RetrogeneDB ID: retro_pcap_175

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_13704:14754..15366(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMP1
• Ensembl ID: ENSPCAG00000014112
• Aliases: None
• Description: TIMP metallopeptidase inhibitor 1 [Source:HGNC Symbol;Acc:11820]

Sequence

>retro_pcap_175
ATGGCTCCCTTCACGTCCCTGGCATCTGGCATCCTGTTGTTCCTTCGGCTGATCACCCCCAGCAGAGCACGCACCTGTGC
GGCACTGCACCCGCAGACAGCATTCTGCAGATCTGACCTAGTCATCAGAGCCACACTCATGGGGACTGCTGACGTCAACC
AGACCACCTGATACAAACGGTATGAAATCAAGATGTTCAAAGGGTTTGATGCATTCAGGAATGCCCCTGACATTCACTTC
ATCTACACCACTGCCATAGAGAGTGTCTGCGGATATCTGCACAGGTCCCAGAACCACAGCAAGGAGTTTCTCATCTCTGG
ACATTTGCGGGAGGGGCACCTGCACATTACCACCTGCAGCTTCATCACTCCTTGGAGCAGTCCGAGCTCTGCTCAGCAAC
GAGGTTTCACCAAGGTCTATGCTGGTGGCTGCGAGGAATACACGGTGTTTCCGTATTCATCCATGCCCTGTGAGCTACAG
AGTGACATTCATTGCTTATGGACAGACCAGCTCCTTTCACGTTCTGAGAAAGGCTTCCAAGGCCGCCACCTTGCCTGCCT
GCCACAGGAGCCAGGGCTGTGCACCTAGCAGTCCCTAAAGCCCAGGAGAGCA

Alignment

ORF - retro_pcap_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPFTSLASGILLLLWLITPSRACTCAAPHPQTAFCSSDLVIRARFMGTAEVNQTTLYKRYEIKMTKMFK
          MAPFTSLASGILL.L.LITPSRA.TCAA.HPQTAFC.SDLVIRA..MGTA.VNQTT.YKRYEI...KMFK
Retrocopy MAPFTSLASGILLFLRLITPSRARTCAALHPQTAFCRSDLVIRATLMGTADVNQTT*YKRYEI---KMFK

Parental  GFDALGNAPDIHFVYTPAMESVCGYLHRSQNHSEEFLIAGQSREGHLHITTCSFIAPWSSLSSAQQRGFT
          GFDA..NAPDIHF.YT.A.ESVCGYLHRSQNHS.EFLI.G..REGHLHITTCSFI.PWSS.SSAQQRGFT
Retrocopy GFDAFRNAPDIHFIYTTAIESVCGYLHRSQNHSKEFLISGHLREGHLHITTCSFITPWSSPSSAQQRGFT

Parental  KVYAAGCEECTVFPCSSIPCKLQSDTHCLWTDQLLSRSEKGFQSRHLACLPQEPGLCTWQSLKPRRA
          KVYA.GCEE.TVFP.SS.PC.LQSD.HCLWTDQLLSRSEKGFQ.RHLACLPQEPGLCT.QSLKPRRA
Retrocopy KVYAGGCEEYTVFPYSSMPCELQSDIHCLWTDQLLSRSEKGFQGRHLACLPQEPGLCT*QSLKPRRA

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_175 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	ENSPCAG00000014112	1 retrocopy	retro_pcap_175 ,
Rattus norvegicus	ENSRNOG00000010208	1 retrocopy	retro_rnor_1969,