TCONS_00056354 (transcript) - C. hemisphaerica

Overview
NameTCONS_00056354
Unique NameTCONS_00056354
Typetranscript
OrganismClytia hemisphaerica (Jellyfish)
Sequence length1089

Sequence
The following sequences are available for this feature:

transcript sequence

>TCONS_00056354 ID=TCONS_00056354|Name=TCONS_00056354|organism=Clytia hemisphaerica|type=transcript|length=1089bp
AAATGAACCATCATGCAATGCTTCAAGGGTTGTCTAGATAGAAATCTCCC
TCCCAATCGCTCATTTCAGCATGCTGTCAAAAGAAATCGTTTCCATCATA
TCTTAACTTGACCTTCAAGATCAAAGGATATCAACTCgtgaaaattgttt
taaaagaaGACGCACACTTGATGATGTTCAGTATGGATAGTCCTACACGC
GATTCACCAACGACCGACAAACGTCACTCGACATCTCCCGTTACACGTCA
CTCCACGTCTCCCGTCAACAGTCCATCTCCTCCGTTAGAACGTCAGAAGA
AACCGTTCTCGATTGACTATCTACTTAATTTTTCACCGACAAAAAAAACG
ACCCTCATCCGACAATCACCACCTGTTGAATACATCCAACCGCCCTTCCA
CACTCGGCCTCCACACTTTATTAATGACCGGTTAAAAGAGCCGGAAGACG
AATCTAAAGTACCATCACCGACTTTATTGACTAACACCTCCAGGAAAAGA
GAGCTTGATCCCACCATAGAATTTCAATGGGATTTGAGCAAATGTTTTCT
ACGAAAACACAAGGCCAATCGTAAACCACGAACGCCCTTCTCCGCCAGTC
AACTTCTCACCTTGGAACAGAAATTTAAACGTAAACAATATTTATCAATA
AACGAGCGATCAGAATTAAGCGCTCAACTGAACTTAACTGAAACACAAAT
CAAAATTTGGTTTCAAAATCGTCGAGCAAAAGAAAAACGTCTTAAAGAAG
CGGAACTCGAGAAAACCGTAAGAACATTTTCACCGGGAAGTGTAACATCA
CCAAACTATTCACCGTGCAGCTGTTGTTATTCGGGCTCTTCCGTATTCAA
CTATCCACCTGTATCGTGCTCTCGGATATCCCGTTTTATGCATTAGTTGA
AAATTCATGTGGGGATGTCTGTTTTGCCTGTTGTTGTATATATCTTTAAT
TTctaagattttaattttgttaatattttgtaaGGTGGCCTCATGTAAGG
TTCGTGATCGACAACCGCTTTTCACAGACCCGCTAGGGTTTTTTCAGCCA
gcggggtaaaaataacggaccaaattCTCGATGAGGATT
Run BLAST on NCBI

protein sequence of TCONS_00056354-protein

>TCONS_00056354-protein ID=TCONS_00056354-protein|Name=TCONS_00056354-protein|organism=Clytia hemisphaerica|type=polypeptide|length=241bp
MMFSMDSPTRDSPTTDKRHSTSPVTRHSTSPVNSPSPPLERQKKPFSIDY
LLNFSPTKKTTLIRQSPPVEYIQPPFHTRPPHFINDRLKEPEDESKVPSP
TLLTNTSRKRELDPTIEFQWDLSKCFLRKHKANRKPRTPFSASQLLTLEQ
KFKRKQYLSINERSELSAQLNLTETQIKIWFQNRRAKEKRLKEAELEKTV
RTFSPGSVTSPNYSPCSCCYSGSSVFNYPPVSCSRISRFMH
Run BLAST on NCBI

