RetrogeneDB ID: retro_ptro_3313

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:26200030..26200406(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNASEH2C
• Ensembl ID: ENSPTRG00000038742
• Aliases: None
• Description: Ribonuclease H2, subunit C [Source:UniProtKB/TrEMBL;Acc:K6ZY76]

Sequence

>retro_ptro_3313
CCCACCACGGTGCGGCGCTTCATCACGCCTGCCATCCGCCAGGGCCCCGAGGGACTCTTAAGTGTAGTTTCGGGGCCGCA
GTCTACGGGGCGACGAGGTGGCAGTGCCGTCCGGCCTCGTGGGATACGTGATGGTGACTGAACAGGAGGAGGTGTCGATG
GGGAAGCCAAACCCCTGGCGGGGTTCCGGGAGTGACAACCAAGAAGAGGAGCTTCTGGAGCGGGACTTTGACCGCTTCCT
CGGAACCACTACCAGCTTCAGCCGCTTCACCCTGTAGGGCACCCTGTGGGGCTTCCTTGGCCCGGAAGCCAAACTGCGTG
GGGCCTTAACTTGGCCCAGCCTCGCGGCAACGATTCACGCGCAGGTGCCCAAGGAC

Alignment

ORF - retro_ptro_3313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.6 %
• Parental protein coverage: 89.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAPVGRFFTPAIRQGPEGLE-VSFRGRCLRGEEVAVPPGLVGYVMVTEEKEVSMGKPDPLRDSGTDDQEE
          P..V.RF.TPAIRQGPEGL..V.FRGR.LRG.EVAVP.GLVGYVMVTE..EVSMGKP.P.R.SG.D.QEE
Retrocopy PTTVRRFITPAIRQGPEGLL>V*FRGRSLRGDEVAVPSGLVGYVMVTEQEEVSMGKPNPWRGSGSDNQEE

Parental  EPLERDFDRFIGATANFSRFTLWG-LETIPGPDAKVRGALTWPSLAAAIHAQVPED
          E.LERDFDRF.G.T..FSRFTL.G.L....GP.AK.RGALTWPSLAA.IHAQVP.D
Retrocopy ELLERDFDRFLGTTTSFSRFTL*GTLWGFLGPEAKLRGALTWPSLAATIHAQVPKD

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	0.02 RPM	11.31 RPM
SRP007412_cerebellum	0.00 RPM	10.54 RPM
SRP007412_heart	0.03 RPM	7.26 RPM
SRP007412_kidney	0.00 RPM	16.66 RPM
SRP007412_liver	0.03 RPM	12.01 RPM
SRP007412_testis	0.00 RPM	9.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3313 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3313 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3313 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000019837	1 retrocopy	retro_mmul_284,
Pan troglodytes	ENSPTRG00000038742	1 retrocopy	retro_ptro_3313 ,