TCONS_00020541 (transcript) - C. hemisphaerica

Overview
NameTCONS_00020541
Unique NameTCONS_00020541
Typetranscript
OrganismClytia hemisphaerica (Jellyfish)
Sequence length1312

Sequence
The following sequences are available for this feature:

transcript sequence

>TCONS_00020541 ID=TCONS_00020541|Name=TCONS_00020541|organism=Clytia hemisphaerica|type=transcript|length=1312bp
gcctttcctctttaccatgaaaaagaatttatttaaaattaaattttttc
tgacacagttaccctccaaactcttatactttttcgtgggtcacccggta
tcaTAACTCTTTTTGCATTGTCATTAGGAATAAGCTAACCTCTCTTCCAA
TTTAAAGgtattaaaatttttcaaaatttgaaggtATTTCCATTACTCAG
GAATGAAATTCACAAGCGAATTTAATACAAATAACATGGAATGTCCTAGT
GAAATAAATGATATGGAATGCTCTACAAACGTTCAGAGACATTGTAAGAA
TGCTGATGTTCTTGAATGTTCCCGATGGATCTCTCTATTTACTAGTTTCG
GTTTATCTTAGAAAGTTCTAGAAAGCTCCTGAATGTTCTGGAATGACCAA
GAACGTCATGAACATCTAAAGACCAcaccatttcaattttatttcaaatt
gcttGTGATGATATAAATATTGTATATGTCAAATGATTCAATTTAGTTGA
GTTGGATAAGCAACAGGGACGGCTCTCTAAATGAAAGAAAGCATACAAAT
TTTATGTAAATTAAATGTTTGTTATTATAAAATTCAACACtttataaata
ataaaaaaagagacAGATGTTTCAAATTTCCCTTGtcataaaaaacaata
aaatcccCTACATATCTTGCAACGGTGTTATGAATCATGTTGACACCAGC
ATTCAAGTTTGTAACACAACAATGACCACATaagttttggttttcaaacc
aTTTAGTAGTCAAATTGACAGAACATAACAATTAGTCTTTAtcctttgtt
tctttttgtttgcGCTGTTGTTCTGATTCTTTACGTGCTGCATCTTGAAG
TAGTTGTACATCAATATCTTCTGGCGGAAGTTGAACATATCGAACAACAG
ATCCACGTAAGAAACAATTTTTAACTGACAACATATGTGGGTATCTGTCT
GGGTCTGTTACGCTGATATCAGTTAGTTTAATGTTCAGGTATTGGTCTAC
AGAATCAAGTACACCAGATATGCTCAGATCATTTTTGAGCtctacaatga
cttcttttccGACAAGTGATTTGAAGAAGGAATAAAACAACATTTTATAT
AGTGATTAGCTTCTCTAAAAGGGGAAAAAGCATCTTTCACAAGCAACAAT
ACCTTTAAAATAACTTACCAAGTATTATAATTGAATTATTTTCTCTGACC
AAGCTTGAACTTTTCAACACCAAACTAAAAATTAGATAAGGGCCATCCTA
CTATTCAGTGCAATCAGatcttttttttaagtttgtgtgtaataaaatat
aatattgtactc
Run BLAST on NCBI

protein sequence of TCONS_00020541-protein

>TCONS_00020541-protein ID=TCONS_00020541-protein|Name=TCONS_00020541-protein|organism=Clytia hemisphaerica|type=polypeptide|length=103bp
MLFYSFFKSLVGKEVIVELKNDLSISGVLDSVDQYLNIKLTDISVTDPDR
YPHMLSVKNCFLRGSVVRYVQLPPEDIDVQLLQDAARKESEQQRKQKETK
DKD
Run BLAST on NCBI

transcript from alignment at sc0000357:298825..300136

Legend: exonfive_prime_UTRCDSthree_prime_UTR
Hold the cursor over a type above to highlight its positions in the sequence below.
>TCONS_00020541 ID=TCONS_00020541|Name=TCONS_00020541|organism=Clytia hemisphaerica|type=transcript|length=1312bp|location=Sequence derived from alignment at sc0000357:298825..300136 (Clytia hemisphaerica)
gagtacaatattatattttattacacacaaacttaaaaaaaagatCTGAT
TGCACTGAATAGTAGGATGGCCCTTATCTAATTTTTAGTTTGGTGTTGAA
AAGTTCAAGCTTGGTCAGAGAAAATAATTCAATTATAATACTTGGTAAGT
TATTTTAAAGGTATTGTTGCTTGTGAAAGATGCTTTTTCCCCTTTTAGAG
AAGCTAATCACTATATAAAATGTTGTTTTATTCCTTCTTCAAATCACTTG
TCggaaaagaagtcattgtagaGCTCAAAAATGATCTGAGCATATCTGGT
GTACTTGATTCTGTAGACCAATACCTGAACATTAAACTAACTGATATCAG
CGTAACAGACCCAGACAGATACCCACATATGTTGTCAGTTAAAAATTGTT
TCTTACGTGGATCTGTTGTTCGATATGTTCAACTTCCGCCAGAAGATATT
GATGTACAACTACTTCAAGATGCAGCACGTAAAGAATCAGAACAACAGCg
caaacaaaaagaaacaaaggaTAAAGACTAATTGTTATGTTCTGTCAATT
TGACTACTAAAtggtttgaaaaccaaaacttATGTGGTCATTGTTGTGTT
ACAAACTTGAATGCTGGTGTCAACATGATTCATAACACCGTTGCAAGATA
TGTAGgggattttattgttttttatgaCAAGGGAAATTTGAAACATCTgt
ctctttttttattatttataaaGTGTTGAATTTTATAATAACAAACATTT
AATTTACATAAAATTTGTATGCTTTCTTTCATTTAGAGAGCCGTCCCTGT
TGCTTATCCAACTCAACTAAATTGAATCATTTGACATATACAATATTTAT
ATCATCACaagcaatttgaaataaaattgaaatggtgTGGTCTTTAGATG
TTCATGACGTTCTTGGTCATTCCAGAACATTCAGGAGCTTTCTAGAACTT
TCTAAGATAAACCGAAACTAGTAAATAGAGAGATCCATCGGGAACATTCA
AGAACATCAGCATTCTTACAATGTCTCTGAACGTTTGTAGAGCATTCCAT
ATCATTTATTTCACTAGGACATTCCATGTTATTTGTATTAAATTCGCTTG
TGAATTTCATTCCTGAGTAATGGAAATaccttcaaattttgaaaaatttt
aatacCTTTAAATTGGAAGAGAGGTTAGCTTATTCCTAATGACAATGCAA
AAAGAGTTAtgataccgggtgacccacgaaaaagtataagagtttggagg
gtaactgtgtcagaaaaaatttaattttaaataaattctttttcatggta
aagaggaaaggc

