RetrogeneDB ID: retro_pcap_147

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_112660:1592..2095(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPCD
• Ensembl ID: ENSPCAG00000004838
• Aliases: None
• Description: deleted in primary ciliary dyskinesia homolog (mouse) [Source:HGNC Symbol;Acc:24542]

Sequence

>retro_pcap_147
ACTGGCTGGCTGGAGAGTCTGTGGGCTGCCGAGAAGACGGCGCTGCTGCAGGATGGGAGAGGGAAGGTGCATTGTCTGTC
CTCAGATGGGAAGGAAACGGCCAAAGAATGTGAAGAAAAGACAAGTGAACTACTTATGAGAAAATGTCATGTGAAAAGTG
TCCCGGGAGCCTTGACCAGTGGTAGATTGAGGTGGGTGATCCAGTTCCCCTGGGAGCAGGAAGCCTGGGGCCAGAACTCA
CAAAGGAAACCAATGCCAATCACATCTTCGTGTGCAAGGACACTGAGATGAATTTTCAGTGGCGAATCTGAAACCTCCCT
TACCCTAAGGACGTCTATAGTGTCTGTACAGACCAGAAGGAGTGCTGTCTTTCTGTCAGAGCTACCAACAAAAAGTACTA
CAAGAAGTTCTCCATTCCTTACCTAGACAGGTACCACCTGCCTCTGGATGACTCCTCTCTGAGCTTTGCTCACGCCACCT
GTACCCCGATAGCCTTGTACCAG

Alignment

ORF - retro_pcap_147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.11 %
• Parental protein coverage: 98.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGWLESLRAAEKTALLQDGRRKVHYLFPDGKEMAEEYDEKTSALLVRKWRVKSTLGAL-GQWQIEVGDPV
          TGWLESL.AAEKTALLQDGR.KVH.L..DGKE.A.E..EKTS.LL.RK..VKS..GAL..QW.IEVGDPV
Retrocopy TGWLESLWAAEKTALLQDGRGKVHCLSSDGKETAKECEEKTSELLMRKCHVKSVPGAL<DQW*IEVGDPV

Parental  PLGAGSLGPELIKESNANPIFMRKDTKTNFQWRIRNLPYPKDVYSVCIDQKERCLVVRTTNKKYYKKFSI
          PLGAGSLGPEL.KE.NAN.IF..KDT..NFQWRI.NLPYPKDVYSVC.DQKE.CL.VR.TNKKYYKKFSI
Retrocopy PLGAGSLGPELTKETNANHIFVCKDTEMNFQWRI*NLPYPKDVYSVCTDQKECCLSVRATNKKYYKKFSI

Parental  PDLDRFHLPLDDSSLSFAHANYTLIISYQ
          P.LDR.HLPLDDSSLSFAHA..T.I..YQ
Retrocopy PYLDRYHLPLDDSSLSFAHATCTPIALYQ

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_147 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	ENSPCAG00000004838	1 retrocopy	retro_pcap_147 ,
Tupaia belangeri	ENSTBEG00000006817	1 retrocopy	retro_tbel_3402,