RetrogeneDB ID: retro_ggor_1031

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:17023720..17024661(+)
• Located in intron of: ENSGGOG00000008354

Retrocopy information

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

Parental gene information

• Parental gene symbol: QRSL1
• Ensembl ID: ENSGGOG00000008261
• Aliases: None
• Description: None

Sequence

>retro_ggor_1031
AATGCTATAGTAGTTCCGAAATTGTTGGATTAGGGAGCTCTACTAATGGAAAAACAAATTTAGATGAGTTTGCTATGAGA
TCTGGAAATGCAGAAGGCGTATTTGGACCAGTTAAAAACCCCTGGAGTTATTCAAAACAATATAGAGAAAAGAGGAAGCA
GAATCTCCACTTTGAGAATGAAGATTCAGACTGGCTGATAACTGGAGGAAGCTCAGGTGGGAGTGCAGTTGCCGTATCGG
CATTCACACGCTATGCGGCTTTAGGATCAGATACAGGAGGGCCGACCAGAAATCCTGCTGCCTACTGTGGGCTCGTTGGT
TTCAAACCAAACTGTGGCTTAGTTTCCCATCATGGTCTCATTTCCCTAGAGAATTTGATGGAAGTGCAAGGAATCTTAAC
CAGATGTGTGGATGATGCAGCAATTGTCTTGGGTGTACTGGCTGAACATGACCCTACGGATTCTACCACAGCACAGGATC
CTGTTAAACCATTCATGCTTCCCAGTTTGACAAATGTGAGCAAACTATGTATAGGTATTCCAAAGGAATATCTTGTACTG
GAATTATCAAGTGAAGTACAGTCTCTTTGGTCCAAAGCTGCTGACCTCTTTGAGTCTGAGGGGGCCAAAGTAATTGAAGT
ATCCTTTTCTCACATCACTTATTCAATTGTCTGCGACCATCTATTGTGCACATCAGAAGCAGCATCGAGTATAGCAAGAT
TTGATGGGCTACAATATGGTCACAGATGTGACGCTGATGTATCTACTGAAGCCATGTATGCTGCAACCAGACGAGAAGGG
TTCAATGATTTTGTAAGAGGAAGAATTCTCTCAGGAAATGTTTTCTTGTTAAAATAAAAATATGAAAATTATTTCATCAA
AGCACAGAAAGTGAGATGCCTCATTGCTAATGATTTTGTGAATGCTTTTAACTCTGGAGTA

Alignment

ORF - retro_ggor_1031 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.18 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NATVVQKLLDQGALLM-GKTNLDEFAMGSGSTDGVFGPVKNPWSYSKQYREKRKQNPHSENEDSDWLITG
          NA.VV.KLLD.GALLM.GKTNLDEFAM.SG...GVFGPVKNPWSYSKQYREKRKQN.H.ENEDSDWLITG
Retrocopy NAIVVPKLLD*GALLM<GKTNLDEFAMRSGNAEGVFGPVKNPWSYSKQYREKRKQNLHFENEDSDWLITG

Parental  GSSGGSAAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFKPSYGLVSRHGLIPLVNSMDVPGILTRCVDD
          GSSGGSA.AVSAFT.YAALGSDTGG.TRNPAA.CGLVGFKP..GLVS.HGLI.L.N.M.V.GILTRCVDD
Retrocopy GSSGGSAVAVSAFTRYAALGSDTGGPTRNPAAYCGLVGFKPNCGLVSHHGLISLENLMEVQGILTRCVDD

Parental  AAIVLGALAGPDPRDSTTVHDPINKPFMLPSLADVSKLCIGIPKEYLVPELSSEVQSLWSKAADLFESEG
          AAIVLG.LA..DP.DSTT..DP..KPFMLPSL..VSKLCIGIPKEYLV.ELSSEVQSLWSKAADLFESEG
Retrocopy AAIVLGVLAEHDPTDSTTAQDPV-KPFMLPSLTNVSKLCIGIPKEYLVLELSSEVQSLWSKAADLFESEG

Parental  AKVIEVSLPHTSYSIVCYHVLCTSEVASNMARFDGLQYGHRCDIDVSTEAMYAATRREGFNDVVRGRILS
          AKVIEVS..H..YSIVC.H.LCTSE.AS..ARFDGLQYGHRCD.DVSTEAMYAATRREGFND.VRGRILS
Retrocopy AKVIEVSFSHITYSIVCDHLLCTSEAASSIARFDGLQYGHRCDADVSTEAMYAATRREGFNDFVRGRILS

Parental  GNFFLLKENYENYFVKAQKVRRLIANDFINAFNSGV
          GN.FLLK..YENYF.KAQKVR.LIANDF.NAFNSGV
Retrocopy GNVFLLK*KYENYFIKAQKVRCLIANDFVNAFNSGV

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	0.10 RPM	7.48 RPM
SRP007412_cerebellum	0.12 RPM	7.72 RPM
SRP007412_heart	0.00 RPM	4.47 RPM
SRP007412_kidney	0.04 RPM	14.07 RPM
SRP007412_liver	0.03 RPM	6.23 RPM
SRP007412_testis	0.10 RPM	16.16 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_1031 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1031 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1321
Pan troglodytes	retro_ptro_902
Pongo abelii	retro_pabe_1100
Callithrix jacchus	retro_cjac_692

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017557	3 retrocopies	retro_btau_476, retro_btau_493, retro_btau_616,
Choloepus hoffmanni	ENSCHOG00000001036	1 retrocopy	retro_chof_2382,
Callithrix jacchus	ENSCJAG00000006200	4 retrocopies	retro_cjac_1421, retro_cjac_3781, retro_cjac_3919, retro_cjac_692,
Cavia porcellus	ENSCPOG00000021670	1 retrocopy	retro_cpor_179,
Homo sapiens	ENSG00000130348	3 retrocopies	retro_hsap_1321, retro_hsap_466, retro_hsap_514,
Gorilla gorilla	ENSGGOG00000008261	3 retrocopies	retro_ggor_1031 , retro_ggor_445, retro_ggor_474,
Macaca mulatta	ENSMMUG00000008330	2 retrocopies	retro_mmul_429, retro_mmul_675,
Nomascus leucogenys	ENSNLEG00000013383	2 retrocopies	retro_nleu_1403, retro_nleu_1550,
Pongo abelii	ENSPPYG00000016883	3 retrocopies	retro_pabe_1100, retro_pabe_230, retro_pabe_268,
Pan troglodytes	ENSPTRG00000018462	2 retrocopies	retro_ptro_351, retro_ptro_902,