transcript from alignment at scaffold_273:15813..19376-

Legend: exonfive_prime_UTRCDSthree_prime_UTR
Hold the cursor over a type above to highlight its positions in the sequence below.
>TCONS_00056354 ID=TCONS_00056354|Name=TCONS_00056354|organism=Clytia hemisphaerica|type=transcript|length=3564bp|location=Sequence derived from alignment at scaffold_273:15813..19376- (Clytia hemisphaerica)
AAATGAACCATCATGCAATGCTTCAAGGGTTGTCTAGATAGAAATCTCCC
TCCCAATCGCTCATTTCAGCATGCTGTCAAAAGAAATCGTTTCCATCATA
TCTTAACGTTAGTGAGCCTTTCAAAAATTTGATTGCTCTCTATTGATCAT
TACAAAACCCCCGTCTTTTAATGAATCTTATATTCACTTAAACCCTTTTG
AATGATAAGTCTTATGTTTGAAAAACATTAAACCCTATCAGTTGACCAAT
CAGAATAAATATAAAAATCAGAGAAAGAAATTTTATAGTTAAACCCTAAA
GCTATCTCTATTCTTTGATAGGGTGAAACTGTTAACCGTAGGTCGTCGAG
ACAATTCAGCAATTGTTTTTAATTGTTCATTAAGAACTCATCTTCTTATC
GTTGGGGTTCAAGAATTCTTTTATTCTTTTTATTATTCTATTGTGTGTTG
ATAACAATAGAGTGAATACCAGCTTGATTAATTGCTATTCATATCTCTCT
AGTTGACCTTCAAGATCAAAGGATATCAACTCGTGAAAATTGTTTTAAAA
GAAGACGCACACTTGATGATGGTAAGTTTTCATCGTGTATCTATTGACGA
AGAGCTAGAGTGATTTCAAAGAAAAGATCTGGCGGTCTACAGATACAGAA
ATATTGGGTTATTTCCCTTTTTCATTTGAACATTGGAAGACGAATTAGAC
GGTGACATAATCTCCAATTGGCTGTATTGACCTTCAAGAACGAGAACTTC
CCAATACGCTAGTAAGGAAAACTTATTGGAATACTTCTGTTAAATTGTAG
TTCAGTATGGATAGTCCTACACGCGATTCACCAACGACCGACAAACGTCA
CTCGACATCTCCCGTTACACGTCACTCCACGTCTCCCGTCAACAGTCCAT
CTCCTCCGTTAGAACGTCAGAAGAAACCGTTCTCGATTGACTATCTACTT
AATTTTTCACCGACAAAAAAAACGACCCTCATCCGACAATCACCACCTGT
TGAATACATCCAACCGCCCTTCCACACTCGGCCTCCACACTTTATTAATG
ACCGGTTAAAAGAGCCGGAAGACGAATCTAAAGTACCATCACCGACTTTA
TTGACTAACACCTCCAGGAAAAGAGAGCTTGATCCCACCATAGGTATGCA
GATTGTTCATTTCTTTGGATTCATATGTAGTATCTGGCCTCCTTTACTGA
GCACTTTCGTTACTGGTCGATCAATGCCTCTTTGAATCAATTGGATTCAC
GCTGTTTTAGTCCACTTTGCCCTTTTAAAGAGTTTTCTGAACAATGCCTG
ACTCCCGGTGGGGTTACTTAAGCAAAAATGGGTGTTGGGTATGTGCGGAC
AGCAAGGGTCGGTTTTTCAACCTTTTCAAGTCTCTAAGGCTAAGGGTCGC
AAAAATCAGAAATATTTAAATTAGTCTCTTTAAGGGTCGGAACATTTACA
ATTTCTAGGAAAGTTTTTTGATTTAGAGTGGAAAAATTGTAAAAAAGTCT
CTCTAAGGGAATTTTTCAGAAATTGAAGAAAGTTAAGCATTAAAGTAAAC
GATTTGGATGTGTATATAAGAAATTTCCTTGGGCATCTATTAGAGAATCT
