RetrogeneDB ID: retro_pcap_91

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_5344:70296..71550(-)
• Located in intron of: ENSPCAG00000009498

Retrocopy information

• Ensembl ID: ENSPCAG00000009602
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000004199
• Aliases: None
• Description: None

Sequence

>retro_pcap_91
TTAAGGGCTGTTGAAGAGGCATTTGTACCAGTTATCAAACTGTGTTTTGATGGGATAGAGATTGATATTTTGTTTGCAAG
ATTAGCACTGCAGACAATTCCAGAAGATCTGGACCTGAGAGATGACAGTCTACTTAAAAATTTAGATATTAGATGCATAA
GAAGCCTTAATGGTTGCCGGGTAACCGATGAAATTTTACACTTAGTGCCAAACATTGATAACTTCAGGTTAACTCTGAGA
GCTATCAAATTGTGGGCCAAATGCCACAATATCTATTCTAACATATTAGGTTTCCTTGGAGGTGTTTCCTGGGCTATGTT
AGTTGCAAGAACTTGCCAGCTGTATCCAAATGCAGTAGCATCAACTCTTGTCTGCAAATTTTTTTTGGTATTTTCTGAAT
GGGATTGGCCAAATCCAGTGCTATTGAAAGAGCCTGAAGAAAGGAATCTTAATTTGCCTGTATGGGACCCACGAGTCAAT
CCCAGTGATAGGTACCATCTTATGCCTATAATCACACCAGCATATCCGCAACAGAACTCCACGTACAATGTGTCTGTTTC
AACCCGGATGGTCATGATTGAGGAGTTTAAACAAGGACTTGCTATCACACATGAAATTTTACTGAGTAAAGCAGACTGGG
TCCAAACTTTTTGAAGCCCCAAACTTCTTTCAAAAGTATAAGCATTATATTGTACTTCTAGCAAGTGCGCCAACAGAGAA
ACAACATCTAGAATGGGTGGGCTTGGTGGAATCAAAAATCCGAATTCTGGTTGGAAGCTTGGAGAAGAATGAATTTATCA
CCTTGGCGCATGTGAACCCCCAGTCATTTCCAGCACCCAAAGAAAACCCCGACAAGGATGAATTTCGTACAATGTGGGTA
ATTGGGTTGGTGCTGAAAAAACCAGAAAACTCTGAAACTCTCAGTATTGATCTCACATATGATGTTCAGTCTTTCACTGA
TACAGTTTATAGGCAAGCAATAAACAGCAAGATGTTTGAGATGGATATGAAAATTGATGCAGTGCACTTAAGGAGAAAGG
AACTTCATCAGCTCCTACCTAATCATGTGCTTCAGAAAAAGAAAGCACATTCAACTTAAGGCGTTAGACTGACAGTTTTG
AATGACAGCAGCATTAAATTGTCTGTGGACAGTGACGACAGCTTGTCTGTGCCTTCATCTTCCAGCACTGTGAAACCAGT
CCACTGGCAGGCAGCTCTTAGGGCAGGGGCACTCCTGTCCCAGTTGTAATGGCA

Alignment

ORF - retro_pcap_91 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.26 %
• Parental protein coverage: 63.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVP
          LRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVP
Retrocopy LRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVP

Parental  NIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPV
          NIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNA.ASTLV.K...VFS.W.WPNPV
Retrocopy NIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVCKXXXVFSEWDWPNPV

Parental  LLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSK
          LLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.EILLSK
Retrocopy LLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHEILLSK

Parental  AEW-SRLFEAPN-FQKYKHYIVLLASAPTEKQRLEWVGLVESKVRILVASLEKNEFITLAHVNPQSFPAP
          A.W.S.LFEAPN.FQKYKHYIVLLASAPTEKQ.LEWVGLVESK.RILV.SLEKNEFITLAHVNPQSFPAP
Retrocopy ADW>SKLFEAPNFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAP

Parental  REHPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRRELH
          .E.PDK.EFRTMWVIGLV.KK.ENSE.LS.DLTYD.QSFTDTVYRQAINSKMFE.DMKI.A.H..R.ELH
Retrocopy KENPDKDEFRTMWVIGLVLKKPENSETLSIDLTYDVQSFTDTVYRQAINSKMFEMDMKIDAVHLRRKELH

Parental  QLLPSHVLQKRKKHSTESVRLTALNDSSLDLSMDSDNSMSVPSPTSAVK-TSPVNSSGSSQGRNSPAPAV
          QLLP.HVLQK.K.HST..VRLT.LNDSS..LS.DSD.S.SVPS..S.VK.TSP....GSS.GR..P.P.V
Retrocopy QLLPNHVLQKKKAHST*GVRLTVLNDSSIKLSVDSDDSLSVPSSSSTVK<TSPL--AGSS*GRGTPVPVV

Parental  TA
          .A
Retrocopy MA

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_91 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000090060	1 retrocopy	retro_hsap_30,
Gorilla gorilla	ENSGGOG00000006287	1 retrocopy	retro_ggor_202,
Loxodonta africana	ENSLAFG00000000946	1 retrocopy	retro_lafr_895,
Myotis lucifugus	ENSMLUG00000010922	1 retrocopy	retro_mluc_1396,
Monodelphis domestica	ENSMODG00000012887	2 retrocopies	retro_mdom_1714, retro_mdom_1916,
Mus musculus	ENSMUSG00000021111	1 retrocopy	retro_mmus_37,
Otolemur garnettii	ENSOGAG00000004611	1 retrocopy	retro_ogar_987,
Procavia capensis	ENSPCAG00000004199	1 retrocopy	retro_pcap_91 ,
Rattus norvegicus	ENSRNOG00000004827	1 retrocopy	retro_rnor_863,