Coding sequence (CDS) from alignment at sc0000357:298825..300136

>TCONS_00020541 ID=TCONS_00020541|Name=TCONS_00020541|organism=Clytia hemisphaerica|type=CDS|length=312bp|location=Sequence derived from alignment at sc0000357:298825..300136 (Clytia hemisphaerica)
ATGTTGTTTTATTCCTTCTTCAAATCACTTGTCggaaaagaagtcattgt
agaGCTCAAAAATGATCTGAGCATATCTGGTGTACTTGATTCTGTAGACC
AATACCTGAACATTAAACTAACTGATATCAGCGTAACAGACCCAGACAGA
TACCCACATATGTTGTCAGTTAAAAATTGTTTCTTACGTGGATCTGTTGT
TCGATATGTTCAACTTCCGCCAGAAGATATTGATGTACAACTACTTCAAG
ATGCAGCACGTAAAGAATCAGAACAACAGCgcaaacaaaaagaaacaaag
gaTAAAGACTAA
Gene-mRNA-Prot
This transcript is a part of the following gene feature(s):
Feature NameUnique NameSpeciesType
XLOC_011532XLOC_011532Clytia hemisphaericagene
The following polypeptide feature(s) derives from this transcript:
Feature NameUnique NameSpeciesType
TCONS_00020541-proteinTCONS_00020541-proteinClytia hemisphaericapolypeptide
The following exon feature(s) are a part of this transcript:
Feature NameUnique NameSpeciesType
TCONS_00020541-exon-sc0000357-1491911889:298825..300136TCONS_00020541-exon-sc0000357-1491911889:298825..300136Clytia hemisphaericaexon
TCONS_00020541-exon-sc0000357-1510915933:298825..300136TCONS_00020541-exon-sc0000357-1510915933:298825..300136Clytia hemisphaericaexon
TCONS_00020541-exon-sc0000357-1575043694:298825..300136TCONS_00020541-exon-sc0000357-1575043694:298825..300136Clytia hemisphaericaexon
Position
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
sc0000357supercontigsc0000357:298825..300136 .
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
43.1459	38.7185	61.8074	70.2137	37.3901	25.5903	34.3812	34.9171	32.4992	23.9122	18.2593	19.4453	11.9263	13.9474	16.9595	15.8665	27.7919	26.6705	8.3186	9.97494	22.8311	19.4893	50.1704	42.2845	15.145	17.3209	21.6755	14.8146	24.1685	24.4961
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR001163LSM_dom_euk/arc
IPR016654U6_snRNA_Lsm2
IPR010920LSM_dom
Vocabulary: Biological Process
TermDefinition
GO:0006397mRNA processing
GO Annotation
GO Assignments
This transcript is annotated with the following GO terms.
Category Term Accession Term Name
biological_process GO:0006397 mRNA processing
Blast
[Close]
BLAST of TCONS_00020541 vs. Swiss-Prot (Human)
Match: LSM2 (U6 snRNA-associated Sm-like protein LSm2 OS=Homo sapiens GN=LSM2 PE=1 SV=1)

HSP 1 Score: 167.162 bits (422), Expect = 7.472e-50
Identity = 78/95 (82.11%), Postives = 89/95 (93.68%), Query Frame = -1 
Query:  809 MLFYSFFKSLVGKEVIVELKNDLSISGVLDSVDQYLNIKLTDISVTDPDRYPHMLSVKNCFLRGSVVRYVQLPPEDIDVQLLQDAARKESEQQRK 1093
            MLFYSFFKSLVGK+V+VELKNDLSI G L SVDQYLNIKLTDISVTDP++YPHMLSVKNCF+RGSVVRYVQLP +++D QLLQDAARKE+ QQ++
Sbjct:    1 MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDTQLLQDAARKEALQQKQ 95
The following BLAST results are available for this feature:
BLAST of TCONS_00020541 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
LSM27.472e-5082.11U6 snRNA-associated Sm-like protein LSm2 OS=Homo s... [more]
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