RetrogeneDB ID:

retro_cint_15

Retrocopy
location
Organism:Vase tunicate (Ciona intestinalis)
Coordinates:7:2691299..2692040(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCING00000020743
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CI14-3-3
Ensembl ID:ENSCING00000023856
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cint_15
ATGTCGTCAAGAGAAGACATGATAGCCCGTGCCAAACTGTCAGAACAGGCACAACGTTATAATGAGATGGCCGCAGCCAT
GAAAGTCGTTGTCGAAATGGGCTCGGAGCTGAGCAACGACGAAAGAAACTTGCTGTCAATCGCGTATAAACATACGACGG
GTGCGAGGAGACAATCCTGGCGAGCTATATCAAGTGTGGAACAAAAAGTAGAACTGGAGAGCGAAGGCCGAATAGAATTA
GTGCGTGATTACAGGGAAAAAATCGAGGCAGAGCTCGAGGCCATTTGCCAAGAAATAATTCAGCTCATTGATTCTCACTT
GCTTAAATCCGCTCAGGATAAAGACAGCCAAGTGTTTTACTACAAAATGAAGGGTGACTATTTCCGCTACATGTGTGAAA
TTTCTTCCATTCCGGAGAAAAGGAAAAAAGTTGTCTCGGGAGCAAATAGAGCATATAATGCAGCAAATACAGAAGCTGAA
CGGATGTCAGCAATTAATCCTATAAAGCTGGGTCTTGCGCTTAACCACTCTGTCTTTTTATATGAGATCAAAAACAGCGA
AAGAAAGGCAATTAATATTGCCCAAACTGCGTTCGACGATGCTCTTAAAAAGGTGGAAGAGCTGAGTGCTGACGCATACA
AGGATTCAACACTGATTATGCAACTTATTAGAGACAACCTTACGCAATGGAATTCACCTGATAAAGTTGTGCAGGAGCTG
TTACAGGACACTGAAGATTAA

ORF - retro_cint_15 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 51.07 %
Parental protein coverage: 90.59 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalTEREDLVYKAKLAEQAERYDEMVESMQAVAKLGVELSVEERNLLSVAYKNVIGARRASWRIISSIEQK-E
..RED....AKL.EQA.RY.EM...M..V...G.ELS..ERNLLS.AYK...GARR.SWR.ISS.EQK.E
RetrocopySSREDMIARAKLSEQAQRYNEMAAAMKVVVEMGSELSNDERNLLSIAYKHTTGARRQSWRAISSVEQKVE
ParentalDDKQKSNEMTQNYKKQVEKELNEICNAILSLIDQHLIPNAGQANESKVFYHKMQGDYHRYLAEFES-GDQ
.......E....Y....E.EL..IC..I..LID.HL...A.Q...S.VFY.KM.GDY.RY..E..S....
RetrocopyLESEGRIELVRDYREKIEAELEAICQEIIQLIDSHLLKSA-QDKDSQVFYYKMKGDYFRYMCEISSIPEK
ParentalRKEAAEQSLLAYKAASDVAADNLPPTHPIRLGLALNFSVFYYEILNSSDRACKLAKKAFDDAIAELDTLS
RK........AY.AA....A.......PI.LGLALN.SVF.YEI.NS...A...A..AFDDA......LS
RetrocopyRKKVVSGANRAYNAAN-TEAERMSAINPIKLGLALNHSVFLYEIKNSERKAINIAQTAFDDALKKVEELS
ParentalEESYKDSTLIMQLLRDNLTLWTS
...YKDSTLIMQL.RDNLT.W.S
RetrocopyADAYKDSTLIMQLIRDNLTQWNS

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_15 retrocopy.

TSS - click to see more details

Ciona intestinalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_cint_15 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 19 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000056643 retrocopies
retro_btau_1485, retro_btau_372, retro_btau_954,
Choloepus hoffmanni ENSCHOG000000108612 retrocopies
retro_chof_1912, retro_chof_905,
Ciona intestinalis ENSCING00000023856 1 retrocopy
retro_cint_15 ,
Cavia porcellus ENSCPOG000000080071 retrocopy
retro_cpor_307,
Ciona savignyi ENSCSAVG000000117232 retrocopies
retro_csav_13, retro_csav_9,
Dasypus novemcinctus ENSDNOG000000038082 retrocopies
retro_dnov_1452, retro_dnov_2602,
Echinops telfairi ENSETEG000000120562 retrocopies
retro_etel_1762, retro_etel_738,
Felis catus ENSFCAG000000113681 retrocopy
retro_fcat_1636,
Homo sapiens ENSG000001089534 retrocopies
retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Gorilla gorilla ENSGGOG000000168401 retrocopy
retro_ggor_2596,
Macropus eugenii ENSMEUG0000001546012 retrocopies
retro_meug_1290, retro_meug_1396, retro_meug_1536, retro_meug_16, retro_meug_1926, retro_meug_196, retro_meug_2153, retro_meug_2163, retro_meug_835, retro_meug_9, retro_meug_982, retro_meug_986,
Monodelphis domestica ENSMODG000000101742 retrocopies
retro_mdom_1567, retro_mdom_744,
Nomascus leucogenys ENSNLEG000000006562 retrocopies
retro_nleu_2067, retro_nleu_2868,
Oryctolagus cuniculus ENSOCUG000000146072 retrocopies
retro_ocun_1062, retro_ocun_1576,
Otolemur garnettii ENSOGAG000000061552 retrocopies
retro_ogar_1003, retro_ogar_2144,
Pongo abelii ENSPPYG000000077694 retrocopies
retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pan troglodytes ENSPTRG000000085215 retrocopies
retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Ictidomys tridecemlineatus ENSSTOG000000050841 retrocopy
retro_itri_1175,
Vicugna pacos ENSVPAG000000102883 retrocopies
retro_vpac_230, retro_vpac_411, retro_vpac_559,


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