RetrogeneDB ID: retro_ggor_2833

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:13195877..13196464(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000022145
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRDX2
• Ensembl ID: ENSGGOG00000025089
• Aliases: None
• Description: None

Sequence

>retro_ggor_2833
ATGTCTTCAGGAAATGCTAAAATTGGGCACCCTGCCCCCAACTTCAAAGCCACAGCTGTTATGCCAGACAGTCAGTTTAA
AGATATCAGCCTGTCTGACTACAAAGGAAATATGTTGTATTCTTCTTTTACCTGCTTGACTTCACTTTTGTGTGCCCCAC
AGAGATCATTGCTTTCAGTGATACAGAAGAATTTAAGAAATTCAACTGCCAAGTGATTGGTGCTTCTGTGGATTCTCACT
TCTGTCAGCTGGCATGGATCCACACCCCTAAGAAACAAGGAGGACTGGGACCCAGGAACATTCCTTTGGCCTCAGACCCG
AAGTGCACCATTGCTCAGGATTATGGGATCTTAAAGGCTGAAGAAGGCATCTCATTCAGGGGCCTCTTTATCGTTGATGA
TATGGGTATTCTTCGGCAGATCACTGTAAGTGACCTCCCTGTTGACTGCTCTGTGGATGAGACTTTGAGACTAGTTCAGG
CCTTCCAGTTCACTGACAAACACGGGGAAGTGTGCCTAGCTGGCTGGAAACCTGGCAGTGATACTATCAAGCCTGATGTC
CAAAAGAGCAAAGAATATTTCTCCAAG

Alignment

ORF - retro_ggor_2833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 98.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGNARIGKPAPDFKATAVV-DGAFKEVKLSDYKG-KYVVLFFYPLDFTFVCPTEIIAFSNRAEDFRKL
          M.SGNA.IG.PAP.FKATAV..D..FK...LSDYKG.KYVV.FFY.LDFTFVCPTEIIAFS...E.F.K.
Retrocopy MSSGNAKIGHPAPNFKATAVMPDSQFKDISLSDYKG<KYVVFFFYLLDFTFVCPTEIIAFSD-TEEFKKF

Parental  GCEVLGVSVDSQFTHLAWINTPRKEGGLGPLNIPLLADVTRRLSEDYGVLKTDEGIAYRGLFIIDGKGVL
          .C.V.G.SVDS.F..LAWI.TP.K.GGLGP.NIPL..D.......DYG.LK..EGI..RGLFI.D..G.L
Retrocopy NCQVIGASVDSHFCQLAWIHTPKKQGGLGPRNIPLASDPKCTIAQDYGILKAEEGISFRGLFIVDDMGIL

Parental  RQITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSK
          RQITV.DLPV..SVDE.LRLVQAFQ.TD.HGEVC.AGWKPGSDTIKP.V..SKEYFSK
Retrocopy RQITVSDLPVDCSVDETLRLVQAFQFTDKHGEVCLAGWKPGSDTIKPDVQKSKEYFSK

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	11.80 RPM	144.96 RPM
SRP007412_cerebellum	7.49 RPM	111.50 RPM
SRP007412_heart	3.66 RPM	112.07 RPM
SRP007412_kidney	27.35 RPM	79.24 RPM
SRP007412_liver	11.08 RPM	44.29 RPM
SRP007412_testis	13.36 RPM	26.42 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_2833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2833 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4230
Pan troglodytes	retro_ptro_2874

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012307	3 retrocopies	retro_amel_1188, retro_amel_1710, retro_amel_55,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004882	4 retrocopies	retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Dipodomys ordii	ENSDORG00000009005	1 retrocopy	retro_dord_176,
Felis catus	ENSFCAG00000000473	1 retrocopy	retro_fcat_1755,
Homo sapiens	ENSG00000167815	3 retrocopies	retro_hsap_1184, retro_hsap_3278, retro_hsap_3500,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833 , retro_ggor_923,
Gorilla gorilla	ENSGGOG00000026364	1 retrocopy	retro_ggor_986,
Gorilla gorilla	ENSGGOG00000026790	1 retrocopy	retro_ggor_1351,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061,
Monodelphis domestica	ENSMODG00000006978	1 retrocopy	retro_mdom_1770,
Mustela putorius furo	ENSMPUG00000004591	2 retrocopies	retro_mputfur_28, retro_mputfur_660,
Mus musculus	ENSMUSG00000005161	2 retrocopies	retro_mmus_2403, retro_mmus_472,
Nomascus leucogenys	ENSNLEG00000012800	2 retrocopies	retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii	ENSOGAG00000024998	2 retrocopies	retro_ogar_1993, retro_ogar_244,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000010541	3 retrocopies	retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Rattus norvegicus	ENSRNOG00000003520	2 retrocopies	retro_rnor_2288, retro_rnor_497,
Sorex araneus	ENSSARG00000000146	1 retrocopy	retro_sara_96,
Sarcophilus harrisii	ENSSHAG00000015596	1 retrocopy	retro_shar_305,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,