CAGACCGTTTTCATGTTGAATTCACTTCCATCAATTTAAGGCGGTTTTCA
CAATCCTTTAAGAAATTAATTAATTTGTTTAATTGATTGAGGTCAATAAA
TTGGCAATAAAATGTCGAAATATCTAGCCTATATAGTAGTTAACTTGGTT
TAGCTGACGTGTCTAGATATCTTTAGAAATCGACAGTATCTAAAGCTTTC
AGTGAAGGTGGGGATTAATCTAAACTTTCTTTGAATGTCCCTGAACACTC
CTTTCTAAAATTTCCGGACGAGAATGTGGTTTTATCTTGTGTAATTCGGC
TCCCCATTGAAGTCAATCAGTCATTTAGGTGACAACTGGTGACGTTGCAC
TACGCGCCAACTCAAGGCGTGATTTTAAACGATTAATAAAATTAAAACCC
CTACTTTGTAATAAATTAAGGTTCTTAAAAATTTTAAGATGGCTCGTAAT
TGTTGCGTTAATATTTCAATGTCTTTTTCCGCTCGTGAAACTTTGGTCTA
CACATTTCTAATTGTCATGTTAAACTTTTAAAGCTTAATTAATTTGAAGC
TTACAAATTACAAAATTAAGTCTCGACTTTTAAACCTTACGAAGCCTTGA
CCTTGGAGCCTTGGCCTACAACTTTTTTATAAGAACATCCACAATTTTTA
AATATGCAGGGAGCTTAAACCTGAAAGCCTAAGCTGAACAAGCTTTGAAC
TTATCACTTGCACATAATAATAAACCAATTAGAGTTAATGAGTAATTGAT
CACATAAATTGCCTAGTTGGCGACACGAAATTTTTATCATGTTTTAAAAC
TCGAATTTTGTCATTTTGTGATAGTGGTATAGCTCCTCCTCAAACTTGTT
TCTTCTCACTTAATTTGCGTTTTATCTTTTGATTGGTTAATTGCTCTGAC
TTAATTTGTTTATGATCATGTCATGTATGCCATTTTTACTGCTAATTATC
ATATCCCTTAATTAGCTGAATTGAAATGAGGCTTGTCATCTTGTCACAGA
CCCCTGTGCTAATTTTAAACTTAGTTGCACCCTGTAATCATGCTGTAATC
ACATGAACCATATCAAGTGTCGAACCAATACACGGTTTTTTATAAGAACA
AACTATATAAGAACATAAGATTTCGATGTCCCAAATGTTAAGAATAAGTT
AAGAATAATATATAACTTTACGGACTCAAGAACGCCAAGTTTTATAGGAA
AATGGACAAAAATACTAAAAAAATTGGCGAAAGTAAGAACATTTTAAGAA
TATTTTTAGGCTTAAAACTCAAAAAGTTAAGAACATCCCAAGGCTTCAAA
AATATTGGATGTTCTTGCAAAAAAAAGCGTAACCAATAGCGGAGCTTTGT
TTGAACTTCGATACCATTATAACGTTCCTACTTTTTCATTACAGAATTTC
AATGGGATTTGAGCAAATGTTTTCTACGAAAACACAAGGCCAATCGTAAA
CCACGAACGCCCTTCTCCGCCAGTCAACTTCTCACCTTGGAACAGAAATT
TAAACGTAAACAATATTTATCAATAAACGAGCGATCAGAATTAAGCGCTC
AACTGAACTTAACTGAAACACAAATCAAAATTTGGTTTCAAAATCGTCGA
GCAAAAGAAAAACGTCTTAAAGAAGCGGAACTCGAGAAAACCGTAAGAAC
ATTTTCACCGGGAAGTGTAACATCACCAAACTATTCACCGTGCAGCTGTT
GTTATTCGGGCTCTTCCGTATTCAACTATCCACCTGTATCGTGCTCTCGG
ATATCCCGTTTTATGCATTAGTTGAAAATTCATGTGGGGATGTCTGTTTT
GCCTGTTGTTGTATATATCTTTAATTTCTAAGATTTTAATTTTGTTAATA
TTTTGTAAGGTGGCCTCATGTAAGGTTCGTGATCGACAACCGCTTTTCAC
AGACCCGCTAGGGTTTTTTCAGCCAGCGGGGTAAAAATAACGGACCAAAT
TCTCGATGAGGATT

