RetrogeneDB ID: retro_pcap_317

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_34389:5315..6089(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VIM
• Ensembl ID: ENSPCAG00000007363
• Aliases: None
• Description: vimentin [Source:HGNC Symbol;Acc:12692]

Sequence

>retro_pcap_317
GATGTTGACAATGCCTCCTTGGCACGTCTTGACCTCGAGCGTAAAGTGGAATCCTTGCAGGAAGAGATTGCCTTTTTGAA
GAAACTGCGCGAAGAGGAAATCCAGGAGCTGCAGGCTCAGATTCAAGAACAGCATGTCCAAATTGATGTGGATGTTTCTA
AGCCTGACCTCATGGCTGCCCTGCGTGACGTCCGTCAGCAATATGAAAGTGTGGCTGCCAAGAATCTTCAGGAGGCTGAA
GAATGGTACAAGTCTAAGTTCGCTGACCTTTCTGAGGCTGCTAACCGGAACAATGATGCCCTGCGCCAGGCAAAGCCGGA
GTCGAGTGAGTACCGGAGACAGGTCCAGTCTCTCACCTGTGAAGTGGATGCTCTTAAAGGAACTAATGAGTCTCTGAAGG
GCCAGATGCGTGAAATGGAGGAGAACTTTGCTGTTGAAGCTGCTAACTACCAAGACACTATTGGCCGCCTGCAGGATGAG
ATTCAGAACATGAAGGAAGAAATGGCTCCTCACCTTCGTGAATACCAAGACCTCCTGAATGTTAAGATGGCCCTTGACAT
TGAGATTGCCACCTACAGGAAGCTGCTGGAAGGAGAGGAAAGCAGGATTTCTCTGCCTCTTCCCAACTTTTCTTCACTGA
ATCTGCAGGAAACCAATCTGGAGTCCCTTCCTCTGGTTGACACACACTCAAAAAGGACACTCCTGATTAAGACAGTTGAA
ACTAGAGATGGACAGGTTATCAACAAAACTTCTCAGCATCATGATGACCTTGAG

Alignment

ORF - retro_pcap_317 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.12 %
• Parental protein coverage: 55.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVDNASLARLDLERKVESLQEEIAFLKKLHEEEIQELQAQIQEQHVQIDVNVSKPDLTAALRDVRQQYES
          DVDNASLARLDLERKVESLQEEIAFLKKL.EEEIQELQAQIQEQHVQIDV.VSKPDL.AALRDVRQQYES
Retrocopy DVDNASLARLDLERKVESLQEEIAFLKKLREEEIQELQAQIQEQHVQIDVDVSKPDLMAALRDVRQQYES

Parental  VAAKNLQEAEEWYKSKFADLSEAANRNNDALRQAKQESNEYRRQVQSLTCEVDALKGTNESLERQMREME
          VAAKNLQEAEEWYKSKFADLSEAANRNNDALRQAK.ES.EYRRQVQSLTCEVDALKGTNESL..QMREME
Retrocopy VAAKNLQEAEEWYKSKFADLSEAANRNNDALRQAKPESSEYRRQVQSLTCEVDALKGTNESLKGQMREME

Parental  ENFAVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNF
          ENFAVEAANYQDTIGRLQDEIQNMKEEMA.HLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNF
Retrocopy ENFAVEAANYQDTIGRLQDEIQNMKEEMAPHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNF

Parental  SSLNLRETNLESLPLVDTHSKRTLLIKTVETRDGQVINETSQHHDDLE
          SSLNL.ETNLESLPLVDTHSKRTLLIKTVETRDGQVIN.TSQHHDDLE
Retrocopy SSLNLQETNLESLPLVDTHSKRTLLIKTVETRDGQVINKTSQHHDDLE

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_317 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000007363	1 retrocopy	retro_pcap_317 ,
Procavia capensis	ENSPCAG00000008436	2 retrocopies	retro_pcap_145, retro_pcap_89,