RetrogeneDB ID: retro_pcap_94

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_5645:32303..32993(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPT1
• Ensembl ID: ENSPCAG00000002429
• Aliases: None
• Description: palmitoyl-protein thioesterase 1 [Source:HGNC Symbol;Acc:9325]

Sequence

>retro_pcap_94
AAAATAAGAGGAAAATACCTGGAATTTGTGTCTTTGGAGATTGGGAAGACACCAATAGAGGATGTAAAGAGCAGCTGCTT
CTTGAATGTCCCTTCCCAAGTATTGACAGTGTGTCGGACTCTCGCCATGGATCCTAAAATGCAGCAAGGCTACAGTGCTA
TGGGATTCTCCCAGGGAAGCCAATTTCTGAGGGCAGTGGCTCGGAGACGCCCATCACCTCCCATGGTCAGTGTTATCTCC
ACTGGGGAACAACATCTAGGTGTTTCTGGACTCCCTTGATGCCTGGGAGAGAGCTGTTATGTCTGTGACTTGATCAGGAA
AACACTGAATGTTGGGGTTTCCTCCCAAAGCCATTCAGAAATACTTGGTTCAAGCGGAATACTGACATGACTCCATTAAA
GAGGATGCGTACTGCAACTATAGCATTTTCTTGGTGGATGTAAGTTGGGAGAGGGATGTCAATGAGTCCCACAAGAAAAA
CCTGATGACTTGATGAAATTTGTGATGGTGAAAGTCCTCAGTGATCCCGTCATGGATCCTGTGGATTGTGAGTGCTTTGG
ATTTTATAGAAGTGGCCAAGCCAAAGAAACTGTCCCCTTTCAGAAGATTTCTTTGTACGTACTGGACTGCCTGGGGCTGA
AGGAAATGGACAGTGCAGGGAAACTAGGCTTCCTGGCCACAGTAGGGAAC

Alignment

ORF - retro_pcap_94 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.53 %
• Parental protein coverage: 74.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KIPGIYV--LSLEIGKTIREDVENSFFLNVNSQVSTVCQTLAEDPKLQQGYNAMGFSQGGQFLRAVAQRC
          KI.G.Y....SLEIGKT..EDV..S.FLNV.SQV.TVC.TLA.DPK.QQGY.AMGFSQG.QFLRAVA.R.
Retrocopy KIRGKYLEFVSLEIGKTPIEDVKSSCFLNVPSQVLTVCRTLAMDPKMQQGYSAMGFSQGSQFLRAVARRR

Parental  SSPPMVNLISVGXXXXXVFGLPRCPGESSHICDLIRKTLNVGAYS-KAIQERLVQAEYWHDPIKEDTYRN
          .SPPMV..IS.G.....V.GLP.C.GES...CDLIRKTLNVG..S.KAIQ..LVQAEY.HD.IKED.Y.N
Retrocopy PSPPMVSVISTGEQHLGVSGLP*CLGESCYVCDLIRKTLNVGVSS>KAIQKYLVQAEY*HDSIKEDAYCN

Parental  HSIFLADINQERGVNESYKKNLMA-LKKFVMVKFLNDTIVDPVDSERYGFYRSGQAKETIPLQKTTLYTQ
          .SIFL.D...ER.VNES.KKNLM..L.KFVMVK.L.D...DPVD.E..GFYRSGQAKET.P.QK..LY..
Retrocopy YSIFLVDVSWERDVNESHKKNLMT<LMKFVMVKVLSDPVMDPVDCECFGFYRSGQAKETVPFQKISLYVL

Parental  DRLGLKEMDNAGKLVFLATEGD
          D.LGLKEMD.AGKL.FLAT.G.
Retrocopy DCLGLKEMDSAGKLGFLATVGN

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_94 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013367	1 retrocopy	retro_btau_348,
Canis familiaris	ENSCAFG00000003004	1 retrocopy	retro_cfam_1985,
Loxodonta africana	ENSLAFG00000022663	2 retrocopies	retro_lafr_199, retro_lafr_422,
Procavia capensis	ENSPCAG00000002429	1 retrocopy	retro_pcap_94 ,
Tursiops truncatus	ENSTTRG00000004339	1 retrocopy	retro_ttru_659,