RetrogeneDB ID: retro_ggor_1512

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 20:47736183..47737727(+)
• Located in intron of: ENSGGOG00000001956

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLYR1
• Ensembl ID: ENSGGOG00000016258
• Aliases: None
• Description: None

Sequence

>retro_ggor_1512
CCTCATGGAAAGAAATGCTTCTTTGTGAAATTTTTTTGGAACATAAGATCATGCCTGGATTAAAGTGAAACAGCTGAAGC
CGTATCATGCTCATAAAGAGGAAATGATAAAGATTCTCAAGGGTAAACTATTCCAACAAGCAGTGGATGCCGCCAAAGAG
TTTCTCAGGAGAGCCCAAAGGGAAAGATCAGACGTCATCCCACAATTCTGCTGATGACAAGAATTGGCTTAATTCCAGTG
AGGAGAGAAGCAGGCCAAACTCAGGTGATGAGAAGTGCAAACAGCCTGTCTGAAGGAAAAGTGAAGAAGATCATGGGAGA
TGGAAAGAAGGGGGTGTCTTCGGGCTCTTCAGAGAGAGGCTCCAAATCCCCTCTGAAAAGAATCCAAGAGCAAAGTCCCC
AGAAGCAGGGTCAGCCCCCAAAGAATGAGAAGAATGTCACCATCCTGGAGTCCGGTACCTTGAAGTGGATGATGGCCGGA
CCAGTGGCTGCATTTAAATGGCAGACCAGAAGCGAGCCTGTTAAAGATGCAGATCCTCATTTCCATCATTTCCTGCTAAG
CCAAACAGAAGCCATCTCTGTCTGTTACCAGGCAATCACAAAGAAGTTGAAAATATGTGAAGAGGAAACTGGTTCCACCT
CCATCCGGGCAGCTGACAGCACGGCTGTGAATGGCAGCATCACAGACAAAAAGATGGGATTTGGGGGCCTTGGTCTCATG
AGAAGTGGAATCGTCTCTAACTTGCTAAAAATGGGTCACACAGTGACTGTCTGGAACCGCACTGCCAAGAAACGTGATTT
GTTCATCTAGGAGGGGGCCCGCCTGGGAAGAACCCCTGCTGAAGTCCTCTCAACCTGTGACATCACTTTCGCCCGTGTGT
TGGATCCCAAGGCGGCCAAGGACCTGGTGCTGGGCCCCAGTGGTATGCTACAAGGGATCTGCCCTGGAAAGTGTTACGTG
GACATGTCAACGGTGGACGCTGACATAGTCACTTAGCTGGCCCGGGTGATTGCGTCCAGGTCGGGGGGTCGCTTTCCAGA
AGCTCCCATCTCAGGGAATCAGCAGCTTTCTAATCACGGAATGTTGGTGATCTTAGCAGCTGGAGACAGGGGCCTATAGG
AGGACTGCAGCAGCTGCTTCCAGGCGATAGGGAAGACCTCCTCCTTCCTAGGTGAAGTTGGCAACGCAGCCAAGATGATG
CTGATTGTGAACATAGTCCAAGGGAGCTTCATAGCCATGATCACTGAGGTGCTGACCCTGGCCTAGGTGACAGATCAGGC
CCAGCAGACACTCTTGGACATCCTCAATCAGGGACAGTTGGCCAGCATCTTCCTAGACCAGAAGTGCCAAAATACCCTGC
AAGGAAACTTTAAGCCTGAATTCTACCGAAATACATGCAGAAGGATCTCTGCTTAGCCATTGTGCTGGGCAATGCGGTCA
ACTGTCCGACTCCCATGGCAGCTGCAGCCAACCAGGTGTACAAAAGAGCCAAGGCACTGGACCAGTCCAACAATATGTCC
GCTGTGTCCTGAGCCTACATACAC

Alignment

ORF - retro_ggor_1512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.69 %
• Parental protein coverage: 93.67 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PRGKKCFFVKFF-GTEDHAWIKVEQLKPYHAHKEEMIKINKGKRFQQAVDAVEEFLRRA-KGKDQTSSHN
          P.GKKCFFVKFF.GT.DHAWIKV.QLKPYHAHKEEMIKI.KGK.FQQAVDA..EFLRRA.KGKDQTSS..
Retrocopy PHGKKCFFVKFF>GT*DHAWIKVKQLKPYHAHKEEMIKILKGKLFQQAVDAAKEFLRRA>KGKDQTSS-H

