RetrogeneDB ID: retro_pcap_409

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_73332:3655..4501(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDIA3
• Ensembl ID: ENSPCAG00000012905
• Aliases: None
• Description: protein disulfide isomerase family A, member 3 [Source:HGNC Symbol;Acc:4606]

Sequence

>retro_pcap_409
GGAATTTTCAGCCACCTGAAGAAGCAAGCAGGGCCTGCTTCAGTTTCTCTTTAGAACGAGGAAAAATTTGAGAAGTTCAT
TAGTGAGAAAGATGCCTCTGTGATGGGTTTTTTCACGAACTTACTCAGTGAAGCTTACTGAGTTCCTAAAAGCAGTCAGC
AGTTTGAGGGATAACTCCCCAATCTGTACATACCAGTGCTGAGTCTCTGGAGGACAAGTATGATGATAATAGAGAGGATA
TCAGTTTGTTTCATCCTTCACATTTGATTAACAAGTTTGGGGATACAACTGTGGCATATATGGAACAGAAAATGACCAGT
GGCAAGATTAAACATTTATTCAGGAAAACATTTTTGGGATCTGCCCTCACATGATAGAAGATAAAAAAGATTTGATACAG
AGCAAGGGCTTACTTGTAGCTTACTACGATGTGGACTATGAAAAGAATACTAAAGGTTCCAACTACTGGAGAAACAGAGT
GATAATGGTTGCAAAGAATTTTCTGGATGCTGGACACAAACTCAGCTTTGCTGTAGGTAACTGAAAAACCTTTAGTCATG
AGCTGTCTGATGTTGACTTGGAAAGTAGTGCTGGAGAGACCCTGTGATTGCTATCAGAACTACCAGAGGAGACAAGTTTG
TCATGCAAGAGGAGTTCTTGCATAGCAGCAAGGCTCTTAAGAGATTTCTGCAGGATTACTTGGATGGCAACCTGAAGAGA
TAATTGAAGTCTGAACCTGTCCCAGAAAGCAGTGATGGACCTGTGAAGGTAGTAGCAGAGAATTTTGATTAAATAATGAA
TGATGAAAATAGAGATGTGCCAATTGAATTTCATGCCCCTTAATGT

Alignment

ORF - retro_pcap_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.09 %
• Parental protein coverage: 56.24 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GIVSHLKKQAGPASVPLRSEEEFEKFISEKDASVVGF-FKDL-FSEAHSEFLKAASNLRDNY-RFAHTSV
          GI.SHLKKQAGPASV.L..EE.FEKFISEKDASV.GF.F..L..S....EFLKA.S.LRDN.....HTS.
Retrocopy GIFSHLKKQAGPASVSL*NEEKFEKFISEKDASVMGF<FHEL<YSVKLTEFLKAVSSLRDNS>QSVHTSA

Parental  ESLVNNYDDNGEGITLFRPSHLINKFEDKTVAYMEQKMTSGKIKK-FIQENIFGICPHMTEDNKDLIQGK
          ESL...YDDN.E.I.LF.PSHLINKF.D.TVAYMEQKMTSGKIK..FIQENIFGICPHM.ED.KDLIQ.K
Retrocopy ESLEDKYDDNREDISLFHPSHLINKFGDTTVAYMEQKMTSGKIKH<FIQENIFGICPHMIEDKKDLIQSK

Parental  DLLVAYYDVDYEKNTKGSNYWRNRVMMVAKKFLDAGHKLNFAIASRKTFSHELSDFGLESTTGEI-PVVA
          .LLVAYYDVDYEKNTKGSNYWRNRV.MVAK.FLDAGHKL.FA....KTFSHELSD..LES..GE..PV.A
Retrocopy GLLVAYYDVDYEKNTKGSNYWRNRVIMVAKNFLDAGHKLSFAVGN*KTFSHELSDVDLESSAGET<PVIA

Parental  IRTAKGEKFVMQEEFSRDGKALERFLQDYFDGSLKRYLKSEPIPESNDGPVKVVVAENFDEIVNDENKDV
          IRT..G.KFVMQEEF....KAL.RFLQDY.DG.LKR.LKSEP.PES.DGPVK.VVAENFD.I.NDEN.DV
Retrocopy IRTTRGDKFVMQEEFLHSSKALKRFLQDYLDGNLKR*LKSEPVPESSDGPVK-VVAENFD*IMNDENRDV

Parental  LIEFYAPWC
          .IEF.AP.C
Retrocopy PIEFHAP*C

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_409 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000167004	1 retrocopy	retro_hsap_217,
Gorilla gorilla	ENSGGOG00000023440	1 retrocopy	retro_ggor_287,
Myotis lucifugus	ENSMLUG00000009380	1 retrocopy	retro_mluc_2352,
Otolemur garnettii	ENSOGAG00000004298	1 retrocopy	retro_ogar_1750,
Procavia capensis	ENSPCAG00000012905	1 retrocopy	retro_pcap_409 ,
Pan troglodytes	ENSPTRG00000007002	1 retrocopy	retro_ptro_331,