TCONS_00004179 (transcript) - C. hemisphaerica

Overview
NameTCONS_00004179
Unique NameTCONS_00004179
Typetranscript
OrganismClytia hemisphaerica (Jellyfish)
Sequence length1075

Sequence
The following sequences are available for this feature:

transcript sequence

>TCONS_00004179 ID=TCONS_00004179|Name=TCONS_00004179|organism=Clytia hemisphaerica|type=transcript|length=1075bp
CACAAATTTGATTAAAATGAAAGTCTTATAGGTGATAACGTAGGGTCTGC
ATTTAAGACAAGAAAGCGATTGTGAAAATATGATTCGGGTCTGCACTTTA
ATAAGAAGCTTTCCCACGTGAAAAATATTGATCTATAAAAACTATCTTTG
GTTCGATTGGTGTGTACTGCTGGCTGGCGAAATAAATTACTCCACCAAAT
TCTTTTTACAATGCCGAAATCCAAAAGGAACAAAGTTGTTTCCTTGAGTA
AGACAACTAAGAAAGGGTTTGAATTGAAGAAAGATTTAGTCTCCCAAATT
CAAGCTTGCTGTGATGAGTTTGCGTCGTTATATATTTTTTCGGTCGAAGA
TATGCGAAACCAAAAGCTAAAAGATGTCAGACAACACTGGAGAACGAGTA
GATTCTTCTTTGGAAAGAATAAAGTGATGACAATAGCTTTGGGACGAACA
AAGGAAGACGAGTACAAAGAAAACCTGCACAAAGTTTCAGAGCAACTCAG
TGGTAATGTTGGTCTTATGTTCACAAATGAGCAAGATCATAAAGTGAAAG
AATGGTTCAGCTCATTCACAGAGCCAGATTATGCCAGATCAGGAAATAAA
GCCACAAAGACAATCACTTTGCCAGCCGGACCTCTGGATGAAAATTCATA
TCCTCACAATATGGAACCTGCTCTGAGGTCCCTCAGCTTGCCAACAGAAC
TCAAAAAAGGAATAATTCACTTGACAACAGACTACACTGTATGTAAAAAG
GATGAAGTTTTATCTCCTGAACAATGTAGAGTGCTCAAACTTTTCTTTGA
ACAATTAGCAAGCTTTCATTTGGTTTTAAAAAGTCTTTGGACATCAGATG
GTAAATTTACGGTTTTGGAAGAtgttgaagatgaagatgaatgatattct
tatatataaagttttattattttaatcaaaactttttatgattATGAAAC
TTCACTTATTACatcaacttttgaaaattggttAAATTACTTTTCTTCAA
AGGAATAATCCAAAAGTGTTGTGGAGCAATTTGTTTTTACAGAGATGTCC
GTAGCCGTttgggaggggggggggg
Run BLAST on NCBI

protein sequence of TCONS_00004179-protein

>TCONS_00004179-protein ID=TCONS_00004179-protein|Name=TCONS_00004179-protein|organism=Clytia hemisphaerica|type=polypeptide|length=227bp
MPKSKRNKVVSLSKTTKKGFELKKDLVSQIQACCDEFASLYIFSVEDMRN
QKLKDVRQHWRTSRFFFGKNKVMTIALGRTKEDEYKENLHKVSEQLSGNV
GLMFTNEQDHKVKEWFSSFTEPDYARSGNKATKTITLPAGPLDENSYPHN
MEPALRSLSLPTELKKGIIHLTTDYTVCKKDEVLSPEQCRVLKLFFEQLA
SFHLVLKSLWTSDGKFTVLEDVEDEDE
Run BLAST on NCBI