Coding sequence (CDS) from alignment at scaffold_273:15813..19376-

>TCONS_00056354 ID=TCONS_00056354|Name=TCONS_00056354|organism=Clytia hemisphaerica|type=CDS|length=2178bp|location=Sequence derived from alignment at scaffold_273:15813..19376- (Clytia hemisphaerica)
AATTTCAATGGGATTTGAGCAAATGTTTTCTACGAAAACACAAGGCCAAT
CGTAAACCACGAACGCCCTTCTCCGCCAGTCAACTTCTCACCTTGGAACA
GAAATTTAAACGTAAACAATATTTATCAATAAACGAGCGATCAGAATTAA
GCGCTCAACTGAACTTAACTGAAACACAAATCAAAATTTGGTTTCAAAAT
CGTCGAGCAAAAGAAAAACGTCTTAAAGAAGCGGAACTCGAGAAAACCGT
AAGAACATTTTCACCGGGAAGTGTAACATCACCAAACTATTCACCGTGCA
GCTGTTGTTATTCGGGCTCTTCCGTATTCAACTATCCACCTGTATCGTGC
TCTCGGATATCCCGTTTTATGCATTAGTTCAGTATGGATAGTCCTACACG
CGATTCACCAACGACCGACAAACGTCACTCGACATCTCCCGTTACACGTC
ACTCCACGTCTCCCGTCAACAGTCCATCTCCTCCGTTAGAACGTCAGAAG
AAACCGTTCTCGATTGACTATCTACTTAATTTTTCACCGACAAAAAAAAC
GACCCTCATCCGACAATCACCACCTGTTGAATACATCCAACCGCCCTTCC
ACACTCGGCCTCCACACTTTATTAATGACCGGTTAAAAGAGCCGGAAGAC
GAATCTAAAGTACCATCACCGACTTTATTGACTAACACCTCCAGGAAAAG
AGAGCTTGATCCCACCATAGATGATGAATTTCAATGGGATTTGAGCAAAT
GTTTTCTACGAAAACACAAGGCCAATCGTAAACCACGAACGCCCTTCTCC
GCCAGTCAACTTCTCACCTTGGAACAGAAATTTAAACGTAAACAATATTT
ATCAATAAACGAGCGATCAGAATTAAGCGCTCAACTGAACTTAACTGAAA
CACAAATCAAAATTTGGTTTCAAAATCGTCGAGCAAAAGAAAAACGTCTT
AAAGAAGCGGAACTCGAGAAAACCGTAAGAACATTTTCACCGGGAAGTGT
AACATCACCAAACTATTCACCGTGCAGCTGTTGTTATTCGGGCTCTTCCG
TATTCAACTATCCACCTGTATCGTGCTCTCGGATATCCCGTTTTATGCAT
TAGTTCAGTATGGATAGTCCTACACGCGATTCACCAACGACCGACAAACG
TCACTCGACATCTCCCGTTACACGTCACTCCACGTCTCCCGTCAACAGTC
CATCTCCTCCGTTAGAACGTCAGAAGAAACCGTTCTCGATTGACTATCTA
CTTAATTTTTCACCGACAAAAAAAACGACCCTCATCCGACAATCACCACC
TGTTGAATACATCCAACCGCCCTTCCACACTCGGCCTCCACACTTTATTA
ATGACCGGTTAAAAGAGCCGGAAGACGAATCTAAAGTACCATCACCGACT
TTATTGACTAACACCTCCAGGAAAAGAGAGCTTGATCCCACCATAGATGA
TGAATTTCAATGGGATTTGAGCAAATGTTTTCTACGAAAACACAAGGCCA
ATCGTAAACCACGAACGCCCTTCTCCGCCAGTCAACTTCTCACCTTGGAA
CAGAAATTTAAACGTAAACAATATTTATCAATAAACGAGCGATCAGAATT
AAGCGCTCAACTGAACTTAACTGAAACACAAATCAAAATTTGGTTTCAAA
ATCGTCGAGCAAAAGAAAAACGTCTTAAAGAAGCGGAACTCGAGAAAACC
GTAAGAACATTTTCACCGGGAAGTGTAACATCACCAAACTATTCACCGTG
CAGCTGTTGTTATTCGGGCTCTTCCGTATTCAACTATCCACCTGTATCGT
GCTCTCGGATATCCCGTTTTATGCATTAGTTCAGTATGGATAGTCCTACA
CGCGATTCACCAACGACCGACAAACGTCACTCGACATCTCCCGTTACACG
TCACTCCACGTCTCCCGTCAACAGTCCATCTCCTCCGTTAGAACGTCAGA
AGAAACCGTTCTCGATTGACTATCTACTTAATTTTTCACCGACAAAAAAA
ACGACCCTCATCCGACAATCACCACCTGTTGAATACATCCAACCGCCCTT
CCACACTCGGCCTCCACACTTTATTAATGACCGGTTAAAAGAGCCGGAAG
ACGAATCTAAAGTACCATCACCGACTTTATTGACTAACACCTCCAGGAAA
AGAGAGCTTGATCCCACCATAGATGATG
Gene-mRNA-Prot
This transcript is a part of the following gene feature(s):
Feature NameUnique NameSpeciesType
XLOC_035505XLOC_035505Clytia hemisphaericagene
The following polypeptide feature(s) derives from this transcript:
Feature NameUnique NameSpeciesType
TCONS_00056354-proteinTCONS_00056354-proteinClytia hemisphaericapolypeptide
The following exon feature(s) are a part of this transcript:
Feature NameUnique NameSpeciesType
TCONS_00056354-exon-scaffold_273-1575043694:19270..19376TCONS_00056354-exon-scaffold_273-1575043694:19270..19376Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1575043694:18806..18874TCONS_00056354-exon-scaffold_273-1575043694:18806..18874Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1575043694:18234..18576TCONS_00056354-exon-scaffold_273-1575043694:18234..18576Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1575043694:15813..16382TCONS_00056354-exon-scaffold_273-1575043694:15813..16382Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1510915933:19270..19376TCONS_00056354-exon-scaffold_273-1510915933:19270..19376Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1510915933:18806..18874TCONS_00056354-exon-scaffold_273-1510915933:18806..18874Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1510915933:18234..18576TCONS_00056354-exon-scaffold_273-1510915933:18234..18576Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1510915933:15813..16382TCONS_00056354-exon-scaffold_273-1510915933:15813..16382Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1491911889:19270..19376TCONS_00056354-exon-scaffold_273-1491911889:19270..19376Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1491911889:18806..18874TCONS_00056354-exon-scaffold_273-1491911889:18806..18874Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1491911889:18234..18576TCONS_00056354-exon-scaffold_273-1491911889:18234..18576Clytia hemisphaericaexon
TCONS_00056354-exon-scaffold_273-1491911889:15813..16382TCONS_00056354-exon-scaffold_273-1491911889:15813..16382Clytia hemisphaericaexon
Position
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
scaffold_273supercontigscaffold_273:15813..19376 -
Expression

