RetrogeneDB ID: retro_ggor_471

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:200626941..200628069(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000023958
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ggor_471
GAGGAATCCAGAAAGCTAGAAGACCTGTTGAGGCAGGTTTGAGCCAAGGAGATCAGTTAGTGAACACTCAGCAGGTTAAA
GCTGAAGCTCAATAAAGATATAGTGCTCTCCGTGGGCATTTATAATCTGATCCAGAAGGCTCTCAAGCCTCCTCCAATAA
AGCCCTATCGAGAAATAGATGAATCAGTGAAAACCAAGACCTGGATATTTAACGTAAATACAGGCAGTTGGCTTCTGCCT
AGAGATACCAAGAGGTCTCAGACCTATGGAAGGCGTCAGATTATACTGGAGAAAGAGGAAACAGAAGAGCTAAAACAGTT
TGATAAACCAGGTTTGATTCTCATGGGTTTAAGCCCTTGGTAAAGCTGAAGAAGCACCGTTACCTGAGGCCCTCCTTGTT
TGTGTACTCTGAAGAGTCGCTGATGAGTTAGAGCTCAACCCTGTTCAGTGCTCTACTCATCAAGTGTCTGGAGAAGGAGG
TCACAGCATTGTGCAGATACACACCCTGCAGGAACATCCCCCCTTATTTTGTGGCTTTGGTGCCACAGGAAGAGGAGTTG
GATGATCAGAAAATTCAGGTGCCTCCTGCAGGCTTCCAGCTGGTCTTTTTATGCTATGCTGATAATAAAGGGAGGTGCCC
TTTGCTAAAAAAGTCACGGCAACCCCAGAGCAGGGAGATAAGGTGAAGGCTATTGTTCAGAAGCTCCGATTCAAATACAG
AAGTGACAGCTTTGAGAACTCTGTGCTGCAGCAGCGTTCCAGGAACCTGGAGGCCTTGGCCTTGGATTTGATGGAGCCTG
AACAAGCAGTGGACCTGACATTGCCTGAGGTTGAAGCAATGAATAAAAGACTGGGCTCCCCACTGGTGGATAAGTTTAAG
GAACTTCTCTACCCACCAGATTACAATCCTGAAGGGAAAGTTAGCAACATAAAACACAATAATGAAGGTTTCAGAAGCAA
AAGGCCCAAGGTGGAGTATTCAGAAGAGGAGCTGAAGACCCACATAAGCAACAGCATGCTGGGCAAGTTTGCTGTGCCCA
TGCTGAAAGAGACCTGCTGGGGTATGGGCTAAAGAGCAGGCTGAAGAAGCAGGAGCCACTGGAAGCCCTCACCAATCACT
TCCAGAAC

Alignment

ORF - retro_ggor_471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.74 %
• Parental protein coverage: 61.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTF
          EES.KLEDLLR.V.AKE.....LSRLKLKLNKDIV.SVGIYNL.QKALKPPPIK.YRE..E.VKTKT..F
Retrocopy EESRKLEDLLRQV*AKEIS**TLSRLKLKLNKDIVLSVGIYNLIQKALKPPPIKPYREIDESVKTKTWIF

Parental  NTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLM-GFKPLVLLKKHHYLRPSLFVYPEE
          N..TG..LLP.DTKRSQ.YG.RQIILEKEETEELK.FD.PGL.LM.GFKPLV.LKKH.YLRPSLFVY.EE
Retrocopy NVNTGSWLLPRDTKRSQTYGRRQIILEKEETEELKQFDKPGLILM<GFKPLVKLKKHRYLRPSLFVYSEE

Parental  SLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADD
          SL...SSTLFSALLIKCLEKEV.ALCRYTP.RNIPPYFVALVPQEEELDDQKIQV.P.GFQLVFL..AD.
Retrocopy SLMS*SSTLFSALLIKCLEKEVTALCRYTPCRNIPPYFVALVPQEEELDDQKIQVPPAGFQLVFLCYADN

Parental  K-RKMPFTEKIMATPEQVGKMKAIVDKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKV
          K.R..PF..K..ATPEQ..K.KAIV.KLRF.YRSDSFEN.VLQQ..RNLEALALDLMEPEQAVDLTLP.V
Retrocopy K<REVPFAKKVTATPEQGDKVKAIVQKLRFKYRSDSFENSVLQQRSRNLEALALDLMEPEQAVDLTLPEV

Parental  EAMNKRLGS-LVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPM
          EAMNKRLGS.LVD.FKEL.YPPDYNPEGKV...KH.NEG..SKRPKVEYSEEELKTHIS...LGKF.VPM
Retrocopy EAMNKRLGSPLVDKFKELLYPPDYNPEGKVSNIKHNNEGFRSKRPKVEYSEEELKTHISNSMLGKFAVPM

Parental  LKEAC-RAYGLKSGLKKQELLEALTKHFQD
          LKE.C...YGLKS.LKKQE.LEALT.HFQ.
Retrocopy LKETC<LGYGLKSRLKKQEPLEALTNHFQN

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	0.00 RPM	146.74 RPM
SRP007412_cerebellum	0.00 RPM	119.38 RPM
SRP007412_heart	0.03 RPM	45.69 RPM
SRP007412_kidney	0.00 RPM	146.75 RPM
SRP007412_liver	0.00 RPM	85.49 RPM
SRP007412_testis	0.10 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_471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_471 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_511

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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,