RetrogeneDB ID: retro_pcap_284

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_26492:11917..12505(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIPK
• Ensembl ID: ENSPCAG00000002419
• Aliases: None
• Description: lipase, family member K [Source:HGNC Symbol;Acc:23444]

Sequence

>retro_pcap_284
CAACCTGCAGTGTTCTTGCAACATGATGTGCTCACATTGGCCACCAACTGGATTTCCAATCTGCCCAGCAACAGCCCGGC
CTTTATTCTGGCAGATGCTTGGTATGACGTTTGGCTGGGAAACAGCAGAGGGAATACCAGGGCCTGGAAAAATGTATACT
ATTCACCAGACTCTGTGGAATTCTGGGCTTTCAGTTTTGATGAATTGGCTAAATATGACCATCCATCCACAACTGACTTC
ATTGTAAAGAAAACTGGACAGGAGAAGCTAGACTATGTTGGCCATTCTCAGGAGACCACCACTGGTTTTACTGCTTTGTC
TACCAATCCCAAGCTGGCTGAGAAAACCAAAACCTTTTATGCATTAGCTCCAGTTGCCACTGTGAAGTACACCAAAGGCC
TTTTTGAGTCATTCAAACTTATTCCTCCATTTCTCTTCAGGGCTACTTTTGGTAACACAGTATTCTCCCCACACAATTAT
TTTTATGAATTTGTTGCTACTGAAGCGTGCTCCCATGAGATAATGGATAGGCTCTGCAGCAATACCTTATTTCTCATTTC
TGGATTCGGCACTAAGAACTTGAACGTA

Alignment

ORF - retro_pcap_284 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.51 %
• Parental protein coverage: 60.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPVVYLQHGLVASASNWI-HLP-NSLGFLLADSGYDVWMGNSRGNTWSRRHLKLSPKSTEYWAFSMDEMA
          .P.V.LQH.....A.NWI..LP.NS..F.LAD..YDVW.GNSRGNT........SP.S.E.WAFS.DE.A
Retrocopy QPAVFLQHDVLTLATNWISNLPSNSPAFILADAWYDVWLGNSRGNTRAWKNVYYSPDSVEFWAFSFDELA

Parental  KYDLPATINFIIEKTGQQQLFYVGHSQGTTIAFIAFCTNPELAKRIKIFFALAPITTVKYTRSPLKKLTT
          KYD.P.T..FI..KTGQ..L.YVGHSQ.TT..F.A..TNP.LA...K.F.ALAP..TVKYT.........
Retrocopy KYDHPSTTDFIVKKTGQEKLDYVGHSQETTTGFTALSTNPKLAEKTKTFYALAPVATVKYTKGLFESFKL

Parental  LSRPVIKALFGDKIIYAHTFFDQFIATKVCSQKLFHRICSNFLFTFSGFDPDNLNM
          .......A.FG......H..F..F.AT..CS.....R.CSN.LF..SGF...NLN.
Retrocopy IPPFLFRATFGNTVFSPHNYFYEFVATEACSHEIMDRLCSNTLFLISGFGTKNLNV

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_284 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000002419	1 retrocopy	retro_pcap_284 ,