RetrogeneDB ID: retro_pcap_55

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_3023:96512..96806(-)
• Located in intron of: ENSPCAG00000016991

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2orf61
• Ensembl ID: ENSPCAG00000010167
• Aliases: None
• Description: chromosome 2 open reading frame 61 [Source:HGNC Symbol;Acc:26850]

Sequence

>retro_pcap_55
GACAAACCACGGGCAAGCCCTAGCTCACTGGTTTATAAAGACCAGAAGCCAACCCAGAAGCCATCATCTTTTGAAAGAGA
AGGATGGTGGAGATTGGCACTAACCAATACACCTATACCTGGCACATGCCACTTGAGAACTTTTCTTGAAGAAGTTCTAT
TAAATCCAGTCACGGCAACCTACAACTTTAAAAACAAAGGAAGGAAAAGGCCACCTCTCGTACTCAGAAACAATCCACTA
ATCAATGACATTTCCCAGTATGGGCCTCCTGGCTCGCTGGAGTTGTTAAAGAAG

Alignment

ORF - retro_pcap_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 68.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DQPVTTLSTATVRDTLKPARKPSCFEREGWWRSALTNTPIPGTYHLRTFLEEALLNPVAATYNFKNEGRK
          D.P....S.....D..KP..KPS.FEREGWWR.ALTNTPIPGT.HLRTFLEE.LLNPV.ATYNFKN.GRK
Retrocopy DKPRASPSSLVYKDQ-KPTQKPSSFEREGWWRLALTNTPIPGTCHLRTFLEEVLLNPVTATYNFKNKGRK

Parental  KPPLVLRNNPVINDIPQYVPPDSLELLKK
          .PPLVLRNNP.INDI.QY.PP.SLELLKK
Retrocopy RPPLVLRNNPLINDISQYGPPGSLELLKK

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_55 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000010167	1 retrocopy	retro_pcap_55 ,