RetrogeneDB ID: retro_nleu_1552

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397299.1:2730596..2731435(+)
• 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_1552
GAGGAATCCAGCAAGCTAGAAGATCTGTTGAGGCAGGTTTCAGCCAAGGAGATCAGGAAGTGAACACTCAGCAGGTTAAA
GCTGAAGCTCAACAAAGATATAGTGCTCTTTGTGGGCATTTATAATCTGATCTAGAAGGCTCTCAAGCCTCCTCCAATAA
AGCCCTAACGAGAAATAGATGAATCAGTGAAAATTAAGACCCGGATATTTAATGTAAATACAGGCAGTTTGCTTCTGCCT
AGAGATACCAAGAGGTCTCGGATCTATGGAAGGCATCAGATTATACTGGAGAAAGAGGAAACAGAAGAGCTAAAATAGTT
TGATGAACCAGGTTTGATTCTCATGGGTTTAAGCCCTTGGTAAAGCTGAAGAAGCACCATTACCTGAGGCCCTCCTTGTT
TGTGTACTCTGAGGAGTCGCTGATGAATGGGAGCTCAACCCTGTTCAGTGCTCTACTCATCAAGTGTCTGGAGAAGGAGG
TCACAGCATTGTGCAGATACATACCCTGCAGGAACATCCCCCCTTATTTTGTGGCTTTGGTGCCACAGGAAGAGGAGTTG
GATGATCAGAAAATTCAGGTGACTCCTGCAGGCTTCCAGCTGGTCTTTTTATGCTATGCTGATAATAAAGGGAAGGTGCC
CTTTACTAAAAAAGTCACGGCAACCCCAGAGCAGGTGGACAAGGTGAAGGCTATTGTTCAGAAGCTCCGATTCAAATACA
GAAGTGACAGCTTTGAGAACTCTGTGCTGCAGCAGCACTCCAGGAACCTGGAGGTCTTGGCCTTGGATTTGATGGAGCCT
GAACAAGCAGTGGACCTGATATTGTCTGAGGTTGAAGCA

Alignment

ORF - retro_nleu_1552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.43 %
• Parental protein coverage: 50.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTF
          EESSKLEDLLR.V.AKE.RK..LSRLKLKLNKDIV..VGIYNL..KALKPPPIK..RE..E.VK.KTR.F
Retrocopy EESSKLEDLLRQVSAKEIRK*TLSRLKLKLNKDIVLFVGIYNLI*KALKPPPIKP*REIDESVKIKTRIF

Parental  NTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMG-FKPLVLLKKHHYLRPSLFVYPEE
          N..TG.LLLP.DTKRS.IYG..QIILEKEETEELK.FD.PGL.LMG.FKPLV.LKKHHYLRPSLFVY.EE
Retrocopy NVNTGSLLLPRDTKRSRIYGRHQIILEKEETEELK*FDEPGLILMG<FKPLVKLKKHHYLRPSLFVYSEE

Parental  SLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADD
          SL..GSSTLFSALLIKCLEKEV.ALCRY.P.RNIPPYFVALVPQEEELDDQKIQVTP.GFQLVFL..AD.
Retrocopy SLMNGSSTLFSALLIKCLEKEVTALCRYIPCRNIPPYFVALVPQEEELDDQKIQVTPAGFQLVFLCYADN

Parental  KRKMPFTEKIMATSEQVDKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTCKAVE
          K.K.PFT.K..AT.EQVDK.KAIV.KLRF.YRSDSFEN.VLQQH.RNLE.LALDLMEPEQAVDL....VE
Retrocopy KGKVPFTKKVTATPEQVDKVKAIVQKLRFKYRSDSFENSVLQQHSRNLEVLALDLMEPEQAVDLILSEVE

Parental  S
          .
Retrocopy A

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_1552 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,