RetrogeneDB ID: retro_pcap_59

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_3244:42123..42418(+)
• Located in intron of: ENSPCAG00000005783

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGS10
• Ensembl ID: ENSPCAG00000003150
• Aliases: None
• Description: regulator of G-protein signaling 10 [Source:HGNC Symbol;Acc:9992]

Sequence

>retro_pcap_59
TTTAACTGCACCCTGAGCTAGCTGAACAGAAAGAGGCGAGCTCAGACATCCATGGCAGGGATGACAGTCCCAAAAGCAGC
CTCCAGAACCTCCAAATCACAGCTGAATGGGCAATTTCCTGGAGAATCTGTTTGAAGACACAGAAGTATGAAAAAATTAC
AGCTTTTTTATTTCATTTTTAAAGAAGTGTGGTAAAGAAAATGTTTTGTATTGGCTAGCATGTGAAGATTTTAAGAAAAT
GCATGGCAAGAAATGGATGCAGCAAAAGATAAAGAAGATCTATGTGACCTTTCTC

Alignment

ORF - retro_pcap_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.44 %
• Parental protein coverage: 53.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FNRAVSRLSRKR-PPSDIHDRDGSSSSSHQNLKSTTKWATS-LEDLLEDPEGVKRFREFLK--KEFSEEN
          FN...S.L.RKR...SDIH.RD.S..SS.QNL..T..WA.S.LE.L.ED.E..K....F....K....EN
Retrocopy FNCTLS*LNRKR<ASSDIHGRDDSPKSSLQNLQITAEWAIS<LENLFEDTEV*KNYSFFISFLKKCGKEN

Parental  VLFWLACEDFKKMQDKKQMQEKAKEIYMTFL
          VL.WLACEDFKKM..KK.MQ.K.K.IY.TFL
Retrocopy VLYWLACEDFKKMHGKKWMQQKIKKIYVTFL

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_59 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000008414	1 retrocopy	retro_ggor_2669,
Macaca mulatta	ENSMMUG00000021610	1 retrocopy	retro_mmul_2295,
Nomascus leucogenys	ENSNLEG00000016735	1 retrocopy	retro_nleu_2034,
Procavia capensis	ENSPCAG00000003150	1 retrocopy	retro_pcap_59 ,
Pongo abelii	ENSPPYG00000002702	1 retrocopy	retro_pabe_3268,