RetrogeneDB ID: retro_pcap_89

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_5258:97816..98959(-)
• Located in intron of: ENSPCAG00000002787

Retrocopy information

• Ensembl ID: ENSPCAG00000002825
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DES
• Ensembl ID: ENSPCAG00000008436
• Aliases: None
• Description: desmin [Source:HGNC Symbol;Acc:2770]

Sequence

>retro_pcap_89
GTGGACTTCTCGCTGGCGGACGCCATCAACACTGAGTTCAAGAACACCCGTACCAACGAGAAAGTAGAGCTGCAGGAGCT
CAATGACCGATTCGCCAACTACATCGACAAGGTGCATTTTCTGGAGCAGCAGAACAAGATCCTGCTGGCCGAGCTTGAGC
AGCTGAAGGGCCAGGGGAAGTCCTGCCTGGGGGACCTCTACGAAGAGGAGATGCGGGAGCTGCGTCGGCAGGTGGATCAG
CTCACCAACGACAAGGCCCGCGTCGAGGTGGAGCGTGACAGCCTGGCCGAGGACATCATGCGTCTCCGGGAGAAGTTGCA
GGAGGAGATGATGCAGAGAGAGGAAGCGGAGAGCACCCTGCAGTCTTTCAGACAGGATGTTGACAATGCCTCCTTCGCAC
GTCTTGACCTCGAGCGTAAAGTGGAGTCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAACTACACGAAGAGGAAATCCAG
GAGCTGCAGGCTCAGATTCAAGAACAGCATGTCCAAATTGATGTGGATGTTTCTAAGCCTGACCTCACGGCTGCCCTGCG
TGACGTCCGTCAGCAGTATGAAAGTGTGGGTGCCAAGAATCTTCAGGAGGCTGAAGAATGGTACAAGTCTAAGTTCGCTG
ACCTTTCTGAGGCTGCTAACCGGAACAATGATGCCCTGCGCCAGGCAAAGCAGGAGTCGAATGAGTACCGGAGACAGGTC
CAGTCTCTCACCTGTGAAGTGGATGCTCTTAAAGGAACTAATGAGTCTCTGGAGCGCCAGATGCGTGGAATGGAGAACTT
TGCTGTTGAAGCTGCTAACTACCAAGACACTACTGGCCGCCTGCAGGATGAGATTCAGAACATGAAGGAAGAAATGGCTC
GTCACCTTCGTGAATACCAAGACCTCCTGAATGTTAAGATGGCCCTTGACATTGAGATTGCCACCTACAGGAAGCTGCTG
GAAGGAGAGGAGAGCAGGATTTCTCTGCCTCTTCCTAACTTTTCTTCACTGAATCTGCGGGAAACCAATCTGGAGTCCCT
TCCTCTGGTTGACACACACTCAAAAAGGACACTCCTGATTAAGACAGTTGAAACTAGAGATGGACAGGTTATCAACGAAA
CTTCTCAGCATCATGATGACCTT

Alignment

ORF - retro_pcap_89 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.02 %
• Parental protein coverage: 81.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDFSLADAVNQEFLTTRTNEKVELQELNDRFANYIEKVRFLEQQNAALAAEVNRLKGREPTRVAE-YEEE
          .DFSLADA.N.EF..TRTNEKVELQELNDRFANYI.KV.FLEQQN..L.AE...LKG.........YEEE
Retrocopy VDFSLADAINTEFKNTRTNEKVELQELNDRFANYIDKVHFLEQQNKILLAELEQLKGQGKSCLGDLYEEE

Parental  LRELRRQVEVLTNQRARVDVERDNLLDDLQRLKAKLQEEIQLKEEAENNLAAFRADVDAATLARIDLERR
          .RELRRQV..LTN..ARV.VERD.L..D..RL..KLQEE....EEAE..L..FR.DVD.A..AR.DLER.
Retrocopy MRELRRQVDQLTNDKARVEVERDSLAEDIMRLREKLQEEMMQREEAESTLQSFRQDVDNASFARLDLERK

Parental  IESLNEEIAFLKKVHEEEIRELQAQLQEQQVQVEMDMSKPDLTAALRDIRAQYETIAAKNISEAEEWYKS
          .ESL.EEIAFLKK.HEEEI.ELQAQ.QEQ.VQ...D.SKPDLTAALRD.R.QYE...AKN..EAEEWYKS
Retrocopy VESLQEEIAFLKKLHEEEIQELQAQIQEQHVQIDVDVSKPDLTAALRDVRQQYESVGAKNLQEAEEWYKS

Parental  KVSDLTQAANKNNDALRQAKQEMMEYRHQIQSYTCEIDALKGTNDSLMRQMRELEDRFASEASGYQDNIA
          K..DL..AAN.NNDALRQAKQE..EYR.Q.QS.TCE.DALKGTN.SL.RQMR..E..FA.EA..YQD...
Retrocopy KFADLSEAANRNNDALRQAKQESNEYRRQVQSLTCEVDALKGTNESLERQMRGMEN-FAVEAANYQDTTG

Parental  RLEEEIRHLKDEMARHLREYQDLLNVKMALDVEIATYRKLLEGEESRINLPIQTFSALNFRETSPEQRG-
          RL..EI...K.EMARHLREYQDLLNVKMALD.EIATYRKLLEGEESRI.LP...FS.LN.RET..E....
Retrocopy RLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNFSSLNLRETNLESLPL

Parental  SEVHTKKTVMIKTIETRDGEVVSEATQQQHEV
          ...H.K.T..IKT.ETRDG.V..E..Q.....
Retrocopy VDTHSKRTLLIKTVETRDGQVINETSQHHDDL

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_89 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000007363	1 retrocopy	retro_pcap_317,
Procavia capensis	ENSPCAG00000008436	2 retrocopies	retro_pcap_145, retro_pcap_89 ,