RetrogeneDB ID: retro_pcap_10

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_97530:5621..6134(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000005521
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000001672
• Aliases: None
• Description: None

Sequence

>retro_pcap_10
ATGTGCAATTCCTGTTGTGGCTCTGTCTGCTCTGATGAGGGCTGTGGCCAAGGCCTCTGCCAGGAGACTTGCTGCCAGCC
CAGCTGCTGCAGGCCCAGCTGCTGCATCTCCAGCTGCTGCCGCCCTGTCTGCTGCCAGACCAGCTGCTGCCGCCCTCAGT
GCTATCAGACCAGCTGCTGCAGACCCAGTTGCTGCCAGACCAGCTGCTGCCACCCTCAGTGCTGTCAGACCAGCTGCTGC
CGCCCTCAGTGCTGTCAGACCAGCTGCTGCAGGCCCAGCTGCTGCATCTCCAGTTGCTGCCGCCCTCAGTGCTGCCAGAC
CAGCTGCTGCCGACCTCAGTGCTGCCAGACCAGCTGCTGCAGGCCAAGCTGTTGCGTCTCCAGCTGCTGCCGCCCAGTCT
GCTGCCAGACCAGCTGCTGCCGCCCTCAGTGCTGTCAGACCAGCTGCTGCAGGCCTAGCTGCTGCATCTCCAGCTGCTGC
TGCCCTGTCTGCTGCCAGACCTCCCGCTGCCGC

Alignment

ORF - retro_pcap_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.52 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CNSCCGSICSDEG-CGRGLCQETCCQPSCCESSCCKPSCCRPSCCESSCYRPQCCRPVCCQTSCCRPSCC
          C.S.C.......G.C....CQ..CC.PSCC.SSCC.P.CC..SCC...CY...CCRP.CCQTSCC.P.CC
Retrocopy CGSVCSDEGCGQGLCQETCCQPSCCRPSCCISSCCRPVCCQTSCCRPQCYQTSCCRPSCCQTSCCHPQCC

Parental  VSSCCRPSCCRPSCCVSSCCRPQCCRPQCCQTSCCRPSCCVSSCCRPSCCISSCCRPVCCQTSYCRPTCS
          ..SCCRP.CC..SCC..SCC...CCRPQCCQTSCCRP.CC..SCCRPSCC.SSCCRPVCCQTS.CRP.C.
Retrocopy QTSCCRPQCCQTSCCRPSCCISSCCRPQCCQTSCCRPQCCQTSCCRPSCCVSSCCRPVCCQTSCCRPQCC

Parental  TGSCC
          ..SCC
Retrocopy QTSCC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_10 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000001672	1 retrocopy	retro_pcap_10 ,