RetrogeneDB ID:

retro_csav_3

Retrocopy
location
Organism:Pacific transparent sea squirt (Ciona savignyi)
Coordinates:reftig_11:1397711..1399655(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCSAVG00000009296
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CSA.971
Ensembl ID:ENSCSAVG00000008588
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_csav_3
ATTCAAGATTTATTTTTGAATAACGATATAATAGAATATTATCGAAAGTTTACAAGAGCAAAGATGTCAACTGCAGTAGG
AATTGATCTGGGAACAACATATTCCTGTGTCGGCGTATTTCGACATGGTAAAGTGGAGATTATTGCTAATGACCAGGGAA
ATAGAACAACACCAAGCTACGTTGCTTTCAATGAGACAGAAAGAATAATCGGAGATGGAGCAAAAGATCAAGTCGCACGA
AACCCCGAGAACACCATCTTTGACGCGAAGAGACTCATCGGAAGAAATTTCAGCGACCCCGTTGTTCAGAAAGACATGGA
GCACTGGCCGTTTCAAGTGGTCAATAAGAACGGAAAACCTTTTCTTAAAGCTGAATATCAAGGCCAAGTGAAGACGTTTT
CGCCAGAAGAAATCAGCTCAATGGTTCTTACGAAGATGAAAGACACGGCAGAGGCCTACCTTGGTGAAAGTGTAAAGGAC
GCTGTCATAACAGTACCAGCTTACTTTAACGATTCACAAAGACAAGCAACCAAAGACGCTGGAACAATAGCTGGTTTAAA
TGTGTTGCGAGTCATTAACGAACCAACAGCCGCCGCCCTTGCATACGGGCTGGATAAAAACCTGTCTGGCGAAAAAAGAG
TTCTGATTTTTGATCTTGGAGGTGGTACCTTTGATGTCTCCGTGCTAAGTATAGATGAAGGATCAATCTTTGAAGTCTTA
TCTACCGCTGGTGACACCCACCTTGGAGGTGAAGACTTCGATAACAGAATGGTGAAGCATTTCATGGACGAATTCAAACG
AAAGCACAAGAAAGACATTTCAAAAAATAATAGATCCGTGAGGAGACTGCGCACGGCTTGTGAGAGAGCAAAGAGAGTTC
TTTCAACCTCGACCGAAGCATCTTTGGAGTTGGAGTCATTGTATGAAGGCATTGATTTCTATAGTAAAATCACTCGTGCA
AGATTCGAGGAAATGTGCTCTGATTTGTTTCGCTCTTGTTTGGATCCTGTGGAGAAAGCATTGCGGGATGCCAAGCTTGA
TAAAATGAAGATTGATGATGTGGTATTGGTTGGAGGATCCACTAGAATTCCAAAGATACAAAAATTACTAAGTGACTTCT
TTAATGGAAAGAATCTCAACAAATCGATTAACCCAGACGAGGCAGTCGCATACGGAGCTGCTATCCAGTCTGCTGTTCTC
ACCGGTAACTCTGGAGTGCAAGATGTTCTTCTAGTAGATGTTGCTCCGCTTTCGTTGGGGATTGAAACGGCTGGCGAAGT
GATGACAAAACTGGTTGAGAGGAACGCAAGAATTCCTCACAGCACATCACAAGTCTTTACCACCTACGCTGACAACCAAC
CAGCTGTAACTATACAAGTTTACGAGGGTGAAAGAGCACTGACGAAACACAACAACCTGTTAGGGACCTTTAACCTCTCT
GGAATACCACCCGCACCAAGAGGTGTTCCAAAAATTGAAGTTACTTTCGACATAGATGCCAACGGTATCTTGCAAGTTTC
AGCCAAAGACCAGAGTACCGGCAAAGCGAACAAAATTACCATCAACAAAGGTCGGCTATCAAAGGCAGACATCGAATCAA
TGTTAGCAGATGCTGAAAAATATAAAGAAGAAGACAATAAACAGGTAGAACGATTGAAAGCGAGAAACGATTTGGAAAGC
TACATGTACTCGTGCAAGAATGCCGCCGAAGAAGCCGGAGACAAAATATCATCGGACGACAGGGAACGAGTGGTGCAAAT
GTGCAACGAGACGCAAAAGTGGTTGGATGGAAATTCACTCGCTGAGAAGGAAGAATTCGAAGAGAAAATGAACCAAGTTA
AGAAATGTTGTTCACCTGTCATGACCAAGTTGCATTCAGCCGCCGGTGGGCAGCAAAGCGCCAGGCAAAACGGTGACGGA
CCAGTTGTGGATGAAGTCGACTAA

