RetrogeneDB ID: retro_pcap_106

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_6616:65344..65624(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf70
• Ensembl ID: ENSPCAG00000006583
• Aliases: None
• Description: chromosome 19 open reading frame 70 [Source:HGNC Symbol;Acc:33702]

Sequence

>retro_pcap_106
GTGTGGTCACTGATGAGGTGTCTTCTCAGGGGCAGTATGAAAGGGGTTGCTGGCAGTCTGGTGTATGACCAGGAGCTGCT
GGGGTCCAGAGACAAAAGCCAGGCAGCTATGTGGAAGGCAGAAGAGTTGGTCCCACCCACCATGTGCCAGTTTGGCCACT
GTGTGTACAAGCAGATACTCTACCTTTCTTCTCCCTTCAAAGCTTAACTTTTCCATCTCCAAGTCCTGGAATTCCAGCAT
TTTCATGGTAATATCTGCTATATTAGCAGCTCCCTCCAAG

Alignment

ORF - retro_pcap_106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.1 %
• Parental protein coverage: 81.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VWTLMRFLIKGSVAGGAVYLVYDQDLLGPSDKSQEALRKAEEVVPPAMYQFSQYVCKQTGLQIPQLPQPV
          VW.LMR.L..GS..G.A..LVYDQ.LLG..DKSQ.A..KAEE.VPP.M.QF...V.KQ....I..L..P.
Retrocopy VWSLMRCLLRGSMKGVAGSLVYDQELLGSRDKSQAAMWKAEELVPPTMCQFGHCVYKQ----ILYLSSPF

Parental  K-FNFSFRDSWNSGIITVMSALSVAPAK
          K..NFS...SWNS.I..V.SA...AP.K
Retrocopy K>LNFSISKSWNSSIFMVISAILAAPSK

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_106 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018796	2 retrocopies	retro_cfam_1706, retro_cfam_756,
Callithrix jacchus	ENSCJAG00000017076	2 retrocopies	retro_cjac_2329, retro_cjac_735,
Felis catus	ENSFCAG00000011836	1 retrocopy	retro_fcat_287,
Loxodonta africana	ENSLAFG00000026050	1 retrocopy	retro_lafr_1241,
Macaca mulatta	ENSMMUG00000028920	1 retrocopy	retro_mmul_251,
Monodelphis domestica	ENSMODG00000001268	1 retrocopy	retro_mdom_1960,
Mustela putorius furo	ENSMPUG00000006136	2 retrocopies	retro_mputfur_1001, retro_mputfur_217,
Procavia capensis	ENSPCAG00000006583	1 retrocopy	retro_pcap_106 ,
Tupaia belangeri	ENSTBEG00000013386	1 retrocopy	retro_tbel_1443,