RetrogeneDB ID: retro_ptro_698

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:63553512..63553887(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRI3
• Ensembl ID: ENSPTRG00000019436
• Aliases: None
• Description: Pan troglodytes brain protein I3 (BRI3), mRNA. [Source:RefSeq mRNA;Acc:NM_001252551]

Sequence

>retro_ptro_698
ATGGACCACAAACCTCTGCTGCAGAAGCGGCCTCTGGCCTACAACCTGGAGTCCATCCAGGTCAACTATGCATGCTGCCT
GCACAGCTATGGCGCCACCCCTGCCAGCCCCCGCCAAGGCCCTACCCCTACCTCATCACAGGGGTACCCACCCGCCACCC
CAGGGTCTACAACATCCACAGCCAGACCACCACCTGGTACCCTGCCAACTCCATCATGGTCATGGGAAGCTGTCCCGTCT
GCAGGGTCGGGGGTGCTGGAGGACTGCTTCAGCTTCCTGGGCATTTTCTTGGTCATCATCCTGTTCCCCTTTGGGTTCAT
CTGCCGTTTTGCCTTGAGGAAGCGAAGATGCCCCAACTGCGGAGAGACCTTCGCT

Alignment

ORF - retro_ptro_698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDHKPLLQERPPAYNLEAGQGDYACGPHGYGAIPAAP-PPPPYPYLVTGIPTHHPRVYNIHSRTVTRYPA
          MDHKPLLQ.RP.AYNLE..Q..YAC..H.YGA.PA.P.PP.PYPYL.TG.PT.HPRVYNIHS.T.T.YPA
Retrocopy MDHKPLLQKRPLAYNLESIQVNYACCLHSYGATPASP<PPRPYPYLITGVPTRHPRVYNIHSQTTTWYPA

Parental  NSIVVVGGCPVCRV-GVLEDCFTFLGIFLAIILFPFGFICCFALRKRRCPNCGATFA
          NSI.V.G.CPVCRV.GVLEDCF.FLGIFL.IILFPFGFIC.FALRKRRCPNCG.TFA
Retrocopy NSIMVMGSCPVCRV>GVLEDCFSFLGIFLVIILFPFGFICRFALRKRRCPNCGETFA

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	27.22 RPM
SRP007412_cerebellum	0.00 RPM	18.86 RPM
SRP007412_heart	0.00 RPM	52.81 RPM
SRP007412_kidney	0.00 RPM	72.75 RPM
SRP007412_liver	0.00 RPM	86.22 RPM
SRP007412_testis	0.00 RPM	30.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_698 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_698 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_698 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1095
Pongo abelii	retro_pabe_910

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015227	1 retrocopy	retro_cjac_2527,
Homo sapiens	ENSG00000164713	3 retrocopies	retro_hsap_1095, retro_hsap_1811, retro_hsap_195,
Gorilla gorilla	ENSGGOG00000009646	1 retrocopy	retro_ggor_205,
Microcebus murinus	ENSMICG00000002888	1 retrocopy	retro_mmur_372,
Macaca mulatta	ENSMMUG00000013275	2 retrocopies	retro_mmul_1248, retro_mmul_849,
Otolemur garnettii	ENSOGAG00000000638	1 retrocopy	retro_ogar_63,
Pongo abelii	ENSPPYG00000025815	3 retrocopies	retro_pabe_1484, retro_pabe_50, retro_pabe_910,
Pan troglodytes	ENSPTRG00000019436	1 retrocopy	retro_ptro_698 ,
Tursiops truncatus	ENSTTRG00000015705	2 retrocopies	retro_ttru_706, retro_ttru_91,