RetrogeneDB ID:

retro_csav_11

Retrocopy
location
Organism:Pacific transparent sea squirt (Ciona savignyi)
Coordinates:reftig_551:260490..260817(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCSAVG00000006630
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CSA.3865
Ensembl ID:ENSCSAVG00000006859
Aliases:None
Description:Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:H2Z293]


Retrocopy-Parental alignment summary:






>retro_csav_11
ATGGGTGTGGAAATTGAGACGATAAAGCCTGGAGATGGTGTGAATTTCCCCAACCGTGGACAGACCGTCGCAGTTCATTA
CACTGGTACCTTGGAGAACGGAACGAAGTTTGACTCTTCATATGATCGTGGGAAGCCATTTACATTTCGGATCGGGTTGG
GCCAAGTTATAAGGGGTTGGGACGAAGGAGTAGCTCAAATGTCGATCGGACAAAAAGCCAAGTTGACATGTAGTCCAGAT
TATGCATACGGTAGTCGCGGCCATCCAGGAGTAATTCCACCAAACGCTACTCTTATCTTCGTAGTTGAACTACTCGGTAT
AGATTAG

ORF - retro_csav_11 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.29 %
Parental protein coverage: 97.22 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMGVTVETITAGDGTNFPKSGQTVCVHYTGTLTNGKKFDSSRDRGKAFEFVIGKAQVIRGWDEGVMQMSVG
MGV..ETI..GDG.NFP..GQTV.VHYTGTL.NG.KFDSS.DRGK.F.F.IG..QVIRGWDEGV.QMS.G
RetrocopyMGVEIETIKPGDGVNFPNRGQTVAVHYTGTLENGTKFDSSYDRGKPFTFRIGLGQVIRGWDEGVAQMSIG
ParentalQRATLTCTPDYAYGANGIGGVIPPNATLVFDVELL
Q.A.LTC.PDYAYG..G..GVIPPNATL.F.VELL
RetrocopyQKAKLTCSPDYAYGSRGHPGVIPPNATLIFVVELL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ciona savignyi was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ciona savignyi was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_csav_11 retrocopy.

TSS - click to see more details

Ciona savignyi was not studied using FANTOM5 data.

Lab - click to see more details

retro_csav_11 was not experimentally validated.

Retrocopy orthology:
Ciona savignyi 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.
Parental genes homology:
Parental genes homology involve 36 parental genes, and 75 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000027971 retrocopy
retro_amel_1717,
Bos taurus ENSBTAG000000083034 retrocopies
retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Callithrix jacchus ENSCJAG000000077001 retrocopy
retro_cjac_696,
Callithrix jacchus ENSCJAG000000209084 retrocopies
retro_cjac_1544, retro_cjac_3889, retro_cjac_4157, retro_cjac_537,
Ciona savignyi ENSCSAVG00000006859 1 retrocopy
retro_csav_11 ,
Dasypus novemcinctus ENSDNOG0000000586816 retrocopies
retro_dnov_1289, retro_dnov_1577, retro_dnov_1666, retro_dnov_2236, retro_dnov_228, retro_dnov_2404, retro_dnov_2418, retro_dnov_2544, retro_dnov_2589, retro_dnov_263, retro_dnov_584, retro_dnov_621, retro_dnov_670, retro_dnov_684, retro_dnov_707, retro_dnov_937,
Equus caballus ENSECAG000000156641 retrocopy
retro_ecab_752,
Erinaceus europaeus ENSEEUG000000139202 retrocopies
retro_eeur_135, retro_eeur_514,
Echinops telfairi ENSETEG000000074541 retrocopy
retro_etel_2059,
Echinops telfairi ENSETEG000000189902 retrocopies
retro_etel_186, retro_etel_2071,
Felis catus ENSFCAG000000260972 retrocopies
retro_fcat_168, retro_fcat_751,
Homo sapiens ENSG000000888321 retrocopy
retro_hsap_1198,
Homo sapiens ENSG000001197821 retrocopy
retro_hsap_1329,
Gorilla gorilla ENSGGOG000000017293 retrocopies
retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Macropus eugenii ENSMEUG000000106891 retrocopy
retro_meug_14,
Microcebus murinus ENSMICG000000015301 retrocopy
retro_mmur_257,
Macaca mulatta ENSMMUG000000123411 retrocopy
retro_mmul_2171,
Macaca mulatta ENSMMUG000000159961 retrocopy
retro_mmul_10,
Monodelphis domestica ENSMODG000000195542 retrocopies
retro_mdom_151, retro_mdom_733,
Mustela putorius furoENSMPUG000000179461 retrocopy
retro_mputfur_1649,
Mus musculus ENSMUSG000000329661 retrocopy
retro_mmus_1293,
Nomascus leucogenys ENSNLEG000000008001 retrocopy
retro_nleu_1406,
Nomascus leucogenys ENSNLEG000000093565 retrocopies
retro_nleu_2009, retro_nleu_2628, retro_nleu_2728, retro_nleu_2730, retro_nleu_604,
Otolemur garnettii ENSOGAG000000026291 retrocopy
retro_ogar_673,
Procavia capensis ENSPCAG000000088162 retrocopies
retro_pcap_289, retro_pcap_37,
Pongo abelii ENSPPYG000000108525 retrocopies
retro_pabe_1654, retro_pabe_1686, retro_pabe_2364, retro_pabe_2365, retro_pabe_998,
Pongo abelii ENSPPYG000000126041 retrocopy
retro_pabe_1105,
Pan troglodytes ENSPTRG000000117081 retrocopy
retro_ptro_906,
Pan troglodytes ENSPTRG000000131632 retrocopies
retro_ptro_2983, retro_ptro_818,
Pteropus vampyrus ENSPVAG000000138401 retrocopy
retro_pvam_1367,
Rattus norvegicus ENSRNOG000000088221 retrocopy
retro_rnor_453,
Sorex araneus ENSSARG000000138081 retrocopy
retro_sara_24,
Sus scrofa ENSSSCG000000071881 retrocopy
retro_sscr_98,
Tupaia belangeri ENSTBEG000000122821 retrocopy
retro_tbel_56,
Tursiops truncatus ENSTTRG000000035473 retrocopies
retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos ENSVPAG000000115111 retrocopy
retro_vpac_171,


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