RetrogeneDB ID: retro_nleu_2287

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397341.1:6841679..6843230(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000013567
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2287
ATGTCAGGGTGGGAGTCATATTACAAAACCGAGGGCGATGAAGAAGCTGAAGAAGAACAAGAAGAGAACCTTGAAGCAAG
AGGAGACTATAAATATTCAGAAAAAGATAGTTCGATTTTTTTGGTTGATGCCTCCAAGGCTATGTTTGAATCTCCTAGTG
AAGATGAGTTGACACCTTTTGACATGAGCATCCAGTGTATTCAAAGTAAGATCATAAGCAGTGATCGAGATCTCTTGGCT
GTGGTGTTCTATGGTACCGAGAAAGACAAAAATTCAGTGAATTTAAAAAATATTTACATCTTACAGGAGCTGGATAATCC
AGGTGCAAAACAAATTCTAGAGCTTGACCAGTTTAAGGGGCAGCAGGGACAAAAACGTTTCCAAGACCTGATGGGCCATG
GATCTGACTACTCACTCAGTGAAGTGCTGTGGGTCCATGCCAACCTCTTTAGTGATGTCCAATTCAAGATGAGTCATAAG
AAGATCATGCTCTTCACCAATGAAGACAACCCCCATGGCAATGAGAGTGCCAAAGCCAGCCAGGCCAGGACCAAAGCCAG
TGATCTCCGAGACACAGGCATCTTCCTTGACTTGATGCATCTGAAGAAACCTGGAGGCTTTGATAGATCCTTGTTCTACA
GAGATATCATCAGCATAGCAGAGGATGAGGACCTCAGGGTTCACTTTGAGGAATCCAGCAAGCTAGAAGACCTGTTGCAG
AAGGTTCACGCCAAAGAGACCAGGAAGTGAGCACTCAGCAGGTTAAAGCTGAAGCTCAACAAAGATATAGTGATCTCTGT
GGGCATTTATAATCTGGTCCAGAAGGCTCTCAAGCCTCCTCCAATAAAGCTCTATCGGGAAATAAATGAACCAGTGAAAA
CCAAGACCCAGACCTTTAATATAAGTACAGACGGTTTGCTTCTGCCTAGCGATACCAAGAGGTCTCAGATCTATGGGAGT
CGTCAGATTATACTGGAGAAAGAGGAAACAGAAGAGCTAAAACGGTTTGATGATCCAGGTTTGATGCTCATGGGTTTCAA
GCCATTGGTACTGCTGAAGAAAGGCCATTACCTGAGGCCCTCCCTGTTCGTGTACCCAGAGGAGTCGCTGGTGATTGGGA
GCTCAACCCTGTTCAGTGCTCTGCTCATGAAGTGTCTGGAGAAGGAGGTTGCAGCATTGTGCAGATACACACCCCACAGG
AACATCTCCCCTTATTTTGTGGCTTTGGTGACTCAGGAAGAAGAGTTGGATGACCAGAAAATTCAGGTGACTCCTCCAGG
CTTCCAGCTGGTCTTTTTGCCCTTTGCTGATGATAAAAGGAAGATGCCCTTTACTGAAAGAGTCATGGCAACTCCAGAGC
AGGTGGACAAGATGAAGGCTATCGTTGAGAAGCTTCGCTTCACATGCAGAAGTGACAGCTTTAAGAACCCTGTGCTGCAG
CAGCACTTCAGGAACCTGGAGGCCTTGGCCTTGGATTTGATGGAGCCAGAACAAGCAGTGGACCTGACATTGCCCAAGGT
TGAAGCAATAAATAAAAGACTGGGCTCCTTG

Alignment

ORF - retro_nleu_2287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.17 %
• Parental protein coverage: 93.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSENELTPFDMSIQCIQSV
          MSGWESYYKTEGDEEAEEEQEENLEA.GDYKYS..DS.IFLVDASKAMFES.SE.ELTPFDMSIQCIQ..
Retrocopy MSGWESYYKTEGDEEAEEEQEENLEARGDYKYSEKDSSIFLVDASKAMFESPSEDELTPFDMSIQCIQ--

Parental  YISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDLMGHGSD
          ..SKIISSDRDLLAVVFYGTEKDKNSVN.KNIY.LQELDNPGAK.ILELDQFKGQQGQKRFQDLMGHGSD
Retrocopy --SKIISSDRDLLAVVFYGTEKDKNSVNLKNIYILQELDNPGAKQILELDQFKGQQGQKRFQDLMGHGSD

Parental  YSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGG
          YSLSEVLWV.ANLFSDVQFKMSHK.IMLFTNEDNPHGN.SAKAS.ARTKA.DLRDTGIFLDLMHLKKPGG
Retrocopy YSLSEVLWVHANLFSDVQFKMSHKKIMLFTNEDNPHGNESAKASQARTKASDLRDTGIFLDLMHLKKPGG

Parental  FDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKA
          FD.SLFYRDIISIAEDEDLRVHFEESSKLEDLL.KV.AKETRK.ALSRLKLKLNKDIVISVGIYNLVQKA
Retrocopy FDRSLFYRDIISIAEDEDLRVHFEESSKLEDLLQKVHAKETRK*ALSRLKLKLNKDIVISVGIYNLVQKA

Parental  LKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGF
          LKPPPIKLYRE.NEPVKTKT.TFN.ST.GLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGF
Retrocopy LKPPPIKLYREINEPVKTKTQTFNISTDGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGF

Parental  KPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
          KPLVLLKK.HYLRPSLFVYPEESLVIGSSTLFSALL.KCLEKEVAALCRYTP.RNI.PYFVALV.QEEEL
Retrocopy KPLVLLKKGHYLRPSLFVYPEESLVIGSSTLFSALLMKCLEKEVAALCRYTPHRNISPYFVALVTQEEEL

Parental  DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATSEQVDKMKAIVEKLRFTYRSDSFENPVLQQHFRNL
          DDQKIQVTPPGFQLVFLPFADDKRKMPFTE..MAT.EQVDKMKAIVEKLRFT.RSDSF.NPVLQQHFRNL
Retrocopy DDQKIQVTPPGFQLVFLPFADDKRKMPFTERVMATPEQVDKMKAIVEKLRFTCRSDSFKNPVLQQHFRNL

Parental  EALALDLMEPEQAVDLTCKAVESSSSFHGRL
          EALALDLMEPEQAVDLT...VE......G.L
Retrocopy EALALDLMEPEQAVDLTLPKVEAINKRLGSL

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_2287 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,