RetrogeneDB ID: retro_pcap_24

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_1037:52167..52659(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPPP3
• Ensembl ID: ENSPCAG00000010498
• Aliases: None
• Description: tubulin polymerization-promoting protein family member 3 [Source:HGNC Symbol;Acc:24162]

Sequence

>retro_pcap_24
AAGACGTTCCAGCGATTTGCAGTCTTTGGCGATTCGTCAAGCAGCGGGACTGAAATGAACAACAAGAACTTCTCCAAGCT
TTGCAAAGACTGTGGCATCATGGATGGCAAGAAGGTCACCTCTACGGATGTGGACATCGTGTTTAGCAAAGTCAAGGCCA
AGAATGCCCGGACCATCACATTTGCAGAGTTCCAGGAGGCCATGAAGGAGCTGGGCCCCAAACGGTTCAAGGGCAAGAGC
CCTGATGAAGCCCTGGAGGACATCTACAAACTCATGGAGGGCAAGGACCCTGCCACCACCGGCACCACTAAAGCAACAAC
AGCCGGCGCGGTGGACCGGCTGACCGACACCAGCAAGTACACGGGCACCCACAAGGAACGCTTCGACGACAGCGGCAAAG
GCAAGGGCATCGCAGGACGGGAAGACGTGCATGACAACTCAGGCTACGTGAGTGGCTACAAGGGTGCTGGCACCTATGAT
AAGGACAAAAAG

Alignment

ORF - retro_pcap_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.85 %
• Parental protein coverage: 93.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESFRKFAIHGDPKASGQEMNGKNWAKLCKDCKVADGKAVTGTDVDIVFSKVKAKSARVINYEEFKRALEE
          ..F..FA..GD...SG.EMN.KN..KLCKDC...DGK.VT.TDVDIVFSKVKAK.AR.I...EF..A..E
Retrocopy KTFQRFAVFGDSSSSGTEMNNKNFSKLCKDCGIMDGKKVTSTDVDIVFSKVKAKNARTITFAEFQEAMKE

Parental  LATKRFKGKSKEEAFDAICQLVAGKEPANVGVTKAKTGGAVERLTDTSKYTGSHKERFDESGKGKGIAGR
          L..KRFKGKS..EA...I..L..GK.PA..G.TKA.T.GAV.RLTDTSKYTG.HKERFD.SGKGKGIAGR
Retrocopy LGPKRFKGKSPDEALEDIYKLMEGKDPATTGTTKATTAGAVDRLTDTSKYTGTHKERFDDSGKGKGIAGR

Parental  QDILDDSGYVSAYKNAGTYDTKVK
          .D..D.SGYVS.YK.AGTYD...K
Retrocopy EDVHDNSGYVSGYKGAGTYDKDKK

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_24 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	ENSPCAG00000010498	1 retrocopy	retro_pcap_24 ,
Tursiops truncatus	ENSTTRG00000000453	1 retrocopy	retro_ttru_529,