ORF - retro_csav_3 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.95 %
Parental protein coverage: 96.74 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKEKKMSKAPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVGFSDTERMIGDAAKNQIAMNPTNT
K........A.GIDLGTTYSCVGVF.HGKVEIIANDQGNRTTPSYV.F..TER.IGD.AK.Q.A.NP.NT
RetrocopyKFTRAKMSTAVGIDLGTTYSCVGVFRHGKVEIIANDQGNRTTPSYVAFNETERIIGDGAKDQVARNPENT
ParentalIFDAKRLIGRRFDEDTVQSDMKHWPFTVKNDSGKPKFEVEYKGDTKTFYPEEISSMILLKMKETAEAYLG
IFDAKRLIGR.F....VQ.DM.HWPF.V.N..GKP....EY.G..KTF.PEEISSM.L.KMK.TAEAYLG
RetrocopyIFDAKRLIGRNFSDPVVQKDMEHWPFQVVNKNGKPFLKAEYQGQVKTFSPEEISSMVLTKMKDTAEAYLG
ParentalKSVTDAVVTVPAYFNDSQRQATKDAGTISGLNILRIINEPTAAAIAYGLDKKVSGDINVLIFDLGGGTFD
.SV.DAV.TVPAYFNDSQRQATKDAGTI.GLN.LR.INEPTAAA.AYGLDK..SG...VLIFDLGGGTFD
RetrocopyESVKDAVITVPAYFNDSQRQATKDAGTIAGLNVLRVINEPTAAALAYGLDKNLSGEKRVLIFDLGGGTFD
ParentalVSVLNIDEG-IFEVKSTSGNTHLGGEDFDNRMVDFFCKEFEKKHKKNLRSSKRALRRLRTACERVKRALS
VSVL.IDEG.IFEV.ST.G.THLGGEDFDNRMV..F..EF..KHKK......R..RRLRTACER.KR.LS
RetrocopyVSVLSIDEGSIFEVLSTAGDTHLGGEDFDNRMVKHFMDEFKRKHKKDISKNNRSVRRLRTACERAKRVLS
ParentalSSTQANMEIDSLFEGIDFYTSVTRARFEELNNDLFRGTLDPVEKALRDAKLEKGKIDEVVLVGGSTRIPR
.ST.A..E..SL.EGIDFY...TRARFEE...DLFR..LDPVEKALRDAKL.K.KID.VVLVGGSTRIP.
RetrocopyTSTEASLELESLYEGIDFYSKITRARFEEMCSDLFRSCLDPVEKALRDAKLDKMKIDDVVLVGGSTRIPK
ParentalIQKLLSDFFNGKELNKSINPDEAVAYGAAVQAAILSGVKSDVVQDLLLLDVAPLSLGLETAGGVMTPLIK
IQKLLSDFFNGK.LNKSINPDEAVAYGAA.Q.A.L.G.....VQD.LL.DVAPLSLG.ETAG.VMT.L..
RetrocopyIQKLLSDFFNGKNLNKSINPDEAVAYGAAIQSAVLTG--NSGVQDVLLVDVAPLSLGIETAGEVMTKLVE
ParentalRNSTVPKKETQKFTTYSDNQPGVLIQVYEGERGMTVNNNLLGKFELTGIPPAPRGIPQIEVTFDIDANGI
RN...P....Q.FTTY.DNQP.V.IQVYEGER..T..NNLLG.F.L.GIPPAPRG.P.IEVTFDIDANGI
RetrocopyRNARIPHSTSQVFTTYADNQPAVTIQVYEGERALTKHNNLLGTFNLSGIPPAPRGVPKIEVTFDIDANGI
ParentalLNVSACDISTGKQNKITITNDKGRLSKEEIDRMVNDAEKYKEEDDQQRQRIQAKNNLESYAFNVKSSLED
L.VSA.D.STGK.NKITI...KGRLSK..I..M..DAEKYKEED..Q..R..A.N.LESY....K...E.
RetrocopyLQVSAKDQSTGKANKITI--NKGRLSKADIESMLADAEKYKEEDNKQVERLKARNDLESYMYSCKNAAEE
ParentalDKVRDKVTDDDRKAVLDKAKEILDWLDMNQAAGKEEYEHQQKELEKVANPVFSKLYQTGGEMPS
....DK...DDR..V.....E...WLD.N..A.KEE.E.......K...PV..KL....G...S
Retrocopy--AGDKISSDDRERVVQMCNETQKWLDGNSLAEKEEFEEKMNQVKKCCSPVMTKLHSAAGGQQS

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_3 retrocopy.

TSS - click to see more details

Ciona savignyi was not studied using FANTOM5 data.

Lab - click to see more details

retro_csav_3 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 34 parental genes, and 118 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
retro_amel_126,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Bos taurus ENSBTAG000000131621 retrocopy
retro_btau_354,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Callithrix jacchus ENSCJAG000000076485 retrocopies
retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG00000008588 1 retrocopy
retro_csav_3 ,
Dipodomys ordii ENSDORG000000154671 retrocopy
retro_dord_16,
Equus caballus ENSECAG000000135102 retrocopies
retro_ecab_291, retro_ecab_628,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Felis catus ENSFCAG000000011326 retrocopies
retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens ENSG000001099718 retrocopies
retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Gorilla gorilla ENSGGOG000000083818 retrocopies
retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Loxodonta africana ENSLAFG000000303124 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta ENSMMUG000000046967 retrocopies
retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 retrocopies
retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus ENSMUSG000000156568 retrocopies
retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Nomascus leucogenys ENSNLEG000000074198 retrocopies
retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Oryctolagus cuniculus ENSOCUG000000155334 retrocopies
retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pongo abelii ENSPPYG000000039879 retrocopies
retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Pan troglodytes ENSPTRG000000044045 retrocopies
retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Ictidomys tridecemlineatus ENSSTOG000000037561 retrocopy
retro_itri_51,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Tursiops truncatus ENSTTRG000000111396 retrocopies
retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,




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