RetrogeneDB ID: retro_pcap_335

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_40661:14073..14451(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000005107
• Aliases: None
• Description: None

Sequence

>retro_pcap_335
ATGCCAGCAGGGGAGCGTGGGAGCGGGATGTGTCTCTTGCTGGGAGCCACGGGTGCCGGGAAGACACTCCTGGTGAAGCG
ACTACAGAAGCTGAGCTCCAGCAACAGGAAGGGTGACTTGGGGGACCCTCCCGCGATGCGGCCCATGGTGGGCACCAACC
TCACCGACATCGTGGTCCAGAAGAAGATCACCATCAGGGAGCTGGGGGGGTGCATGAGCCCCATTTGTCCCAGTTACTAC
GGAAAGTGCCATGCCCTCCTGTTTGTGCTGGATGCCTCTGACCCCGTGCAGCTCTCTGCCTCCTGTTCCCAGCTCCTGGG
TCTCCTTTCTGCAGAACAACTTGCAGGAGCGGCTGTCCTTATCCTCTTCAACAAAATC

Alignment

ORF - retro_pcap_335 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.13 %
• Parental protein coverage: 85.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPGGAR-DGMCLLLGAAGVGKTVLVKRLQNLSSRDGKGDLGDPPATQPTVGTDLTDIVAQKKITIRELGG
          .P.G.R..GMCLLLGA.G.GKT.LVKRLQ.LSS...KGDLGDPPA..P.VGT.LTDIV.QKKITIRELGG
Retrocopy MPAGERGSGMCLLLGATGAGKTLLVKRLQKLSSSNRKGDLGDPPAMRPMVGTNLTDIVVQKKITIRELGG

Parental  CMSPIWPSYYGNCHALLFVLDASDPTQLSASCSQLLGLLSAEQLAGAAVLILFNKI
          CMSPI.PSYYG.CHALLFVLDASDP.QLSASCSQLLGLLSAEQLAGAAVLILFNKI
Retrocopy CMSPICPSYYGKCHALLFVLDASDPVQLSASCSQLLGLLSAEQLAGAAVLILFNKI

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_335 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000005107	1 retrocopy	retro_pcap_335 ,
Tursiops truncatus	ENSTTRG00000007609	1 retrocopy	retro_ttru_1190,