RetrogeneDB ID: retro_ptro_11

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:124835169..124836147(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000002353
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCGF2
• Ensembl ID: ENSPTRG00000009074
• Aliases: None
• Description: None

Sequence

>retro_ptro_11
ATGCATCGAACAACGAGAATCAAGATCACTGAGCTAAATCCCCACCTGATGTGTGTGCTTTGTGGAGGGTACTTCATTGA
TGCCACAACCATAATAGAATGTCTACATTCCTTCTGTAAAACGTGTATTGTTCGTTACCTGGAGACCAGCAAGTATTGTC
CTATTTGTGATGTCCAAGTTCACAAAACCAGACCACTACTGAATATAAGGTCAGATAAAACTCTCCAAGATATTGTATAC
AAATTAGTTCCAGGGCTTTTCAAAAATGAAATGAAGAGAAGAAGGGATTTTTATGCAGCTCATCCTTCTGCTGATGCTGC
CAATGGCTCTAATGAAGATAGAGGAGAGGTTGCAGATGAAGATAAGAGAATTATAACTGATGATGAGATAATAAGCTTAT
CCATTGAATTCTTTGACCAGAACAGATTGGATCGGAAAGTAAACAAAGACAAAGAGAAATCTAAGGAGGAGGTGAATGAT
AAAAGATACTTACGATGCCCAGCAGCAATGACTGTGATGCACTTAAGAAAGTTTCTCAGAAGTAAAATGGACATACCTAA
TACTTTCCAGATTGATGTCATGTATGAGGAGGAACCTTTAAAGGATTATTATACACTAATGGATATTGCCTACATTTATA
CCTGGAGAAGGAATGGTCCACTTCCATTGAAATACAGAGTTCGACCTACTTGTAAAAGAATGAAGATCAGTCACCAGAGA
GATGGACTGACAAATGCTGGAGAACTGGAAAGTGACTCTGGAAGTGACAAGGCCAACAGCCCAGCAGGAGGTATTCCCTC
CACCTCTTCTTGTTTGCCTAGCCCCAGTACTCCAGTGCAGTCTCCTCATCCACAGTTTCCTCACATTTCCAGTACTATGA
ATGGAACCAGCAACAGCCCCAGCGGTAACCACCAATCTTCTTTTGCCAATAGACCTCGAAAATCATCAGTAAATGGGTCA
TCAGCAACTTCTTCTGGT

Alignment

ORF - retro_ptro_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.22 %
• Parental protein coverage: 69.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHRTTRIKITELNPHLMCALCGGYFIDATTIVECLHSFCKTCIVRYLETNKYCPMCDVQVHKTRPLLSIR
          MHRTTRIKITELNPHLMC.LCGGYFIDATTI.ECLHSFCKTCIVRYLET.KYCP.CDVQVHKTRPLL.IR
Retrocopy MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIR

Parental  SDKTLQDIVYKLVPGLFKDEMKRRRDFYAAYPLTEVPNGSNEDRGEVLEQEKGTLSDDEIVSLSIEFYEG
          SDKTLQDIVYKLVPGLFK.EMKRRRDFYAA.P.....NGSNEDRGEV....K....DDEI.SLSIEF...
Retrocopy SDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEDKRIITDDEIISLSIEFFD-

Parental  ARDRDEKKGPLENGDGDKEKTGVRFLRCPAAMTVMHLAKFLRNKMDVPSKYKVEVLYEDEPLKEYYTLMD
          ...R...K..........E....R.LRCPAAMTVMHL.KFLR.KMD.P......V.YE.EPLK.YYTLMD
Retrocopy -QNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYEEEPLKDYYTLMD

Parental  IAYIYPWRRNGPLPLKYRVQPACKRLTLA
          IAYIY.WRRNGPLPLKYRV.P.CKR....
Retrocopy IAYIYTWRRNGPLPLKYRVRPTCKRMKIS

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	22.00 RPM
SRP007412_cerebellum	0.00 RPM	38.97 RPM
SRP007412_heart	0.00 RPM	16.82 RPM
SRP007412_kidney	0.00 RPM	60.44 RPM
SRP007412_liver	0.00 RPM	14.21 RPM
SRP007412_testis	0.00 RPM	6.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_11 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_11 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_11 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000011789	1 retrocopy	retro_eeur_392,
Pan troglodytes	ENSPTRG00000009074	1 retrocopy	retro_ptro_11 ,
Pan troglodytes	ENSPTRG00000012094	1 retrocopy	retro_ptro_704,