RetrogeneDB ID: retro_pcap_158

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_120703:5061..5466(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS29
• Ensembl ID: ENSPCAG00000012049
• Aliases: None
• Description: vacuolar protein sorting 29 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14340]

Sequence

>retro_pcap_158
GACTATCTCAAGACTCAAGCTGGTAATGTTCATATTGTAAGAAGAGACCATGATAAGAATTTGAATTATCCAAAACAGAA
AGTTGCGACTATTAGACAATTCAAAACTAGTTTGATCCATGGACATCAAGTTATTTCGTGAGAAGATATGGCCAGCTTAG
CCCTGTTACAGAAGCAGTTTGATGTGAACATTCTTATCTTGTGATACACACACATATTTGAAGCATTTGAGCATGAAAAT
AAATTCCACATTAACCCAGGTTCTGCCACCGGATCATGTAATGCCTTGGAAACAAATATTCCTTCATTTATGGTGATTAA
TATCCAGGCTTATACAGTTGTCACTTATGTTTGCCAGCTAGTTGGAGATGACACAGAACTAGAAAAAATCAAACACAACA
AATCT

Alignment

ORF - retro_pcap_158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.06 %
• Parental protein coverage: 75.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHT
          DYLKT.AG.VHIVR.D.D.NLNYP.QKV.T..QFK..LIHGHQVI...DMASLALLQ.QFDV.ILI...T
Retrocopy DYLKTQAGNVHIVRRDHDKNLNYPKQKVATIRQFKTSLIHGHQVIS*EDMASLALLQKQFDVNILIL*YT

Parental  HKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS
          H.FEAFEHENKF.INPGSATG..NALETN.IPSF....IQA.TVVTYV.QL.GDD...E.I...KS
Retrocopy HIFEAFEHENKFHINPGSATGSCNALETN-IPSFMVINIQAYTVVTYVCQLVGDDTELEKIKHNKS

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_158 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001891	1 retrocopy	retro_acar_30,
Loxodonta africana	ENSLAFG00000006176	1 retrocopy	retro_lafr_1115,
Monodelphis domestica	ENSMODG00000011577	1 retrocopy	retro_mdom_450,
Procavia capensis	ENSPCAG00000012049	1 retrocopy	retro_pcap_158 ,