RetrogeneDB ID: retro_pcap_275

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_253762:842..1186(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000016124
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIF
• Ensembl ID: ENSPCAG00000009406
• Aliases: None
• Description: peptidylprolyl isomerase F [Source:HGNC Symbol;Acc:9259]

Sequence

>retro_pcap_275
CAAGGTTTCCACTTTCACAGAAATGTTCTTGGGTTTATGTGCCAGGGTGGTAGCTTAACATGCCCTAATAGCACTGTGGC
AAGTCTGTCTACAGGGAGAAATTTGATGAGGAGAAATTCATCCTGAAGCATACAAGTTCTGGCATCCTGTCCATGGCAAG
TGCTGAACCCAATGAAAATGGTTCCCAGTTTTTTATCTACACTGTTAAGACTGAATGGTTAGATGGCAAACATGTTGTCT
TTGGCAAGGTGAAAGAAGGCATGAACACTGTGAAAGCCATGGAGCACTTTGGGTCCAGGAATGGCAAGACCAGGAAGAAA
ATCATCATTGGTGACTGTGGACAA

Alignment

ORF - retro_pcap_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.07 %
• Parental protein coverage: 56.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGSTFHRVIPSFMCQAGDFTNHNGTG-GKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTI
          .G..FHR....FMCQ.G..T..N.T..GKS.Y...F..E.F.LKH...G.LSMA.A.PN.NGSQFFI.T.
Retrocopy QGFHFHRNVLGFMCQGGSLTCPNSTV<GKSVYREKFDEEKFILKHTSSGILSMASAEPNENGSQFFIYTV

Parental  KTDWLDGKHVVFGHVKEGMDVVKKIESFGSKSGKTSKKIVITDCGQ
          KT.WLDGKHVVFG.VKEGM..VK..E.FGS..GKT.KKI.I.DCGQ
Retrocopy KTEWLDGKHVVFGKVKEGMNTVKAMEHFGSRNGKTRKKIIIGDCGQ

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_275 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000008796	3 retrocopies	retro_ecab_507, retro_ecab_649, retro_ecab_732,
Homo sapiens	ENSG00000108179	1 retrocopy	retro_hsap_1436,
Microcebus murinus	ENSMICG00000007086	8 retrocopies	retro_mmur_1266, retro_mmur_218, retro_mmur_515, retro_mmur_568, retro_mmur_605, retro_mmur_694, retro_mmur_769, retro_mmur_87,
Nomascus leucogenys	ENSNLEG00000010567	1 retrocopy	retro_nleu_70,
Procavia capensis	ENSPCAG00000009406	1 retrocopy	retro_pcap_275 ,
Pan troglodytes	ENSPTRG00000002669	1 retrocopy	retro_ptro_979,
Pteropus vampyrus	ENSPVAG00000001713	2 retrocopies	retro_pvam_380, retro_pvam_623,
Tupaia belangeri	ENSTBEG00000015457	1 retrocopy	retro_tbel_1906,
Xenopus tropicalis	ENSXETG00000018981	1 retrocopy	retro_xtro_20,