transcript from alignment at sc0000039:472001..473075

Legend: exonthree_prime_UTRCDSfive_prime_UTR
Hold the cursor over a type above to highlight its positions in the sequence below.
>TCONS_00004179 ID=TCONS_00004179|Name=TCONS_00004179|organism=Clytia hemisphaerica|type=transcript|length=1075bp|location=Sequence derived from alignment at sc0000039:472001..473075 (Clytia hemisphaerica)
ccccccccccctcccaaACGGCTACGGACATCTCTGTAAAAACAAATTGC
TCCACAACACTTTTGGATTATTCCTTTGAAGAAAAGTAATTTaaccaatt
ttcaaaagttgatGTAATAAGTGAAGTTTCATaatcataaaaagttttga
ttaaaataataaaactttatatataagaatatcattcatcttcatcttca
acaTCTTCCAAAACCGTAAATTTACCATCTGATGTCCAAAGACTTTTTAA
AACCAAATGAAAGCTTGCTAATTGTTCAAAGAAAAGTTTGAGCACTCTAC
ATTGTTCAGGAGATAAAACTTCATCCTTTTTACATACAGTGTAGTCTGTT
GTCAAGTGAATTATTCCTTTTTTGAGTTCTGTTGGCAAGCTGAGGGACCT
CAGAGCAGGTTCCATATTGTGAGGATATGAATTTTCATCCAGAGGTCCGG
CTGGCAAAGTGATTGTCTTTGTGGCTTTATTTCCTGATCTGGCATAATCT
GGCTCTGTGAATGAGCTGAACCATTCTTTCACTTTATGATCTTGCTCATT
TGTGAACATAAGACCAACATTACCACTGAGTTGCTCTGAAACTTTGTGCA
GGTTTTCTTTGTACTCGTCTTCCTTTGTTCGTCCCAAAGCTATTGTCATC
ACTTTATTCTTTCCAAAGAAGAATCTACTCGTTCTCCAGTGTTGTCTGAC
ATCTTTTAGCTTTTGGTTTCGCATATCTTCGACCGAAAAAATATATAACG
ACGCAAACTCATCACAGCAAGCTTGAATTTGGGAGACTAAATCTTTCTTC
AATTCAAACCCTTTCTTAGTTGTCTTACTCAAGGAAACAACTTTGTTCCT
TTTGGATTTCGGCATTGTAAAAAGAATTTGGTGGAGTAATTTATTTCGCC
AGCCAGCAGTACACACCAATCGAACCAAAGATAGTTTTTATAGATCAATA
TTTTTCACGTGGGAAAGCTTCTTATTAAAGTGCAGACCCGAATCATATTT
TCACAATCGCTTTCTTGTCTTAAATGCAGACCCTACGTTATCACCTATAA
GACTTTCATTTTAATCAAATTTGTG

