RetrogeneDB ID: retro_pcap_38

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_176:83740..84231(+)
• Located in intron of: ENSPCAG00000007775

Retrocopy information

• Ensembl ID: ENSPCAG00000007818
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CA1
• Ensembl ID: ENSPCAG00000004468
• Aliases: None
• Description: carbonic anhydrase I [Source:HGNC Symbol;Acc:1368]

Sequence

>retro_pcap_38
ATGGCAAGTACTGACTGGGGGTATGATGACAAAAACGGTCCTGAGCAATGGGGCAAACTGTACTCTATCGCCAAGGGAAA
TAATCAATCTCCTATCGAAATTAAAACCAAAGAAACCAAACATGACACTGCTCTAAAACCTATCAATGTCTCCTACAATC
CAGCCACAGCCACAGAAATTGTCAACGTTGGACATTCATTTCATGTGTGTTTTGAGGATAATGATAACTGGTCAGTGCTG
AAAGGCGGCCCTCTCTCTGGAAGCTACAGGCTCTGCCAGTTCCACTTTCACTGGAGCAGCACAGATGACTATGGCTCTGA
GCACACAGTAAATAGAGAAAAATTTTCTGCAAAGCTTCACATAGTTCACTGGAATTCTGAAAAGTACTCCAGTTTTGTTG
AAGCTGCCTCCAACGCTGATGGCTTGGCAATTATTGTGCTGATGAGCCTGGTCAGGCCAACTCATCGCTGCAGAAAGTAC
TTAATGCCTTA

Alignment

ORF - retro_pcap_38 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.55 %
• Parental protein coverage: 63.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGTDWGYDDKNGPEQWGKLYPIANGNNQSPIDIKTKETKHDTALKPFSVSYNPATAKEIVNVGHSFHVC
          MA.TDWGYDDKNGPEQWGKLY.IA.GNNQSPI.IKTKETKHDTALKP..VSYNPATA.EIVNVGHSFHVC
Retrocopy MASTDWGYDDKNGPEQWGKLYSIAKGNNQSPIEIKTKETKHDTALKPINVSYNPATATEIVNVGHSFHVC

Parental  FEDNDNRSVLKGGPVSGSYRLCQFHFHWGSTDDYGCEHTVNGEKFSAELHIVHWNSEKYSSFAEAASKAD
          FEDNDN.SVLKGGP.SGSYRLCQFHFHW.STDDYG.EHTVN.EKFSA.LHIVHWNSEKYSSF.EAAS.AD
Retrocopy FEDNDNWSVLKGGPLSGSYRLCQFHFHWSSTDDYGSEHTVNREKFSAKLHIVHWNSEKYSSFVEAASNAD

Parental  GLAIIGALMKL-GQANSSLQKVLNAL
          GLAII..LM.L.GQANSSLQKVLNAL
Retrocopy GLAII-VLMSL<GQANSSLQKVLNAL

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_38 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	ENSPCAG00000004468	1 retrocopy	retro_pcap_38 ,