RetrogeneDB ID: retro_ggor_599

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:94095398..94095856(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000024160
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPA2
• Ensembl ID: ENSGGOG00000015287
• Aliases: None
• Description: None

Sequence

>retro_ggor_599
ACTGTCATTCCTCCAGAAAAATATGTCATTGTGGCAGGCGATTTGAGACCTCTTCAGGACAAAAAGAGCCTGGTACCCTT
TAAAATCATGCCCCTGGAGGATATGAATTAGTTCACCATACATATTCTGGAAGTGATCAATGTACACATGATACTAAGCA
AAGCTAACAGGCAGCCCTCAGCAGGGAGAGCACCTATCAGCAATCCAGGAATGAGTGAAGCAGGGAAATTTGGTGGGAAT
AACTTCATGCCAGCAAAGGACCTACTGTGGCCCAAAACCAGGTGTTGAATTTGATTAAGCGTTGCCCAAGACCGAAAGAA
TTGAACTTTCAGGATCTTAAGAACCAGCTCAACCACATGTCTGTATCCTCAATCAAGCAAGCTGTGGATTTTCTGAGCAA
TGAGGGGCACATCTATTCTTCTGTGGATGATTATCATTTTAAATCCACAGATGCAGAA

Alignment

ORF - retro_ggor_599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.42 %
• Parental protein coverage: 56.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPG
          TV.PPE.YV.VAG.LR..Q.KKSLV.FKIMPLEDMN.FT.HILEVIN.HM.LSKAN.QPSAGRAPISNPG
Retrocopy TVIPPEKYVIVAGDLRPLQDKKSLVPFKIMPLEDMN*FTIHILEVINVHMILSKANRQPSAGRAPISNPG

Parental  MSEAGNFGGNSFMPA-NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIY
          MSEAG.FGGN.FMPA..G.TVAQNQVLNLIK.CPRP..LNFQDLKNQL.HMSVSSIKQAVDFLSNEGHIY
Retrocopy MSEAGKFGGNNFMPA<KGPTVAQNQVLNLIKRCPRPKELNFQDLKNQLNHMSVSSIKQAVDFLSNEGHIY

Parental  STVDDDHFKSTDAE
          S.VDD.HFKSTDAE
Retrocopy SSVDDYHFKSTDAE

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	0.05 RPM	16.02 RPM
SRP007412_cerebellum	0.00 RPM	22.50 RPM
SRP007412_heart	0.00 RPM	7.29 RPM
SRP007412_kidney	0.00 RPM	20.77 RPM
SRP007412_liver	0.00 RPM	14.03 RPM
SRP007412_testis	0.10 RPM	89.20 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_599 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_599 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_704
Pongo abelii	retro_pabe_523

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225,
Homo sapiens	ENSG00000117748	2 retrocopies	retro_hsap_704, retro_hsap_815,
Gorilla gorilla	ENSGGOG00000015287	2 retrocopies	retro_ggor_599 , retro_ggor_668,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519,
Macaca mulatta	ENSMMUG00000018172	2 retrocopies	retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys	ENSNLEG00000009702	3 retrocopies	retro_nleu_1409, retro_nleu_250, retro_nleu_2511,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180,
Otolemur garnettii	ENSOGAG00000015583	2 retrocopies	retro_ogar_1838, retro_ogar_2066,
Pongo abelii	ENSPPYG00000001651	2 retrocopies	retro_pabe_523, retro_pabe_728,
Pan troglodytes	ENSPTRG00000000420	1 retrocopy	retro_ptro_566,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257, retro_itri_773,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,