Coding sequence (CDS) from alignment at sc0000039:472001..473075

>TCONS_00004179 ID=TCONS_00004179|Name=TCONS_00004179|organism=Clytia hemisphaerica|type=CDS|length=684bp|location=Sequence derived from alignment at sc0000039:472001..473075 (Clytia hemisphaerica)
tcattcatcttcatcttcaacaTCTTCCAAAACCGTAAATTTACCATCTG
ATGTCCAAAGACTTTTTAAAACCAAATGAAAGCTTGCTAATTGTTCAAAG
AAAAGTTTGAGCACTCTACATTGTTCAGGAGATAAAACTTCATCCTTTTT
ACATACAGTGTAGTCTGTTGTCAAGTGAATTATTCCTTTTTTGAGTTCTG
TTGGCAAGCTGAGGGACCTCAGAGCAGGTTCCATATTGTGAGGATATGAA
TTTTCATCCAGAGGTCCGGCTGGCAAAGTGATTGTCTTTGTGGCTTTATT
TCCTGATCTGGCATAATCTGGCTCTGTGAATGAGCTGAACCATTCTTTCA
CTTTATGATCTTGCTCATTTGTGAACATAAGACCAACATTACCACTGAGT
TGCTCTGAAACTTTGTGCAGGTTTTCTTTGTACTCGTCTTCCTTTGTTCG
TCCCAAAGCTATTGTCATCACTTTATTCTTTCCAAAGAAGAATCTACTCG
TTCTCCAGTGTTGTCTGACATCTTTTAGCTTTTGGTTTCGCATATCTTCG
ACCGAAAAAATATATAACGACGCAAACTCATCACAGCAAGCTTGAATTTG
GGAGACTAAATCTTTCTTCAATTCAAACCCTTTCTTAGTTGTCTTACTCA
AGGAAACAACTTTGTTCCTTTTGGATTTCGGCAT
Gene-mRNA-Prot
This transcript is a part of the following gene feature(s):
Feature NameUnique NameSpeciesType
XLOC_002329XLOC_002329Clytia hemisphaericagene
The following polypeptide feature(s) derives from this transcript:
Feature NameUnique NameSpeciesType
TCONS_00004179-proteinTCONS_00004179-proteinClytia hemisphaericapolypeptide
The following exon feature(s) are a part of this transcript:
Feature NameUnique NameSpeciesType
TCONS_00004179-exon-sc0000039-1491911889:472001..473075TCONS_00004179-exon-sc0000039-1491911889:472001..473075Clytia hemisphaericaexon
TCONS_00004179-exon-sc0000039-1510915933:472001..473075TCONS_00004179-exon-sc0000039-1510915933:472001..473075Clytia hemisphaericaexon
TCONS_00004179-exon-sc0000039-1575043694:472001..473075TCONS_00004179-exon-sc0000039-1575043694:472001..473075Clytia hemisphaericaexon
Position
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
sc0000039supercontigsc0000039:472001..473075 .
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
69.9723	68.7533	19.5746	16.9724	97.3448	73.6926	80.1638	92.8489	67.802	68.6323	58.6057	66.2457	88.9313	98.6093	88.3049	88.8731	71.5647	70.0102	32.6184	36.3658	109.204	103.691	181.783	167.232	52.7818	68.0689	47.7482	52.0373	107.993	119.849
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR001790Ribosomal_L10P
IPR033867Mrt4
Vocabulary: Cellular Component
TermDefinition
GO:0005622intracellular
Vocabulary: Biological Process
TermDefinition
GO:0042254ribosome biogenesis
GO:0000027ribosomal large subunit assembly
GO Annotation
GO Assignments
This transcript is annotated with the following GO terms.
Category Term Accession Term Name
biological_process GO:0000027 ribosomal large subunit assembly
biological_process GO:0042254 ribosome biogenesis
cellular_component GO:0005622 intracellular
Blast
[Close]
BLAST of TCONS_00004179 vs. Swiss-Prot (Human)
Match: MRT4 (mRNA turnover protein 4 homolog OS=Homo sapiens GN=MRTO4 PE=1 SV=2)

HSP 1 Score: 266.929 bits (681), Expect = 2.999e-87
Identity = 123/217 (56.68%), Postives = 166/217 (76.50%), Query Frame = 1 
Query:  211 MPKSKRNKVVSLSKTTKKGFELKKDLVSQIQACCDEFASLYIFSVEDMRNQKLKDVRQHWRTSRFFFGKNKVMTIALGRTKEDEYKENLHKVSEQLSGNVGLMFTNEQDHKVKEWFSSFTEPDYARSGNKATKTITLPAGPLDENSYPHNMEPALRSLSLPTELKKGIIHLTTDYTVCKKDEVLSPEQCRVLKLFFEQLASFHLVLKSLWTSD-GKF 858
            MPKSKR+K VSL+KT KKG ELK++L+ +++ C D +  L+IFSV +MRN KLKD+R  W+ SR FFGKNKVM +ALGR+  DEYK+NLH+VS++L G VGL+FTN    +V EWF+ +TE DYAR+GNKA  T++L  GPL++  +PH+MEP LR L LPT LK+G++ L +DY VCK+ +VL+PEQ RVLKLF  ++A F + +K +W S  G+F
Sbjct:    1 MPKSKRDKKVSLTKTAKKGLELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKHSRMFFGKNKVMMVALGRSPSDEYKDNLHQVSKRLRGEVGLLFTNRTKEEVNEWFTKYTEMDYARAGNKAAFTVSLDPGPLEQ--FPHSMEPQLRQLGLPTALKRGVVTLLSDYEVCKEGDVLTPEQARVLKLFGYEMAEFKVTIKYMWDSQSGRF 215
The following BLAST results are available for this feature:
BLAST of TCONS_00004179 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
MRT42.999e-8756.68mRNA turnover protein 4 homolog OS=Homo sapiens GN... [more]
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