Hover the mouse over a column in the graph to view expression values in transcripts per million (tpm).
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Values : 
    GrOo_1	 GrOo_2	 FGOo_1	 FGOo_2	 EG_1	 EG_2	 P1_1	 P1_2	 P2_1	 P2_2	 P3_1	 P3_2	 PoPr_1	 PoPr_2	 St_1	 St_2	 GO_1	 GO_2	 PH_1	 PH_2	 BMF_1	 BMF_2	 MMF_1	 MMF_2	 M_1	 M_2	 GEC_1	 GEC_2	 GEN_1	 GEN_2
0.164685	0	0	0	0.924254	0.539429	0.424673	0.485246	0.0339732	0.673301	0.490141	0.156952	0.791806	1.09145	0	0.221105	6.51002	7.85875	0.358492	0.250993	3.08307	7.34204	0	0.410979	1.80688	2.30916	0	0	0	0.182361
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR020479Homeobox_metazoa
IPR000047HTH_motif
IPR001356Homeobox_dom
IPR017970Homeobox_CS
IPR009057Homeobox-like
Vocabulary: Molecular Function
TermDefinition
GO:0003677DNA binding
GO:0043565sequence-specific DNA binding
Vocabulary: Biological Process
TermDefinition
GO:0006355regulation of transcription, DNA-templated
GO Annotation
GO Assignments
This transcript is annotated with the following GO terms.
Category Term Accession Term Name
biological_process GO:0006355 regulation of transcription, DNA-templated
molecular_function GO:0003677 DNA binding
molecular_function GO:0043565 sequence-specific DNA binding
Blast
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BLAST of TCONS_00056354 vs. Swiss-Prot (Human)
Match: MSX2 (Homeobox protein MSX-2 OS=Homo sapiens GN=MSX2 PE=1 SV=3)

HSP 1 Score: 100.523 bits (249), Expect = 2.929e-24
Identity = 45/59 (76.27%), Postives = 52/59 (88.14%), Query Frame = 3 
Query:  543 CFLRKHKANRKPRTPFSASQLLTLEQKFKRKQYLSINERSELSAQLNLTETQIKIWFQN 719
            C LRKHK NRKPRTPF+ SQLL LE+KF++KQYLSI ER+E S+ LNLTETQ+KIWFQN
Sbjct:  134 CTLRKHKTNRKPRTPFTTSQLLALERKFRQKQYLSIAERAEFSSSLNLTETQVKIWFQN 192
The following BLAST results are available for this feature:
BLAST of TCONS_00056354 vs. Swiss-Prot (Human)
Analysis Date: 2017-10-03 (blastx Clytia hemisphaerica v1.0 mRNA vs SwissProt (Homo sapiens))
Total hits: 1
Match NameE-valueIdentityDescription
MSX22.929e-2476.27Homeobox protein MSX-2 OS=Homo sapiens GN=MSX2 PE=... [more]
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