Parental  SSDDKNRRNSSEERSRPNSGDEKR-KLSLSEGKVKKNMGEGKKRVSSGSSERGSKSPLKRAQEQSPRKRG
          .S.D......S.E..............SLSEGKVKK.MG.GKK.VSSGSSERGSKSPLKR.QEQSP.K.G
Retrocopy NSADDKNWLNSSEERSRPNSGDEK>ANSLSEGKVKKIMGDGKKGVSSGSSERGSKSPLKRIQEQSPQKQG

Parental  RPPKDEKDLTIPESSTVKGMMAGPMAAFKWQPTASEPVKDADPHFHHFLLSQTEKPAVCYQAITKKLKIC
          .PPK.EK..TI.ES.T.K.MMAGP.AAFKWQ.T.SEPVKDADPHFHHFLLSQTE...VCYQAITKKLKIC
Retrocopy QPPKNEKNVTILESGTLKWMMAGPVAAFKWQ-TRSEPVKDADPHFHHFLLSQTEAISVCYQAITKKLKIC

Parental  EEETGSTSIQAADSTAVNGSITPTDKKIGFLGLGLMGSGIVSNLLKMGHTVTVWNRTAEKCDLFIQEGAR
          EEETGSTSI.AADSTAVNGSIT..DKK.GF.GLGLM.SGIVSNLLKMGHTVTVWNRTA.K.DLFI.EGAR
Retrocopy EEETGSTSIRAADSTAVNGSIT--DKKMGFGGLGLMRSGIVSNLLKMGHTVTVWNRTAKKRDLFI*EGAR

Parental  LGRTPAEVVSTCDITFACVSDPKAAKDLVLGPSGVLQGIRPGKCYVDMSTVDADTVTELAQVIVSR-GGR
          LGRTPAEV.STCDITFA.V.DPKAAKDLVLGPSG.LQGI.PGKCYVDMSTVDAD.VT.LA.VI.SR.GGR
Retrocopy LGRTPAEVLSTCDITFARVLDPKAAKDLVLGPSGMLQGICPGKCYVDMSTVDADIVT*LARVIASRSGGR

Parental  FLEAPVSGNQQLSNDGMLVILAAGDRGLYEDCSSCFQAMGKTSFFLGEVGNAAKMMLIVNMVQGSFMATI
          F.EAP.SGNQQLSN.GMLVILAAGDRGL.EDCSSCFQA.GKTS.FLGEVGNAAKMMLIVN.VQGSF.A.I
Retrocopy FPEAPISGNQQLSNHGMLVILAAGDRGL*EDCSSCFQAIGKTSSFLGEVGNAAKMMLIVNIVQGSFIAMI

Parental  AEGLTLAQVTGQSQQTLLDILNQGQLASIFLDQKCQNILQGNFKPDFYL-KYIQKDLRLAIALGDAVNHP
          .E.LTLA.VT.Q.QQTLLDILNQGQLASIFLDQKCQN.LQGNFKP.FY..KY.QKDL.LAI.LG.AVN.P
Retrocopy TEVLTLA*VTDQAQQTLLDILNQGQLASIFLDQKCQNTLQGNFKPEFYR<KYMQKDLCLAIVLGNAVNCP

Parental  TPMAAAANEVYKRAKALDQSDNDMSAVYRAYIH
          TPMAAAAN.VYKRAKALDQS.N.MSAV..AYIH
Retrocopy TPMAAAANQVYKRAKALDQS-NNMSAVS*AYIH

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	0.19 RPM	113.75 RPM
SRP007412_cerebellum	0.28 RPM	77.97 RPM
SRP007412_heart	0.00 RPM	23.64 RPM
SRP007412_kidney	0.04 RPM	64.73 RPM
SRP007412_liver	0.16 RPM	32.02 RPM
SRP007412_testis	0.00 RPM	64.13 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_1512 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1512 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_2514

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019912	1 retrocopy	retro_cjac_2514,
Erinaceus europaeus	ENSEEUG00000011783	1 retrocopy	retro_eeur_477,
Homo sapiens	ENSG00000140632	1 retrocopy	retro_hsap_2432,
Gorilla gorilla	ENSGGOG00000016258	1 retrocopy	retro_ggor_1512 ,
Macaca mulatta	ENSMMUG00000009567	1 retrocopy	retro_mmul_621,
Nomascus leucogenys	ENSNLEG00000009950	1 retrocopy	retro_nleu_240,
Oryctolagus cuniculus	ENSOCUG00000010486	1 retrocopy	retro_ocun_680,
Pongo abelii	ENSPPYG00000007072	1 retrocopy	retro_pabe_1791,
Pan troglodytes	ENSPTRG00000007730	1 retrocopy	retro_ptro_1404,