RetrogeneDB ID: retro_pcap_263

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_239409:87..1152(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT6A
• Ensembl ID: ENSPCAG00000015532
• Aliases: None
• Description: chaperonin containing TCP1, subunit 6A (zeta 1) [Source:HGNC Symbol;Acc:1620]

Sequence

>retro_pcap_263
ATGGCAGTGATTAGGACCCTGAACCCCAAGGCTGAGATAGAGTGAACCCAGGTGGCTCTGCTCATCAACATCAGCATGGC
CCAGGGGCTGCAGGTCATGTAGAGGATCAACCTGGGCCCCAAGGGCACCATGGAGATTCTAGTACCCGATGTGGAGACAT
CGGGCTTACTAAAGATGGCAATGTGCTGCTTCATGAAATGCAAGTTCAACACCCAACAGCCTCCTTAATAACAAAAGTAG
CAACAGCCCAAGATGACATAACAGGTGATACTACTAATTCCAAGGTCCTGATTCTTGGAGAGTTGCTGAAACAAGTGACA
GGTCTGCATTTCTGAAGGTTTGCATATCAGAATAACTGAAGGATTTGAAGCTGCAAAGGAAAAGCTCTATAAGTTATAGA
ACAAAGTGAAGTAAGCAGAGAGAAGGACAGAGAAACACTTAAATACATGTGGTCAGAACATCTCTGCATACTAAAGTTCA
TGTTGAAGTTGCTGATGTCTTAACAGAGGCTGTAGCTGAATCCATTTTGGTTATTCAAAAGATGAACATGGTTCATCTTT
TCATGGTTGAAATTACGGAGATAAAATATAAATCTGAAATTGATACAACCTTAATTAGAGGGCTTATTTTGGATCATGGG
GCAAGGCATCCTGATATGAAAAGAAGAGTAGAAGATGTGTACATCCTCACATGCAGTGTGTCATTAGAATATGAAAAAAA
CAGAAGTGAACTCTGGCTTCTTTTACAAGAGTGCAGAAGAGAGAGACAAACTTGTAAAATCTGAAAGAAAATTCATTGAA
GATAGAGTTAACAAAATAATAGAACAAGAAAGAAAATCTGTGGTGATTCAAATAAAGGATTCATCATTATTAAGCAAAGG
GAATTGACCCTTTGTCTTTAGATGTCCTTGCAAAAGAAGGCATAGTAGCTCTCTACGGAACTGTATGAAGAAATATGGAG
AGGCTGACACTTGCTGGTGGTGGGGTAGCTGTAAATTCTTTAGACGACCTAAATTCTGACTGTTTGGGACATGCAGAACT
CATCTATGAGTATATACTGTGAGAG

Alignment

ORF - retro_pcap_263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.1 %
• Parental protein coverage: 67.11 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAAVKTLNPKAEVARAQAALAVNISAARGLQDVLRTNLGPKGTMKMLV-SGAGDIKLTKDGNVLLHEMQI
          MA...TLNPKAE....Q.AL..NIS.A.GLQ...R.NLGPKGTM..LV....GDI.LTKDGNVLLHEMQ.
Retrocopy MAVIRTLNPKAEIE*TQVALLINISMAQGLQVM*RINLGPKGTMEILV<TRCGDIGLTKDGNVLLHEMQV

Parental  QHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQA-DLYISEGLHPRIITEGFEAAKEKALEVLEQIK
          QHPTASLI.KVATAQDDITGD.T.S.VLI.GELLKQ.....ISEGLH.RI.TEGFEAAKEK........K
Retrocopy QHPTASLITKVATAQDDITGDTTNSKVLILGELLKQV>QVCISEGLHIRI-TEGFEAAKEKLYKL*NKVK

Parental  -VSKEMDRQTLIDVARTSLHTKVHAELADVLTEAV-DSILAIKQNEPIDLFMVEIMEMKHKSETDTSLIR
          ....E..R.T.I.V.RTSLHTKVH.E.ADVLTEAV..SIL.I.......LFMVEI.E.K.KSE.DT.LIR
Retrocopy >KQREGQRNT*IHVVRTSLHTKVHVEVADVLTEAVAESILVIQKMNMVHLFMVEITEIKYKSEIDTTLIR

Parental  GLVLDHGARHPDMKKRVEDAYILTCNVSLEYE-KTEVNSSFFYKSAEEREKLVKAERKFIEDRVNKIIE-
          GL.LDHGARHPDMK.RVED.YILTC.VSLEYE.KTEVNS.FFYKSAEER.KLVK.ERKFIEDRVNKIIE.
Retrocopy GLILDHGARHPDMKRRVEDVYILTCSVSLEYE>KTEVNSGFFYKSAEERDKLVKSERKFIEDRVNKIIE<

Parental  LKKKVCGDSNKGFVVINQ-KGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVALNSLDDLNSDSLG
          ..KK.CGDSNKGF..I.Q.KGIDP.SLD.LAKEGIVAL.....RNMERLTLA.GGVA.NSLDDLNSD.LG
Retrocopy TRKKICGDSNKGFIIIKQ<KGIDPLSLDVLAKEGIVALYGTV*RNMERLTLAGGGVAVNSLDDLNSDCLG

Parental  HAGLVYEYTLGE
          HA.L.YEY.L.E
Retrocopy HAELIYEYIL*E

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_263 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 19 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016077	1 retrocopy	retro_amel_855,
Canis familiaris	ENSCAFG00000010149	1 retrocopy	retro_cfam_431,
Choloepus hoffmanni	ENSCHOG00000000654	3 retrocopies	retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus	ENSCJAG00000021279	2 retrocopies	retro_cjac_1320, retro_cjac_580,
Dipodomys ordii	ENSDORG00000001249	1 retrocopy	retro_dord_617,
Felis catus	ENSFCAG00000027654	2 retrocopies	retro_fcat_1102, retro_fcat_320,
Homo sapiens	ENSG00000146731	2 retrocopies	retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla	ENSGGOG00000011439	1 retrocopy	retro_ggor_133,
Loxodonta africana	ENSLAFG00000012791	1 retrocopy	retro_lafr_808,
Macaca mulatta	ENSMMUG00000015272	1 retrocopy	retro_mmul_2582,
Monodelphis domestica	ENSMODG00000006565	1 retrocopy	retro_mdom_1330,
Nomascus leucogenys	ENSNLEG00000015664	1 retrocopy	retro_nleu_1355,
Oryctolagus cuniculus	ENSOCUG00000017674	1 retrocopy	retro_ocun_468,
Procavia capensis	ENSPCAG00000015532	1 retrocopy	retro_pcap_263 ,
Pongo abelii	ENSPPYG00000025820	1 retrocopy	retro_pabe_2719,
Pan troglodytes	ENSPTRG00000019206	2 retrocopies	retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus	ENSPVAG00000001421	1 retrocopy	retro_pvam_663,
Rattus norvegicus	ENSRNOG00000000923	1 retrocopy	retro_rnor_2226,
Tursiops truncatus	ENSTTRG00000015158	1 retrocopy	retro_ttru_1552,