RetrogeneDB ID: retro_pcap_69

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_387:207112..207616(+)
• Located in intron of: ENSPCAG00000010242

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000007530
• Aliases: None
• Description: None

Sequence

>retro_pcap_69
AGGTGGGCCACGGTGGACACGATGTGCAGACACAACTACGAGGTGTTGTCTGAGCGCCTCACCCTGAAGCGCCGAGTCCA
GCCTAAAGTGAACGTCTCCCCCTCCAAGAAGCGGGCCCTACAGCACCACAGCTTGCTTGTCTGCCATGCGACAAACTTCT
GTCCAGACAACCTTGAAATCTGGTGGTTCCGAAATGGACCGGAGGAAACAGCTGGGATTGTGTCCACTGAACTAATCCGT
ATTGGAGACTGGACCTTCCAGATCCTGGTGATACTGGAAATGACCCCCCAGCAGGGCGATGTCTACACCTGCCAAGTGGA
GCACCCCAGCCTGGACAGTCCTGTCACTGTGGAACGGAAGGCACAGTCTCATTCTGCCAAAAACAAAATGCTGACCAGAG
TCGGGGGCTTTGTGCTAGGATTCATCATCTTTGGAGTGGGCTTCTTCATGCATAACAGGAGCAAGAAAGTTCAACAAGGT
TCTGGATAAACAGGGTTCCTGACC

Alignment

ORF - retro_pcap_69 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 63.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRAAVDAFCRHNYGVV-QSFSLRRRVEPLVTVYPAKTRPLQQHNLLVCSVNGFYPGHIEVRWFRNGQEEE
          R.A.VD..CRHNY.V......L.RRV.P.V.V.P.K.R.LQ.H.LLVC....F.P...E..WFRNG.EE.
Retrocopy RWATVDTMCRHNYEVLSERLTLKRRVQPKVNVSPSKKRALQHHSLLVCHATNFCPDNLEIWWFRNGPEET

Parental  AGVISTGLIRNGDWTFQILVMLEAIPQRGEVYSCQVEHASLTAPVTVEWRAQSESAQKKMLSGIGGLVLG
          AG..ST.LIR.GDWTFQILV.LE..PQ.G.VY.CQVEH.SL..PVTVE..AQS.SA..KML...GG.VLG
Retrocopy AGIVSTELIRIGDWTFQILVILEMTPQQGDVYTCQVEHPSLDSPVTVERKAQSHSAKNKMLTRVGGFVLG

Parental  LLFLGVGLFIHVRNQKAHSGLQPTGLLS
          ....GVG.F.H.R..K...G...TG.L.
Retrocopy FIIFGVGFFMHNRSKKVQQGSG*TGFLT

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_69 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	ENSPCAG00000007530	1 retrocopy	retro_pcap_69 ,