RetrogeneDB ID:

retro_cint_18

Retrocopy
location
Organism:Vase tunicate (Ciona intestinalis)
Coordinates:9:4229563..4230856(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCING00000002360
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CIN.21501
Ensembl ID:ENSCING00000002649
Aliases:None
Description:Histone deacetylase [Source:UniProtKB/TrEMBL;Acc:F6YDI9]


Retrocopy-Parental alignment summary:






>retro_cint_18
AGTAACAACAAAGTGGCTTACTTCTATGACATGGATGTTTCACGGTTCCACTATGGCCCTGGTCACCCCATGAAACCTCA
CCGTCTTGCTCTTACCCACACTCTAGTGTTGCACTATGGCCTTCACAACAAGATGCAAATGTTTAAGCCGTACCGCGCCA
CTAGCCACGACATGTGTAGATTTCACTCTGAAGATTACATCAATTTCCTTCAGCGTATAACACCTATGAATCTAGCTGGT
TTCACGAAAAACTTAAAACTGTTTAATGTGGGCGATGACTGTCCTGTTTTCCCTGGTCTTTATGACTTTTGCTCCATGTA
CACTGGTGCCTCTTTGCAAGCAGCGACAATGCTTAATAATAAGAAAAGTGATATCGCTATAAACTGGTCAGGTGGTTTGC
ACCATGCTAAGAAGTATGAAGCATCTGGCTTCTGTTACGTGAATGATATCGTCATTGCAATTTTGGAACTTTTAAAGTAT
CACCCTAGAGTATTATACCTCGACATTGATGTACACCACGGTGATGGTGTCCAAGAGGCTTTTTATTTAACGGACCGTGT
GATGACTGTATCCTTTCATAAGTATGGCAATTACTTTTTCCCAGGCACTGGCGACATGTATGAGATTGGAGCTGAGAGTG
GCCGCTATTATTCATTAAATGTACCACTTAAGGATGGCATTAACGATCAGGCTTATCAGCAACTTCTTAAGCCTATTATG
AAAGCTGTAATGCAGTCATACCAACCCACTTGCATTGTTATGCAGTGTGGTGCAGACTCCCTTGGCTGTGACAGACTTGG
CTGCTTCAACCTGACCATAGACGGACATGGAGAATGCGTGAAGTTCATGAAAGAGTTTGGCGTCCCAATGATGGTCCTTG
GCGGCGGTGGGTACACTGTACGCAATGTGGCCAGGTGCTGGACACATGAAACTTCTATCATAGTAGGTCAGGAAATTAAT
GACGAATTACCTTATAACGAATACTTTGAGTATTTTGGTCCTGACTACACTCTTAGACCGGACACAAGTCGAGGTATAGA
AAACCAGAACACTAAGCAGTATCTTGATCAACTGCGACAGATGTGTCTTGAGAGTTTAAAGATGATCACGCATGCTCCGA
GTGTTCAGATGCATGAGGTTCCTCCGGATCTGCTCTCCTTTGACAACTACGAGTCCCTCAGTGAGTTGGATGTGAGAGAG
AGGCAAGAAGACGTGGATCAGAGGATTGAACCAGATAATGAGTTTTATGACGGCGAAAAAGACAATGATAAAGAAAGTGA
TGTCAGCATATGA

