RetrogeneDB ID: retro_pcap_127

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_7640:51981..53434(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000006070
• Aliases: None
• Description: None

Sequence

>retro_pcap_127
GACAGTGGCGGAGAGAGGAAGCATCAAAAGCTTCTGGAAACAATCAGTTCCCTTGATGGAAAGAATAGGTGGAAATTGGC
TGAAAGGTCAGAGGCCAGCCTGAATGTGTCAGAGTTCAATGTCACGTCTGATGAATCGGAAGAAAAGCTGGTCCTTTCAG
ATCTGCTTCAGCCCATTAAATCTTCCTTTTCTTTGGCCACTGTGCAAAAGCAACTAAAGAGAATCAAAGCAAAGAAAGCT
GTAGAGTTGCCCCTTAACAAAGAAGAGGTTGCTCGGATCCACAGAGAAGTGGCATTCAGTAAAACTGCTCAAGCTCTCTC
CAAGTGGGATCCCGTAGTTTTAAAGAACTGGAAAGCAGAGCAATTGGTTTTTCCCCTGAAGAAGGAGCCTGCAGCCTTTC
ATCCTATTGAACATAAGCTCAGTGTCTGGAAGACAGAAAGTCCCCTGGAACAGGAAATTTTTAACGTCCTCCACAAGAAG
AGGCAGCCAATGACAGACCCTTTACTGACTCCAGTAGAGAAAGCCTCTCTCAAAGCCATGAGCCTGGAAGAGGCTAAGAT
GTGCCGAGCAGAGCATTAGAGGGCCCGGGCCCTGCAGTCCTACTATGAGGCCAAGGCTCAGAGAGAGAAGAAAATCAAAA
GCAAACAGCATCACCGAGTTGTGAAGAAAGGAGAGGCCAAGAAAGCCCTCAAAGACTTGGAGACTCTGCAGAAGGGCAGC
CCTATCGCAGCATTGGGAGAACTGGAGAAAATGGAAAAAACCCGAATGGCTGAGCGAATGACCCTGAAGCACCAGAACAG
TGGCAAGTGGGCCAAATCAAAGGCAGTGATGGCCAAATAACAATCTCGAGGCACGCTGGGCCACACAGGAACAGTTGGCC
AAGAGCAAAGCACTGATGCAGAAGCTCCGGCACCGTCTGAGAGTGAGGAAGAGGAGCGAGGTGCACAGGAGGATGGAATC
CTTGTCCCTGATGTCGTGAATGAAATCCAGATGAACACAGATGGGTCAAATCCCTGGATGTGCACAGGTTGCCCCAGTGA
CGTGAAAGAAGCTGAAATCCAGGACTCGGAACAACTTGCTGAGCATCTCTCCCGAGCAGAATCCAGAAAGGGAGGGAGAA
GAAAGCCCAGTAGCAGAAGAAGAAACCTGGTTGAAAGAATTTGAGGAAAGGCGATCCGTTAGGAAAAGGCACGAGCTCAA
CCAGGGTGCTGGACCTGTAGGCCATCAGGAAACCCAAGGCTCTGGCAGCAGGGAGGTGCTGTCCCAATTGAGGGCACTGT
CTCAAAAACTCAGCAAGGCCGACTGTGAGTCCTAGAAGCAAAAAGTGACTTCAGTGGAGGCTGTTCTCCCAGTCCAGAGA
GAAGCTCTGGTCCCCGTGGAGGAGGAAGCCTTGCTGCAGAAGCTGGAGAGAGTGCAGACTTTTAGGGAGCTGGAAGAGCT
AGGCAGAGGATGC

Alignment

ORF - retro_pcap_127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.57 %
• Parental protein coverage: 63.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DSDGERKHQKLLEAISSLDGKNRRKLAERSEASLKVSEFNVSSEGTGEKLVLADLLPPTKTSASLATVKK
          DS.GERKHQKLLE.ISSLDGKNR.KLAERSEASL.VSEFNV.S....EKLVL.DLL.P.K.S.SLATV.K
Retrocopy DSGGERKHQKLLETISSLDGKNRWKLAERSEASLNVSEFNVTSDESEEKLVLSDLLQPIKSSFSLATVQK

Parental  QLNRVKSRKTVELPLNKEEVARIHREVAFNKTSQVLSKWDPIVVKNRKAEQLVFPLEKEQPAFAPIEHVL
          QL.R.K..K.VELPLNKEEVARIHREVAF.KT.Q.LSKWDP.V.KN.KAEQLVFPL.KE..AF.PIEH.L
Retrocopy QLKRIKAKKAVELPLNKEEVARIHREVAFSKTAQALSKWDPVVLKNWKAEQLVFPLKKEPAAFHPIEHKL

Parental  GGWKARTPLEQEIFNILHKNKQPVTDPLLTPVEKASLKAMSLEEAKMRRAELQRARALQSYYEAKARREK
          ..WK...PLEQEIFN.LHK..QP.TDPLLTPVEKASLKAMSLEEAKM.RAE..RARALQSYYEAKA.REK
Retrocopy SVWKTESPLEQEIFNVLHKKRQPMTDPLLTPVEKASLKAMSLEEAKMCRAEH*RARALQSYYEAKAQREK

Parental  KIKSKKYHKVVKKGKAKKALKDFETLRKVDPTAALEELEKIEKARMMERMSLKHQNSGKWAKSKAIMAK-
          KIKSK..H.VVKKG.AKKALKD.ETL.K..P.AAL.ELEK.EK.RM.ERM.LKHQNSGKWAKSKA.MAK.
Retrocopy KIKSKQHHRVVKKGEAKKALKDLETLQKGSPIAALGELEKMEKTRMAERMTLKHQNSGKWAKSKAVMAK>

Parental  YDLEARQAMQEQLAKNKELTQKLQ-AASESEEEEGGVEENE-LIPDVVNEVHTTTNEPNPWMHRSCTGDT
          ..LEAR.A.QEQLAK.K.L.QKL..A.SESEEEE.G..E...L.PDVVNE....T...NPWM...C..D.
Retrocopy NNLEARWATQEQLAKSKALMQKLR<APSESEEEERGAQEDGILVPDVVNEIQMNTDGSNPWMCTGCPSDV

Parental  KEAEIPKDAGPPHEPVACEDSESEG-EEGPAA-EDTLLEEFEKRRSLRKRPELSQDAESAGSQEAQDASS
          KEAEI..D.....E......S...G.EE.P.A.E.T.L.EFE.RRS.RKR.EL.Q.A...G.QE.Q...S
Retrocopy KEAEI-QDSEQLAEHLSRAESRKGG>EESPVAEEETWLKEFEERRSVRKRHELNQGAGPVGHQETQGSGS

Parental  QEVLSELRALSQKLNQKKHQSGKQKGNSARTVLLVQREELAQEEEEPVLLQRPERVQTLEELEVLGEEGC
          .EVLS.LRALSQKL......S.KQK..S...VL.VQRE.L...EEE..LLQ..ERVQT..ELE.LG..GC
Retrocopy REVLSQLRALSQKLSKADCES*KQKVTSVEAVLPVQREALVPVEEE-ALLQKLERVQTFRELEELG-RGC

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_127 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127 ,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,