RetrogeneDB ID: retro_ggor_239

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:53370558..53371455(+)
• Located in intron of: ENSGGOG00000004787

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A6
• Ensembl ID: ENSGGOG00000023004
• Aliases: None
• Description: None

Sequence

>retro_ggor_239
TCCGCTGCCCGCTGGCCAGCAGGATGGAACAGGCCACACTCCTTTGTCAAGGACTTACTGGCCGGAGGCATTGCCCTCGC
TATTTCCAAGAGGGCAGCGATCCGAGTTGAGCCAGTCAAGGCACTGCTGCAGGTGCAACATGCCAGTAAGCAGACTGTGG
TGACACTGTACAAAGGTGTGGTGTGGTGGGCTGCAAGGTCCACATCCCCAAGGAGCAGGGCACTTGTCCTTCTGGAGGGG
CACCTGGCCAGCACCATCCACTGCTTCCCCATGCAAGCCCTCAACTTTGCCTTTAGGGATAAGTACAAGCAGGTCTTTCT
GGGAGGCGTGCATAAGCATGCACAGTTCTGGAGATATTTTGCAGGCAACCTGGCTTCCTGAGGGGCAGCTGGGGCCATCT
CCCTGTGCTTCTTCTACCCCCTGGAATTTGCCAGAACCCTCCTGGCAGCCAACGTTGGGAAATTGGGCATATAGTGGGAG
CTCAAAGGCCTGGCAGACTGCCTGGAGAAGATCAAGGCTGATGGGATCCGAGGCCTGTCCCAGGGCTTCAGCATCTCGGT
GCAGGGCATCCATATGTACTGGGCAACCTACCTCAGCGTGTATGATACAGCCAAGGGCATGCTCCCTGACCCCAAGAACA
CCCACCACATGGTGAGCTGGATGATTGCCCAGGCAATGACAGTGGCCCATGTGGCCTCCTACCTACTCCTCACAGTGCGG
GCGGATGGTGATGCAGTCCAGGTGCAAAGGAGGTGATATTACGAACACAGGTGCCCTTGATTGTTGGCAGAAGCTCTCCT
AAAATGAAGGGGCAAAGCCTCCTTCAAGGATGCATGGTCCAACATCCTCACAGGCATGGGGCCAAGTCTGGGCCTGTATT
ATGAGCTGAAGAAAGTC

Alignment

ORF - retro_ggor_239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.19 %
• Parental protein coverage: 94.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAARPATMTEQAISFAKDFLAGGIAAAISKTAVAPIERVKLLLQVQHASKQIAADKQYKGIVDCIVRIPK
          SAAR.........SF.KD.LAGGIA.AISK.A....E.VK.LLQVQHASKQ......YKG.V....R...
Retrocopy SAARWPAGWNRPHSFVKDLLAGGIALAISKRAAIRVEPVKALLQVQHASKQTVV-TLYKGVVWWAARSTS

Parental  EQG-VLSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKHTQFWRYFAGNLASGGAAGATSLCFVY
          .....L....G.LA..I..FP.QALNFAF.DKYKQ.FLGGV.KH.QFWRYFAGNLAS.GAAGA.SLCF.Y
Retrocopy PRSRALVLLEGHLASTIHCFPMQALNFAFRDKYKQVFLGGVHKHAQFWRYFAGNLAS*GAAGAISLCFFY

Parental  PLDFARTRLAADVGKSGTEREFRGLGDCLVKITKSDGIRGLYQGFSVSVQGIIIYRAAYFGVYDTAKGML
          PL.FART.LAA.VGK.G...E..GL.DCL.KI.K.DGIRGL.QGFS.SVQGI..Y.A.Y..VYDTAKGML
Retrocopy PLEFARTLLAANVGKLGI*WELKGLADCLEKI-KADGIRGLSQGFSISVQGIHMYWATYLSVYDTAKGML

Parental  PDPKNTHIVVSWMIAQTVTAVAGVVSYPFDTVR-RRMMMQSGRKGADIMYTGTVDCWRKIFRDEG-GKAF
          PDPKNTH..VSWMIAQ..T.VA.V.SY...TVR.R..M.QS..KG.DI..TG..DCW.K....EG.GKA.
Retrocopy PDPKNTHHMVSWMIAQAMT-VAHVASYLLLTVR>RMVM-QSRCKGGDITNTGALDCWQKLS*NEG<GKAS

Parental  FKGAWSNVLRGMGGAFVLVLYDELKKV
          FK.AWSN.L.GMG....L.LY.ELKKV
Retrocopy FKDAWSNILTGMGPS--LGLYYELKKV

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	223.08 RPM
SRP007412_cerebellum	0.08 RPM	203.69 RPM
SRP007412_heart	0.00 RPM	158.54 RPM
SRP007412_kidney	0.00 RPM	279.56 RPM
SRP007412_liver	0.03 RPM	73.28 RPM
SRP007412_testis	0.00 RPM	87.54 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_239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_239 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_150
Pan troglodytes	retro_ptro_146

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005609	1 retrocopy	retro_amel_255,
Homo sapiens	ENSG00000169100	5 retrocopies	retro_hsap_1207, retro_hsap_150, retro_hsap_2460, retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla	ENSGGOG00000014279	8 retrocopies	retro_ggor_1673, retro_ggor_1674, retro_ggor_2146, retro_ggor_2377, retro_ggor_2512, retro_ggor_2517, retro_ggor_2840, retro_ggor_941,
Gorilla gorilla	ENSGGOG00000023004	2 retrocopies	retro_ggor_239 , retro_ggor_2785,
Loxodonta africana	ENSLAFG00000001584	1 retrocopy	retro_lafr_713,
Microcebus murinus	ENSMICG00000006136	2 retrocopies	retro_mmur_1021, retro_mmur_922,
Macaca mulatta	ENSMMUG00000006899	1 retrocopy	retro_mmul_1182,
Nomascus leucogenys	ENSNLEG00000000389	1 retrocopy	retro_nleu_895,
Otolemur garnettii	ENSOGAG00000000963	2 retrocopies	retro_ogar_2492, retro_ogar_2499,