RetrogeneDB ID: retro_ptro_704

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:76014248..76014640(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF1
• Ensembl ID: ENSPTRG00000012094
• Aliases: None
• Description: None

Sequence

>retro_ptro_704
TCCCGAGGTTTGGACTGGGTCACCCAGCCCAGTCGGGAAGCACCAGCAGTGAGCAACCCTGGCCTCCCCTTCAGCAGCTT
TGACCACTCTAAAGCCCCCTGCTATGGCTATGATGAGCAGCTGAGCCTGTGCCCAGAGTGGCTGAGTTCTGGCAAAGACA
AGAATAAAAGCATCCTGCAGAACAAGTATGTCCGATGTTCTGTTAGAACTGAGGTATGCCATCTCTGGATGGTCCTGTGT
CACCGCTTGATGCTAAATCCTCAGCATGTGCAGCTCCTTTTTGACAATGAAGTTCTCCCTGATCACATGACAGTAAAGCA
GCTATGGCTCTCCGCTGGTTCGACAAGCTATCCCCTTTGCTTTTACAATACAGTGTGAAAGAGAAGAGGAGG

Alignment

ORF - retro_ptro_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 50.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRGLDRVTQPTGEEPALSNLGLPFSSFDHSKAHYYRYDEQLNLCLERLSSGKDKNKSVLQNKYVRCSVRA
          SRGLD.VTQP..E.PA.SN.GLPFSSFDHSKA..Y.YDEQL.LC.E.LSSGKDKNKS.LQNKYVRCSVR.
Retrocopy SRGLDWVTQPSREAPAVSNPGLPFSSFDHSKAPCYGYDEQLSLCPEWLSSGKDKNKSILQNKYVRCSVRT

Parental  EVRHLRRVLCHRLMLNPQHVQLLFDNEVLPDHMTMKQIWLS-RWFGKPSPLLLQYSVKEKRR
          EV.HL..VLCHRLMLNPQHVQLLFDNEVLPDHMT.KQ.WLS.RWF.K.SPLLLQYSVKEKRR
Retrocopy EVCHLWMVLCHRLMLNPQHVQLLFDNEVLPDHMTVKQLWLS<RWFDKLSPLLLQYSVKEKRR

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	11.85 RPM
SRP007412_cerebellum	0.04 RPM	10.65 RPM
SRP007412_heart	0.00 RPM	5.45 RPM
SRP007412_kidney	0.03 RPM	10.96 RPM
SRP007412_liver	0.00 RPM	10.28 RPM
SRP007412_testis	0.00 RPM	17.49 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_704 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_704 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1029
Pongo abelii	retro_pabe_862

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000115289	1 retrocopy	retro_hsap_1029,
Mus musculus	ENSMUSG00000069678	1 retrocopy	retro_mmus_2722,
Nomascus leucogenys	ENSNLEG00000000752	1 retrocopy	retro_nleu_907,
Pongo abelii	ENSPPYG00000012270	1 retrocopy	retro_pabe_862,
Pan troglodytes	ENSPTRG00000009074	1 retrocopy	retro_ptro_11,
Pan troglodytes	ENSPTRG00000012094	1 retrocopy	retro_ptro_704 ,
Sorex araneus	ENSSARG00000007319	1 retrocopy	retro_sara_448,
Sus scrofa	ENSSSCG00000008277	1 retrocopy	retro_sscr_1069,