RetrogeneDB ID: retro_pcap_133

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_870:5268..5780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRRG2
• Ensembl ID: ENSPCAG00000012419
• Aliases: None
• Description: proline rich Gla (G-carboxyglutamic acid) 2 [Source:HGNC Symbol;Acc:9470]

Sequence

>retro_pcap_133
GTCTTCTTGGACTTCCCAAAGGCCTAGAACTTCCTGAGCAGCCGCAGATGGATTCCACATGCCAACCACTGGGACCTGGA
ACTACTGACATCTGGAAACCTGGAACGGGAGTGCCTTGAGGAGTGTTCCTGGGAGGAGGCCCGCGAGTACTTTGAGGACA
ATGCCCAGACTGATCACTTTTGGGACACTTACATCTACAATGGCAAAGGAGGGCACAAATAAGTGGATGTAGCAGGCTTG
GCAGAGCGGCTGACATCCAGTTTCCTGCTTATCAACCTGACTGGTCTCAGAGCCCTTTGGTACCTACACTACCAAAGTGC
CCAAGGCTAGCATTTCTGTCTCCAAGAGTCCAGGTTCATGAGCCCCATGAACCCCCTGAGCTGTGTGGGCCCGCCGACGC
CTCTGTCCCCACACCCATGCCAGGCCTCCCCACCTATAAGCAGGCTCTGGAGGCCTTGGGAGTCCACAACGCACCTCAAC
CTCCTTACACCAGCCTCAGGAGGTCTCCTAAC

Alignment

ORF - retro_pcap_133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.99 %
• Parental protein coverage: 86.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VFLDSPKAQNFLSSHRRIPRANHWDLELLTPGNLERECLEEKCSWEEAREYFEDNAQTNDFWDSYIYNGK
          VFLD.PKA.NFLSS.R.IP.ANHWDLELLT.GNLERECLEE.CSWEEAREYFEDNAQT..FWD.YIYNGK
Retrocopy VFLDFPKA*NFLSSRRWIPHANHWDLELLTSGNLERECLEE-CSWEEAREYFEDNAQTDHFWDTYIYNGK

Parental  GGRRQVDVAGLAVGLTSGVLLIILIGLGAFWYLHYRRGRGQHSCPQESGLMSPLNRPSSLGPPTPLS-PP
          GG...VDVAGLA..LTS..LLI.L.GL.A.WYLHY....G.H.C.QES..MSP.N..S..GPPTPLS.P.
Retrocopy GGHK*VDVAGLAERLTSSFLLINLTGLRALWYLHYQSAQG*HFCLQESRFMSPMNPLSCVGPPTPLS<PT

Parental  PPPGLPTYEQALEASGAHDAPPPPYSSLRRSSN
          P.PGLPTY.QALEA.G.H.AP.PPY.SLRRS.N
Retrocopy PMPGLPTYKQALEALGVHNAPQPPYTSLRRSPN

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_133 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	ENSPCAG00000012419	1 retrocopy	retro_pcap_133 ,