RetrogeneDB ID: retro_pcap_128

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_7658:12754..13174(+)
• Located in intron of: ENSPCAG00000018869

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000012043
• Aliases: None
• Description: None

Sequence

>retro_pcap_128
CTGCAGAAAGAACTGTTGGCTTTGCAAAATGACCCACCTCCTGGGATGACTTTAAATGAAAAGAGTGTTCAAAATTCAAT
TATACAGTTGATTGTAGACATGGAAAGTGCACCAGGCACCTTTTATGAAGGTGAAAACTTTCAACTTCTATTTAAGTTTA
GTAGTCAATATCCTTTTGACTCTCCTCAAGTCATGTTTACTGGTGAAAATATTCCTGTTCATCCTCATGTTTATAGCAAT
GGTCGTATCTGTTTGGCTATTCTAACAGAAGACTGGTCCCCAGTGCTCTCAGTTCAATCAGTTTGTCTTAGCATTATTAG
TATGCTTTCCAGCTGCAAAGAGAAGAGACGACCACCAGATAATTCTTTTTATGTTCAAACATATAACAAGAATCCAAAGA
AAACAAAGTAGTAGTATCAT

Alignment

ORF - retro_pcap_128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.71 %
• Parental protein coverage: 98.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQKELLALQNDPPPGMTLNEKSVQNSITQWIVDMEGAPGTLYEGEKFQLLFKFSSRYPFDSPQVMFTGEN
          LQKELLALQNDPPPGMTLNEKSVQNSI.Q.IVDME.APGT.YEGE.FQLLFKFSS.YPFDSPQVMFTGEN
Retrocopy LQKELLALQNDPPPGMTLNEKSVQNSIIQLIVDMESAPGTFYEGENFQLLFKFSSQYPFDSPQVMFTGEN

Parental  IPVHPHVYSNGHICLSILTEDWSPALSVQSVCLSIISMLSSCKEKRRPPDNSFYVRTCNKNPKKTKWWYH
          IPVHPHVYSNG.ICL.ILTEDWSP.LSVQSVCLSIISMLSSCKEKRRPPDNSFYV.T.NKNPKKTK..YH
Retrocopy IPVHPHVYSNGRICLAILTEDWSPVLSVQSVCLSIISMLSSCKEKRRPPDNSFYVQTYNKNPKKTK**YH

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_128 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000025939	1 retrocopy	retro_mmus_3516,
Ornithorhynchus anatinus	ENSOANG00000008597	1 retrocopy	retro_oana_106,
Oryctolagus cuniculus	ENSOCUG00000010245	1 retrocopy	retro_ocun_1189,
Otolemur garnettii	ENSOGAG00000027181	2 retrocopies	retro_ogar_460, retro_ogar_766,
Procavia capensis	ENSPCAG00000012043	2 retrocopies	retro_pcap_128 , retro_pcap_278,