RetrogeneDB ID:

retro_cint_29

Retrocopy
location
Organism:Vase tunicate (Ciona intestinalis)
Coordinates:9:6523900..6524344(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CIN.22448
Ensembl ID:ENSCING00000018711
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cint_29
ATGGCTCTCAGGAGAATAAAGAAAGAGCTTAAAGATTTGGAGAAAGATGGCCCGTGTAATTGTACAGCAGCTCCTGCTGG
AGAAGGTTTAGACTTGTTTCAATGGGAAGCCACAATAATGGGCCCTGTTGATTCACCCTATGAAGGGGGAGCCTTCTATC
TTAAAATACATTTCCCCATTGACTACCCATTTAAACCACCCAAGGTTGTTTTCACTACAAAGATATATCATCCCAATATT
AACAGCACTGGGAATATTTGTTTGGATATTTTGCGTTCGCAATGGTCACCTGCGCTAAATGTATCCAAAGTACTTTTGTC
GATCAGTTCGCTTCTGTGCGATCCCAACCCAGGACACCCATTGGTCCCTGAGATTGCCAAGTTATATGTTGATAACAGGG
AGAAATATTTGCAGAATGCGATAGAGTGGACAAGAAAATATGCA

ORF - retro_cint_29 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.95 %
Parental protein coverage: 98.65 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALKRINKELADISRDPPAQCSAGPVGD--DLFQWQATIMGPSDSPYQGGVFFLSIHFPTDYPFKPPKVA
MAL.RI.KEL.D...D.P..C.A.P.G...DLFQW.ATIMGP.DSPY.GG.F.L.IHFP.DYPFKPPKV.
RetrocopyMALRRIKKELKDLEKDGPCNCTAAPAGEGLDLFQWEATIMGPVDSPYEGGAFYLKIHFPIDYPFKPPKVV
ParentalFSTKIYHPNINSNGSICLDILRSQWSPALTVAKVLLSICSLLCDPNPDDPLVPDIARVFKNDRSKYNDLA
F.TKIYHPNINS.G.ICLDILRSQWSPAL.V.KVLLSI.SLLCDPNP..PLVP.IA......R.KY...A
RetrocopyFTTKIYHPNINSTGNICLDILRSQWSPALNVSKVLLSISSLLCDPNPGHPLVPEIAKLYVDNREKYLQNA
ParentalREWTRKYA
.EWTRKYA
RetrocopyIEWTRKYA

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

2 EST(s) were mapped to retro_cint_29 retrocopy
EST ID Start End Identity Match Mis-match Score
AV957614 6523923 6524083 97.5 156 1 154
AV998132 6523914 6524088 100 174 0 174

