RetrogeneDB ID: retro_ggor_3067

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:148089122..148090964(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000026303
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: XRCC6
• Ensembl ID: ENSGGOG00000015885
• Aliases: None
• Description: None

Sequence

>retro_ggor_3067
GCAGTAGCCAACTTGTCAGGGTGGGAGTCATATTACAAAACCGAGGGCAGTGAAGAAGCTGAAGAAGAACAAGAAGAGAA
CCTTGAAGCAAGAGGAGACTATAAATATTCAGAAAGAGATAGTTTGATTTTTCTGGTTGATGCCTCCAAGGCTATGTTTG
AATCTCCTAGTGAAGATGAATTGACACCTTTTGACATGAGCATCCAGTGTATTCAAAGTGTGTACATCAGTAAGATCATA
AGCAGTGATCGAGATCTCTTGGCTGTGGTGTTCTATGGTACCGAGAAAGACAAAAATTCAGTGAATTTAAAAAATATTTA
CGTCTTATAGGAGCTGGATAATCCAGGTGCAAAATGAATTCTAGAGCTTGACCAGTTTAAGGGGCAGCAGGGACAAAAAC
GTTTCCAAGACCTGATGGGCCATGGATCTGACTACTCACTCAGTGAAGTGCTGTGGGTCCGTGCCAACCTCTTTAGTGAT
GTCCAATTCAAGATGAGTCATAAGAAGATCACGCTCTTCACCAATGAAGACAACCCCCATGGCAATGACAGTGCCAAAGC
CAGCCAGGCCAGGACCAAAGCCGATGATCTCCGAGATACAGGCATCTTCCTTGACTTGATGCATCTGAAGAAACCTGGAG
GCTTTGACATATCCTTGTTCTACAGAGATATCATCAGCATAGCAGAGGATGAGGACCTCAGGGTTCACTTTGAGGAATCC
AGCAAGCTAGAAGACCTGTTGCAGAAGGTTCACGCCAAAGAGACCGGGAAGTGAGCACTCAGCAGGTTAAAGCTGAAGCT
CAACAAAGATATAGTGATCTCTGTGGGCATTTATAATCTGGTCCAGAAGGCTCTCAAGCCTCCTCCAATAAAGCTCTATC
GGGAAATAAATGAACCAGTGAAAACCAAGACCCGGACCTTTAATACAAGTACAGACGATTTGCTTCTGCCTAGCGATACC
AAGTGGTCTCAAATCTATGGGAGTCGTCAGATTATACTGGAGAAAGAGGAAACAGAAGAGCTAAAACGGTTTGATGATCC
AGGTTTGATGCTCATGGGTTTCAAGCCATTGGTACTGCTGAAGAAACGCCATTACCTGAGGCCCTCCCTGTTTGTGTACC
CAGAGGAGCCGCTGGTGATTGGGAGCTTAACCCTGTTCAGTCCTCTGCTCATCAAGTGTCTGGAGAAGGAGGTGGCAGCA
TTGTGCAGATACACACCCCGCAGGAACATCCCCCCTTATTTTGTGGCTTTGGTGACACAGGAAGAAGTGTTGGATGACCA
GAAAATTCAGGTGACTCCTCTGGGCTTCCAGCTGGTCTTTTTACCCTTTGCTGATGATAAAAGGAAGATGCCCTTTACGG
AAAAAGTCACGGCAACTCCAGAGCAGGTGGACAAGATGAAGGCTATCGTTGAGAAGCTTCGCTTCATGTACAGTGACAGC
TTTGAGAACCCCGTGCTGCAGCAGCACTTCAGGAACCTGGAGGCCGAGGCCTTGGCCTTGGATTTGATGGAGCCAGAACA
AGCAGTGGACCTGACATTGCCCAAGGTTGAAGCAATAAATAGAAGACTGGGCTCCTTGGTGGATGAGTTTAAGGAGCTTG
TTTACCCACCAGATTACAATCCTGAAGGGAAAGTTACCAAGAGAAAACATGATAATGAAGGTTCTGGAAGCAAAAGGCCC
AAGGTGGAGTATTCAGAAGAGGAGCTGAAGACCCACATTAGCAAGGGCACGCTGGGCAAGTTCACTGTGCCCATGCTGAA
AGAGGCCTGCCGGGCTTACGGGCTGAAGAGTGGGCTGAAGAAGCAGGAGCTGCTGGAAGCCCTCACCAAGCACTTCCAGG
AT

