RetrogeneDB ID: retro_pcap_285

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_265244:56..923(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000005424
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SPPL2C
• Ensembl ID: ENSPCAG00000011127
• Aliases: None
• Description: signal peptide peptidase like 2C [Source:HGNC Symbol;Acc:28902]

Sequence

>retro_pcap_285
GAAGACGACAAGAACACACCAGTGGACTTCACGCCGGCCATGACAGGTACCGTGGTCCTCATGTCCTGCTCCGTCATGCT
GCTCCTTTACTTCTTCTATGACTGCTTTGTCTACGTCATGATTGGGATCTTTGGCCTGGGCGCCGGCACTGGCCTTTACA
GCTGCCTGGCCCCGCTGGTGTACCAGCTGTCCCTGCAGCAATGCCAATGGCCCCTGCCTGGCCATCGGGGCTGTCTACAG
CTGCCCCTGCTTCTGCTGGCCGGCCTGTGCCTGGCAGTGACCATCCTCTGGGTGGCTTACCGCAACGAGGACAGTTGGGT
GTGGCTCCTGCAGGACACATTGGGTGTGGCCTATTGCCTCTTTGTCCTTCGGCGTGTGCGGCTACCCACACTCAGGAACT
GTGCCTCTTTCCTGCTGATCCTGCTGGCCTTGGACGTCTTCTTTGTCTTTGTCACACCCTTCTTCACCAGGACTGGCAAG
AGCGTGATGGTAGAAGTGGCCACGGGCCCGGCAGATTCCTCTAGCCATGAGAAGCTGCCCATGGTATTCAAAGTGCCCAA
GATAAGTTTCTCAACCTTGACCTTCTGTGACCGATCCTTCTCCATCCTTGGCTTTGGTGACATCGTGGTCCCTGGCTTCC
TAGTGGCCTACTGTCATCGCTTTGATGTCCAAATCAGCTCACACCAGGTCTACTTTATGGCTTGCATCTTGGCCTACGCT
GTGGGCCTGCTGGTCACTTTTATTGCCATGGCCCTCACGCAGATGGGCCAGCCCGCCCTGCTCTACCTTGTGTCCAGCAC
ACTGCTCAGTAGCCTGACTGTGGCCACCTGCCGCCAAGAGCTCAGCCTCTTCTGGATTGGCCAGGGC

Alignment

ORF - retro_pcap_285 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.59 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKQEDEAVDVTPVMICVFVVMCCSMLVLLYCFYDQLVYVVIGIFCLASSTGLYSCLAPLVRRLPFGQCRV
          E......VD.TP.M....V.M.CS...LLY.FYD..VYV.IGIF.L...TGLYSCLAPLV..L...QC..
Retrocopy EDDKNTPVDFTPAMTGTVVLMSCSVMLLLYFFYDCFVYVMIGIFGLGAGTGLYSCLAPLVYQLSLQQCQW

Parental  PDNSLPYLHKRPQVRMLLLALACVAVSVVWGVFRNEDQWAWVLQDALGIAFCLYMLRTIRLPTFKACALL
          P...LP......Q...LLLA..C.AV...W...RNED.W.W.LQD.LG.A.CL..LR..RLPT...CA..
Retrocopy P---LPGHRGCLQLPLLLLAGLCLAVTILWVAYRNEDSWVWLLQDTLGVAYCLFVLRRVRLPTLRNCASF

Parental  LLVLFVYDVFFVFITPFLTKSGNSIMVEVATGPSDSATHEKLPMVLKVPRLNASPLALCDRPFSLLGFGD
          LL.L...DVFFVF.TPF.T..G.S.MVEVATGP.DS..HEKLPMV.KVP....S.L..CDR.FS.LGFGD
Retrocopy LLILLALDVFFVFVTPFFTRTGKSVMVEVATGPADSSSHEKLPMVFKVPKISFSTLTFCDRSFSILGFGD

Parental  ILVPGLLVAYCHRFDVQVQSSRVYFVACTVAYGIGLLVTFVALALMQRGQPALLYLVPCTLVTSCGVALW
          I.VPG.LVAYCHRFDVQ..S..VYF.AC..AY..GLLVTF.A.AL.Q.GQPALLYLV..TL..S..VA..
Retrocopy IVVPGFLVAYCHRFDVQISSHQVYFMACILAYAVGLLVTFIAMALTQMGQPALLYLVSSTLLSSLTVATC

Parental  RRELGLFWTGSG
          R.EL.LFW.G.G
Retrocopy RQELSLFWIGQG

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_285 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000011710	1 retrocopy	retro_nleu_2146,
Procavia capensis	ENSPCAG00000011127	1 retrocopy	retro_pcap_285 ,
Pelodiscus sinensis	ENSPSIG00000017155	1 retrocopy	retro_psin_63,