATCTCTGTGGGCATTTACAATCTCATCCAGAAGGCTCTCAAGCCTC
CTCCAATAAAACTCTATCGGAAAACAAATGAACCAGTGAAAACCAAGTCCCGGAAATTTAATGTTAATACCGGCAGTTTG
CTTCTGCCTAGCGCTACCAAGAGGTCTCAGATCTATGGGAGTCATCAGATTATACTGGAGAAAGAGGAAACAGAAGAGCT
AAAATGGTTTGATGAACCAGCTTTGATGCTCATGGTTTTCAAGCCCTTGGTAATGCTGAAGGAGCACCATTACCTGAGGC
CCTCCTTGTTCACGTACCCTGAGGAGTCGCTGGTGAGTGGGAGTTCAACTCTGTTCAGTGCTCTGCTCATCAAGTGTCTG
GAGAAGGTGGTCATAGCATTGTGCAGATACATACCCCGCAGGAACATCCCCCCTTATTTTGTGGCTTTGGTGTCACAGGA
AGAGGAGTTGGATGACCAGAAAATTCAGTTGACTACTGCAGGTTTCCAGCTGGTCATTTTAACCTTTGCTGATGATAAAA
GGAAGGTGCCCTTTACTGAAAAAGTCATAGCAACTCCAGAGCAGGTGGACAACATGAAGGCTATCATTCAGAAGCTCTGC
TTCACATACAGAAGTGACAGCTTTGAGAACCCCGTGCTGCAGCAGCACTTTGGGAACCTGGAGCCCTTGATCTTGTATTT
GATGAAGCCTGAACAAGCAGTGGACCTTATATTACCCAAGGTTGAAGAAATGAATAAAAGACTGGGCTCCATG

Alignment

ORF - retro_nleu_2676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.1 %
• Parental protein coverage: 52.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
          VHFEESSKLEDLL.KV.AKETRK.ALSRLKLKLNKD.VISVGIYNL.QKALKPPPIKLYR.TNEPVKTK.
Retrocopy VHFEESSKLEDLLQKVCAKETRK*ALSRLKLKLNKDTVISVGIYNLIQKALKPPPIKLYRKTNEPVKTKS

Parental  RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYP
          R.FN..TG.LLLPS.TKRSQIYGS.QIILEKEETEELK.FD.P.LMLM.FKPLV.LK.HHYLRPSLF.YP
Retrocopy RKFNVNTGSLLLPSATKRSQIYGSHQIILEKEETEELKWFDEPALMLMVFKPLVMLKEHHYLRPSLFTYP

Parental  EESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFA
          EESLV.GSSTLFSALLIKCLEK.V.ALCRY.PRRNIPPYFVALV.QEEELDDQKIQ.T..GFQLV.L.FA
Retrocopy EESLVSGSSTLFSALLIKCLEKVVIALCRYIPRRNIPPYFVALVSQEEELDDQKIQLTTAGFQLVILTFA

Parental  DDKRKMPFTEKIMATSEQVDKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTCKA
          DDKRK.PFTEK..AT.EQVD.MKAI..KL.FTYRSDSFENPVLQQHF.NLE.L.L.LM.PEQAVDL....
Retrocopy DDKRKVPFTEKVIATPEQVDNMKAIIQKLCFTYRSDSFENPVLQQHFGNLEPLILYLMKPEQAVDLILPK

Parental  VESSSSFHGRL
          VE......G..
Retrocopy VEEMNKRLGSM

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_2676 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 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000196419	4 retrocopies	retro_hsap_4066, retro_hsap_4880, retro_hsap_4913, retro_hsap_511,
Gorilla gorilla	ENSGGOG00000015885	2 retrocopies	retro_ggor_3067, retro_ggor_471,
Macaca mulatta	ENSMMUG00000001856	2 retrocopies	retro_mmul_2346, retro_mmul_430,
Nomascus leucogenys	ENSNLEG00000015610	3 retrocopies	retro_nleu_1552, retro_nleu_2287, retro_nleu_2676 ,
Pongo abelii	ENSPPYG00000011876	1 retrocopy	retro_pabe_3821,
Tupaia belangeri	ENSTBEG00000011736	3 retrocopies	retro_tbel_1474, retro_tbel_1523, retro_tbel_3859,
Tursiops truncatus	ENSTTRG00000006749	1 retrocopy	retro_ttru_289,