ORF - retro_cint_18 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.19 %
Parental protein coverage: 97.52 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSRKVCYYYDSDIGNNYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKCNAEEMSRYHSDDYIKFLR
..KV.Y.YD.D.....YG.GHPMKPHR...TH.L.L.YGL..KM....P.......M.R.HS.DYI.FL.
RetrocopyNNKVAYFYDMDVSRFHYGPGHPMKPHRLALTHTLVLHYGLHNKMQMFKPYRATSHDMCRFHSEDYINFLQ
ParentalSIRPDNMSEYTKQMQRFNVGEDCPVFDGLYEFCQLSGGGSIAGAVKINKHQTDIAINWAGGLHHAKKSEA
.I.P.N....TK....FNVG.DCPVF.GLY.FC....G.S...A...N....DIAINW.GGLHHAKK.EA
RetrocopyRITPMNLAGFTKNLKLFNVGDDCPVFPGLYDFCSMYTGASLQAATMLNNKKSDIAINWSGGLHHAKKYEA
ParentalSGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEY-FPGTGDLRDIGA
SGFCYVNDIV.AILELLKYH.RVLY.DID.HHGDGV.EAFY.TDRVMTVSFHKYG.Y.FPGTGD...IGA
RetrocopySGFCYVNDIVIAILELLKYHPRVLYLDIDVHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEIGA
ParentalGKGKYYALNFPLRDGMDDECYEQIFQPVITKVMEYYQPSAVVLQCGADSLG-DRLGCFNLTVKGHAKCLE
..G.YY.LN.PL.DG..D..Y.Q...P....VM..YQP...V.QCGADSLG.DRLGCFNLT..GH..C..
RetrocopyESGRYYSLNVPLKDGINDQAYQQLLKPIMKAVMQSYQPTCIVMQCGADSLGCDRLGCFNLTIDGHGECVK
ParentalYVKKFNVPILMLGGGGYTIRNVARCWTYETAVALGQEIPNELPYNDYFEYFGPDFKLHISPS-NMSNQNT
..K.F.VP...LGGGGYT.RNVARCWT.ET....GQEI..ELPYN.YFEYFGPD..L....S....NQNT
RetrocopyFMKEFGVPMMVLGGGGYTVRNVARCWTHETSIIVGQEINDELPYNEYFEYFGPDYTLRPDTSRGIENQNT
ParentalMEYLQKIRQRLFENLRMLPHAPGVQMQDIPPDAVVSGSDDEAMDDPD
..YL...RQ...E.L.M..HAP.VQM...PPD...S....E.....D
RetrocopyKQYLDQLRQMCLESLKMITHAPSVQMHEVPPD-LLSFDNYESLSELD

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Ciona intestinalis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cint_18 retrocopy.

TSS - click to see more details

Ciona intestinalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_cint_18 was not experimentally validated.

Retrocopy orthology:
Ciona intestinalis 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 23 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Ciona intestinalis ENSCING00000002649 1 retrocopy
retro_cint_18 ,
Callithrix jacchus ENSCJAG000000009702 retrocopies
retro_cjac_2490, retro_cjac_830,
Echinops telfairi ENSETEG000000084681 retrocopy
retro_etel_488,
Homo sapiens ENSG000001164781 retrocopy
retro_hsap_826,
Gorilla gorilla ENSGGOG000000117411 retrocopy
retro_ggor_676,
Myotis lucifugus ENSMLUG000000031174 retrocopies
retro_mluc_1570, retro_mluc_225, retro_mluc_2548, retro_mluc_935,
Myotis lucifugus ENSMLUG000000138371 retrocopy
retro_mluc_283,
Macaca mulatta ENSMMUG000000099482 retrocopies
retro_mmul_1085, retro_mmul_2518,
Monodelphis domestica ENSMODG000000178601 retrocopy
retro_mdom_597,
Mus musculus ENSMUSG000000288001 retrocopy
retro_mmus_153,
Nomascus leucogenys ENSNLEG000000024731 retrocopy
retro_nleu_259,
Ornithorhynchus anatinus ENSOANG000000036311 retrocopy
retro_oana_79,
Otolemur garnettii ENSOGAG000000057093 retrocopies
retro_ogar_2181, retro_ogar_3022, retro_ogar_3313,
Pelodiscus sinensis ENSPSIG000000041341 retrocopy
retro_psin_44,
Pan troglodytes ENSPTRG000000185191 retrocopy
retro_ptro_69,
Pteropus vampyrus ENSPVAG000000133251 retrocopy
retro_pvam_1339,
Rattus norvegicus ENSRNOG000000095683 retrocopies
retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sorex araneus ENSSARG000000003541 retrocopy
retro_sara_651,
Sarcophilus harrisii ENSSHAG000000087871 retrocopy
retro_shar_573,
Ictidomys tridecemlineatus ENSSTOG000000127791 retrocopy
retro_itri_374,
Tarsius syrichta ENSTSYG000000093634 retrocopies
retro_tsyr_1337, retro_tsyr_1355, retro_tsyr_681, retro_tsyr_765,
Tursiops truncatus ENSTTRG000000016131 retrocopy
retro_ttru_1236,
Tursiops truncatus ENSTTRG000000150431 retrocopy
retro_ttru_462,


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