RetrogeneDB ID: retro_pcap_182

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_13987:5975..7060(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf72
• Ensembl ID: ENSPCAG00000008676
• Aliases: None
• Description: chromosome 9 open reading frame 72 [Source:HGNC Symbol;Acc:28337]

Sequence

>retro_pcap_182
ATGTCAACACTCTGCCCGCCACCATCCCCAGCTGTTGCCAAGACAGAGATCCCTTTAAGTGGTGCATCACCTTTATTGGC
AGCCACTTTTGCTTACTGGGACAATATTCTTGGGCCTAGAGTAAGACACATTTGGGCTCCAAAGATGGGACAGGTACTTC
TCAGCTATGGAGAAATAACCTTTCTTGCTAACCACACCCTCAATGGGAAAATCCTTCGAAATGCAGAGAGTGGAGCTATA
GATGTCGCTTTTTGTCTTGTCTGAAAAAGGAGTGATTATTGTTTCTTTAATCTTTGATGGAAACTGGAATGGGAATAGGA
GTACATATGGACTGTCAATTATACTTCCACAGACAGAACTTAGCTTCTATCTCCCACTTCACAGAGTGTGTGTGAATAGG
TTCACACACATTATTCGGAAAGGAAGGATATGGATGCATAAGGAAAGGCAAGAAAATGTTCAGAAGATTGTCCTAGAAGG
CACAGAGAGAATGGAAGATCAGGGTCAGAGTATTATTCCAGTGCTTACTGGAGAGGTAATTCCCATAATGGAGCGGCTTT
CATCTGTGAAATCACACAGTGTTTCTGAAGAAATAGATACAGCTGACACAGTGCTCAATGATGATGATACTGGTGACAGC
TGTCATGAAGGGTTCCTTCTCAATACCATCAGCTCACACCTGCAAACATGCGGCTGTTCTGTAGTTGTAGGTAGTAGTGT
GTAGAAACTAAGTAAGATAGTGCGAACACCATGCCTTTTTCTGACTCCAGCAGAGAGAAAATGCTCCAGATTATGTGAAG
CTGAATCATCATTTACATAAGAGTCAGGGCGGTTTGTACAAGGCCTGCTAAAGGATTCCACTGGAAGCTTTGTGCTCCTT
CCGACAAGACACGTATCCTCCCTACCCCACCACACACATAGATGTGGATGTCAACACTGTCAAGCAGATGCCACCCTGTC
ATGAACATATCTATAACCAGCGCAGGTACATGAGATCCGAGCTGACAGTATTCTGGAGAACCACTTCAGAAGAAGACATG
GCTCAGGATACAATCATCTACACAGATGAAAGCTTCACTCCTGAT

Alignment

ORF - retro_pcap_182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.05 %
• Parental protein coverage: 89.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSTLCPPPSPAV-KTEIALSGESPLLAATFAYWDN-LGPRVRHIWAPKTGQVLLSDGEITFLANHTLNGE
          MSTLCPPPSPAV.KTEI.LSG.SPLLAATFAYWDN.LGPRVRHIWAPK.GQVLLS.GEITFLANHTLNG.
Retrocopy MSTLCPPPSPAVAKTEIPLSGASPLLAATFAYWDNILGPRVRHIWAPKMGQVLLSYGEITFLANHTLNGK

Parental  ILRNAESGAIDVKFFVLSEKG-VIIVSLIFDGNWNGDRSTYGLSIILPQTELSFYLPLHRVCVDRLTHII
          ILRNAESGAIDV.F.........I..SLIFDGNWNG.RSTYGLSIILPQTELSFYLPLHRVCV.R.THII
Retrocopy ILRNAESGAIDVAFCLV*KRS>IIV-SLIFDGNWNGNRSTYGLSIILPQTELSFYLPLHRVCVNRFTHII

Parental  RKGRIWMHKXXXXXXXXXXXXXXXXXXXXGQSIIPMLTGEVIPVMELLSSMKSHSVSEEIDIADTVLNDD
          RKGRIWMHK....................GQSIIP.LTGEVIP.ME.LSS.KSHSVSEEID.ADTVLNDD
Retrocopy RKGRIWMHKERQENVQKIVLEGTERMEDQGQSIIPVLTGEVIPIMERLSSVKSHSVSEEIDTADTVLNDD

Parental  DIGDSCHEGFLLNAISSHLQTCGCSVVVGSSAEKVNKIVRTLCLFLTPAERKCSRLCEAESSFKYESGLF
          D.GDSCHEGFLLN.ISSHLQTCGCSVVVGSS..K..KIVRT.CLFLTPAERKCSRLCEAESSF..ESG.F
Retrocopy DTGDSCHEGFLLNTISSHLQTCGCSVVVGSSV*KLSKIVRTPCLFLTPAERKCSRLCEAESSFT*ESGRF

Parental  VQGLLKDSTGSFV-LPFRQVMYAPYPT-THIDVDVNTVKQMPPCHEHIYNQRRYMRSELTAFWRATSEED
          VQGLLKDSTGSFV.LP.R.V...P..T....DV..NTVKQMPPCHEHIYNQRRYMRSELT.FWR.TSEED
Retrocopy VQGLLKDSTGSFVLLPTRHVSSLPHHT>IDVDV--NTVKQMPPCHEHIYNQRRYMRSELTVFWRTTSEED

Parental  MAQDTIIYTDESFTPD
          MAQDTIIYTDESFTPD
Retrocopy MAQDTIIYTDESFTPD

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_182 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
Macropus eugenii	ENSMEUG00000009026	1 retrocopy	retro_meug_366,
Procavia capensis	ENSPCAG00000008676	1 retrocopy	retro_pcap_182 ,