RetrogeneDB ID: retro_pcap_145

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_111926:6340..7481(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_pcap_145
GTGGACTTCTCGCTGGCGGACGCCATCAACACTGAGTTCAAGAACACCCGTACCAACGAGAAAGTAGAGCTGCAGGAGCT
CAGTGACTGATTCGCCAACTACATCGACAAGGTGCGTTCTGGTGCAGCAGAACAAGATCCTGCTGGCCGAGCTTGAGCAG
CTGAAGGGCCAGGGGAAGTCCCGTCTGGGGGACCTCTGCGAAGAGGAGATGCGGGAGCTGCGTCGGCAGGTGGATCAGCT
CACCAACGACAAGGCCCACGTCGAGGTGGAGCGTGACAACCTGGCCGAGGACATCATGCGTCTCCGGGAGAAGTTGCAGG
AGGAGATGATGCAGACAGAGGAAGCAGAGAGCACCCTGCAGTCTTTCAGACAGGATGCTGACAATGCCTCCTTGGCACTT
CTTGACCTTGAGCGTAAAGTGGAGTCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAACTACACGAAGAGGAAATCCAGGA
GCTGCAGGCTCAGATTCAAGAACAGCATGTCCAAATTGATGTGGATGTTTCTAAGCCTGACCTCACGGCTGCCCTGCGTG
ACGTCCGTCAGCAGTATGAAAGTGTGGCTGCCAAGAATCTTCAGGAGGCTGAAGAATGGTACAAGTCTAAGTTTGCTGAC
CTTTCTGAGGCTGCTAACCGGAACAATGATGCCCTGCGCCAGGCAAAGCAGGAGTCGAATGAGTACCGGAGACAGGTCCA
GTCTCTCACCTGTGAAGTGGATGCTCTTAAAGGAACTAATGAGTCTCTGGAGCGCCAGATGCGTGGAATGGAGAACTTTG
CTGTTGAAGCTGCTAACTACCAAGACACTACTGGCCGCCTGCAGGATGAGATTCAGAACATGAAGGAAGAAATGGCTCGT
CACCTTCGTGAATACCAAGACCTCCTGAATGTTAAGATGGCCCTTGACATTGAGATTGCCACCTACAGGAAGCTGCTGGA
AGGAGAGGAGAGCAGGATTTCTCTGCCTCTTCCTAACTTTTCTTCACTGAATCTGCGGGAAACCAATCTGGAGTCCCTTC
CTCTGGTTGACACACACTCAAAAAGGACACTCCTGATTAAGACAGTTGAAACTAGAGATGGACAGGTTATCAACGAAACT
TCTCAGCATCATGATGACCTT

Alignment

ORF - retro_pcap_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.54 %
• Parental protein coverage: 81.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDFSLADAVNQEFLTTRTNEKVELQELNDRFANYIEKVR-FLEQQNAALAAEVNRLKGREPTRVAEY-EE
          .DFSLADA.N.EF..TRTNEKVELQEL.D.FANYI.KVR....Q.N..L.AE...LKG....R.....EE
Retrocopy VDFSLADAINTEFKNTRTNEKVELQELSD*FANYIDKVR>LVQQ-NKILLAELEQLKGQGKSRLGDLCEE

Parental  ELRELRRQVEVLTNQRARVDVERDNLLDDLQRLKAKLQEEIQLKEEAENNLAAFRADVDAATLARIDLER
          E.RELRRQV..LTN..A.V.VERDNL..D..RL..KLQEE....EEAE..L..FR.D.D.A.LA..DLER
Retrocopy EMRELRRQVDQLTNDKAHVEVERDNLAEDIMRLREKLQEEMMQTEEAESTLQSFRQDADNASLALLDLER

Parental  RIESLNEEIAFLKKVHEEEIRELQAQLQEQQVQVEMDMSKPDLTAALRDIRAQYETIAAKNISEAEEWYK
          ..ESL.EEIAFLKK.HEEEI.ELQAQ.QEQ.VQ...D.SKPDLTAALRD.R.QYE..AAKN..EAEEWYK
Retrocopy KVESLQEEIAFLKKLHEEEIQELQAQIQEQHVQIDVDVSKPDLTAALRDVRQQYESVAAKNLQEAEEWYK

Parental  SKVSDLTQAANKNNDALRQAKQEMMEYRHQIQSYTCEIDALKGTNDSLMRQMRELEDRFASEASGYQDNI
          SK..DL..AAN.NNDALRQAKQE..EYR.Q.QS.TCE.DALKGTN.SL.RQMR..E..FA.EA..YQD..
Retrocopy SKFADLSEAANRNNDALRQAKQESNEYRRQVQSLTCEVDALKGTNESLERQMRGMEN-FAVEAANYQDTT

Parental  ARLEEEIRHLKDEMARHLREYQDLLNVKMALDVEIATYRKLLEGEESRINLPIQTFSALNFRETSPEQRG
          .RL..EI...K.EMARHLREYQDLLNVKMALD.EIATYRKLLEGEESRI.LP...FS.LN.RET..E...
Retrocopy GRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNFSSLNLRETNLESLP

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

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_145 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 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,