RetrogeneDB ID: retro_pcap_77

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_4321:38515..38771(+)
• Located in intron of: ENSPCAG00000000772

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000007865
• Aliases: None
• Description: None

Sequence

>retro_pcap_77
GAGGTCTCTTTGCCACCCTCCTTTGGACCTCTGGCCTCACTCTGCTTGAAATGGACCCAACTGCTGCTGTACCACTGGAG
GCTCCGGTGCCTGCACCAGCTTCTACAAATGCATCTTCTGCTAGGAAGGCTGCAGTTCCTACTGCCCAGCTGGCTGTGCC
AAGTGCACCCAGGGCAGCATCTAAAAAGGGCATCAGACGAGTGGAGCTGTGGCATCTGACATAGGAGAGGCCTGCACCCA
GATGTAAACAGGGTCA

Alignment

ORF - retro_pcap_77 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.99 %
• Parental protein coverage: 78.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EVSSSPSFSPLPHLS-KWT-PTAPALLAAPVPVLAPANAKSANALPARRAAAPAALWAVSSAPRAASAKG
          EVS..PSF.PL..L..KWT.PTA...L.APVP..APA...S.NA..AR.AA.P.A..AV.SAPRAAS.KG
Retrocopy EVSLPPSFGPLASLCLKWT<PTAAVPLEAPVP--APA---STNASSARKAAVPTAQLAVPSAPRAASKKG

Parental  PR-TSAAAAPD-GTACPDVKTAT
          .R.TS.A.A.D.G.AC....T..
Retrocopy IR<TSGAVASDIGEACTQM*TGS

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_77 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000016109	2 retrocopies	retro_mmul_1207, retro_mmul_2513,
Procavia capensis	ENSPCAG00000007865	1 retrocopy	retro_pcap_77 ,
Pteropus vampyrus	ENSPVAG00000016198	1 retrocopy	retro_pvam_245,