RetrogeneDB ID: retro_ptro_817

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:38568476..38568806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLA2G12A
• Ensembl ID: ENSPTRG00000016362
• Aliases: None
• Description: phospholipase A2, group XIIA [Source:HGNC Symbol;Acc:18554]

Sequence

>retro_ptro_817
CCTTTCCCACATTGCAATTATAAACCCTCCTGCCGAATGGATGGGGCTCTCCACTATCTGGAGTTCATCTTAACATTGGC
ATTGCTTCCCAGACTGAGTGCTGCAACTACTGTGACAGGTGCTATGAGACTGGGGGCAAAAGCAAGAACAAATGGGAAGA
GAAGTTCCAGTATTATTGCCTCTTTAACATCTGCCAAAAATGTGCAGAAGACACTGGGACTGGCTCAGCATGTTCAGGCT
TGTGAAACAACAATGCAGCTCTTGTTTGACAGTGTTAGACATTTAGGCTGTAAACCACACCTGGACAGCCAATGGGTCCC
ATATAGGTGC

Alignment

ORF - retro_ptro_817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 57.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PFPRYGYKPSP-PNGCGSPLFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQ-YCLSKIC-RDV
          PFP...YKPS..PNG.GSPL.GVHLNIGI.S.T.CCN..DRCYET.GKSKN...E.FQ.YCL..IC...V
Retrocopy PFPHCNYKPSC<PNGWGSPLSGVHLNIGIASQTECCNYCDRCYETGGKSKNKWEEKFQYYCLFNIC>KNV

Parental  QKTLGLTQHVQACETTVELLFDSVIHLGCKPYLDSQRAACRC
          QKTLGL.QHVQACETT..LLFDSV.HLGCKP.LDSQ....RC
Retrocopy QKTLGLAQHVQACETTMQLLFDSVRHLGCKPHLDSQWVPYRC

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	6.88 RPM
SRP007412_cerebellum	0.00 RPM	9.82 RPM
SRP007412_heart	0.00 RPM	9.71 RPM
SRP007412_kidney	0.10 RPM	15.22 RPM
SRP007412_liver	0.00 RPM	5.66 RPM
SRP007412_testis	0.00 RPM	6.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_817 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_817 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_817 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_929

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172, retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242, retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30, retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817 ,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623, retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,