Alignment

ORF - retro_ggor_3067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVANMSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQQ
          AVAN.SGWESYYKTEG.EEAEEEQEENLEA.GDYKYS.RDSLIFLVDASKAMFES.SEDELTPFDMSIQ.
Retrocopy AVANLSGWESYYKTEGSEEAEEEQEENLEARGDYKYSERDSLIFLVDASKAMFESPSEDELTPFDMSIQ-

Parental  CIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDLM
          CIQSVYISKIISSDRDLLAVVFYGTEKDKNSVN.KNIYVL.ELDNPGAK.ILELDQFKGQQGQKRFQDLM
Retrocopy CIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNLKNIYVL*ELDNPGAK*ILELDQFKGQQGQKRFQDLM

Parental  GHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHL
          GHGSDYSLSEVLWV.ANLFSDVQFKMSHK.I.LFTNEDNPHGNDSAKAS.ARTKA.DLRDTGIFLDLMHL
Retrocopy GHGSDYSLSEVLWVRANLFSDVQFKMSHKKITLFTNEDNPHGNDSAKASQARTKADDLRDTGIFLDLMHL

Parental  KKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYN
          KKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLL.KV.AKET.K.ALSRLKLKLNKDIVISVGIYN
Retrocopy KKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLQKVHAKETGK*ALSRLKLKLNKDIVISVGIYN

Parental  LVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGL
          LVQKALKPPPIKLYRE.NEPVKTKTRTFNTST..LLLPSDTK.SQIYGSRQIILEKEETEELKRFDDPGL
Retrocopy LVQKALKPPPIKLYREINEPVKTKTRTFNTSTDDLLLPSDTKWSQIYGSRQIILEKEETEELKRFDDPGL

Parental  MLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVP
          MLMGFKPLVLLKK.HYLRPSLFVYPEE.LVIGS.TLFS.LLIKCLEKEVAALCRYTPRRNIPPYFVALV.
Retrocopy MLMGFKPLVLLKKRHYLRPSLFVYPEEPLVIGSLTLFSPLLIKCLEKEVAALCRYTPRRNIPPYFVALVT

Parental  QEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVDKLRFTYRSDSFENPVLQQ
          QEE.LDDQKIQVTP.GFQLVFLPFADDKRKMPFTEK..ATPEQV.KMKAIV.KLRF.Y.SDSFENPVLQQ
Retrocopy QEEVLDDQKIQVTPLGFQLVFLPFADDKRKMPFTEKVTATPEQVDKMKAIVEKLRFMY-SDSFENPVLQQ

Parental  HFRNL--EALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSK
          HFRNL..EALALDLMEPEQAVDLTLPKVEA.N.RLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSK
Retrocopy HFRNLEAEALALDLMEPEQAVDLTLPKVEAINRRLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSK

Parental  RPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD
          RPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD
Retrocopy RPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.34 RPM	146.74 RPM
SRP007412_cerebellum	0.32 RPM	119.38 RPM
SRP007412_heart	0.09 RPM	45.69 RPM
SRP007412_kidney	0.25 RPM	146.75 RPM
SRP007412_liver	0.34 RPM	85.49 RPM
SRP007412_testis	2.28 RPM	536.54 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_3067 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3067 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4913
Pongo abelii	retro_pabe_3821

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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,