TSS - click to see more details

Ciona intestinalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_cint_29 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 38 parental genes, and 166 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000021831 retrocopy
retro_acar_182,
Ailuropoda melanoleuca ENSAMEG000000112166 retrocopies
retro_amel_1295, retro_amel_1427, retro_amel_1648, retro_amel_1750, retro_amel_620, retro_amel_995,
Bos taurus ENSBTAG000000041616 retrocopies
retro_btau_1421, retro_btau_1602, retro_btau_1739, retro_btau_1775, retro_btau_1851, retro_btau_1852,
Canis familiaris ENSCAFG000000310415 retrocopies
retro_cfam_1191, retro_cfam_1439, retro_cfam_1602, retro_cfam_2034, retro_cfam_785,
Choloepus hoffmanni ENSCHOG000000046492 retrocopies
retro_chof_2549, retro_chof_439,
Ciona intestinalis ENSCING000000068601 retrocopy
retro_cint_33,
Ciona intestinalis ENSCING00000018711 2 retrocopies
retro_cint_19, retro_cint_29 ,
Callithrix jacchus ENSCJAG000000154923 retrocopies
retro_cjac_512, retro_cjac_657, retro_cjac_791,
Dasypus novemcinctus ENSDNOG0000000932030 retrocopies
retro_dnov_1061, retro_dnov_1125, retro_dnov_113, retro_dnov_114, retro_dnov_1167, retro_dnov_1193, retro_dnov_1198, retro_dnov_1257, retro_dnov_141, retro_dnov_1544, retro_dnov_1752, retro_dnov_1761, retro_dnov_1831, retro_dnov_1862, retro_dnov_1912, retro_dnov_1934, retro_dnov_1995, retro_dnov_2084, retro_dnov_2135, retro_dnov_2289, retro_dnov_2362, retro_dnov_2457, retro_dnov_2622, retro_dnov_436, retro_dnov_574, retro_dnov_750, retro_dnov_795, retro_dnov_83, retro_dnov_889, retro_dnov_917,
Dipodomys ordii ENSDORG000000067622 retrocopies
retro_dord_172, retro_dord_323,
Equus caballus ENSECAG000000206781 retrocopy
retro_ecab_859,
Erinaceus europaeus ENSEEUG000000108201 retrocopy
retro_eeur_84,
Erinaceus europaeus ENSEEUG000000146583 retrocopies
retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi ENSETEG000000012913 retrocopies
retro_etel_1218, retro_etel_1998, retro_etel_36,
Felis catus ENSFCAG000000249182 retrocopies
retro_fcat_1106, retro_fcat_785,
Gorilla gorilla ENSGGOG000000013682 retrocopies
retro_ggor_1156, retro_ggor_2321,
Gorilla gorilla ENSGGOG000000108321 retrocopy
retro_ggor_953,
Loxodonta africana ENSLAFG000000068782 retrocopies
retro_lafr_288, retro_lafr_290,
Macropus eugenii ENSMEUG000000042566 retrocopies
retro_meug_1034, retro_meug_1503, retro_meug_2138, retro_meug_564, retro_meug_787, retro_meug_89,
Macaca mulatta ENSMMUG000000206663 retrocopies
retro_mmul_1298, retro_mmul_2143, retro_mmul_2246,
Monodelphis domestica ENSMODG000000117832 retrocopies
retro_mdom_17, retro_mdom_884,
Mustela putorius furoENSMPUG000000091105 retrocopies
retro_mputfur_1263, retro_mputfur_1637, retro_mputfur_263, retro_mputfur_682, retro_mputfur_703,
Mus musculus ENSMUSG0000007857811 retrocopies
retro_mmus_1818, retro_mmus_1895, retro_mmus_1913, retro_mmus_2293, retro_mmus_2635, retro_mmus_2643, retro_mmus_3119, retro_mmus_3636, retro_mmus_850, retro_mmus_875, retro_mmus_923,
Mus musculus ENSMUSG000000918963 retrocopies
retro_mmus_2267, retro_mmus_27, retro_mmus_629,
Ornithorhynchus anatinus ENSOANG000000054151 retrocopy
retro_oana_51,
Oryctolagus cuniculus ENSOCUG0000002944810 retrocopies
retro_ocun_1220, retro_ocun_1426, retro_ocun_1536, retro_ocun_1660, retro_ocun_1856, retro_ocun_1941, retro_ocun_261, retro_ocun_467, retro_ocun_887, retro_ocun_988,
Otolemur garnettii ENSOGAG000000128606 retrocopies
retro_ogar_1124, retro_ogar_3047, retro_ogar_3048, retro_ogar_3110, retro_ogar_544, retro_ogar_599,
Ochotona princeps ENSOPRG000000116959 retrocopies
retro_opri_1042, retro_opri_1189, retro_opri_206, retro_opri_310, retro_opri_447, retro_opri_457, retro_opri_627, retro_opri_77, retro_opri_838,
Pongo abelii ENSPPYG000000149671 retrocopy
retro_pabe_91,
Pongo abelii ENSPPYG000000158446 retrocopies
retro_pabe_1016, retro_pabe_1164, retro_pabe_1257, retro_pabe_2330, retro_pabe_30, retro_pabe_3670,
Pan troglodytes ENSPTRG000000173033 retrocopies
retro_ptro_26, retro_ptro_3141, retro_ptro_341,
Pteropus vampyrus ENSPVAG000000154381 retrocopy
retro_pvam_234,
Rattus norvegicus ENSRNOG000000137419 retrocopies
retro_rnor_2777, retro_rnor_342, retro_rnor_345, retro_rnor_539, retro_rnor_650, retro_rnor_724, retro_rnor_725, retro_rnor_772, retro_rnor_784,
Sus scrofa ENSSSCG000000243061 retrocopy
retro_sscr_783,
Sus scrofa ENSSSCG000000298224 retrocopies
retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Ictidomys tridecemlineatus ENSSTOG000000134816 retrocopies
retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tupaia belangeri ENSTBEG000000002705 retrocopies
retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,
Tarsius syrichta ENSTSYG000000054591 retrocopy
retro_tsyr_1421,




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