Lipopolysaccharide-induced TNF-alpha factor

Overview
NameLipopolysaccharide-induced TNF-alpha factor
Smed IDSMED30018451
Length (bp)679
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of Lipopolysaccharide-induced TNF-alpha factor (SMED30018451) t-SNE clustered cells

Violin plots show distribution of expression levels for Lipopolysaccharide-induced TNF-alpha factor (SMED30018451) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of Lipopolysaccharide-induced TNF-alpha factor (SMED30018451) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Lipopolysaccharide-induced TNF-alpha factor (SMED30018451) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30018451

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30018451SMESG000020870.1 SMESG000046087.1 SMESG000046084.1 dd_Smed_v4_2768_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30018451SMESG000020870.1 SMESG000046087.1 SMESG000046084.1 dd_Smed_v4_2768_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018451SMESG000020870.1 SMESG000046087.1 SMESG000046084.1 dd_Smed_v4_2768_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30018451SMESG000020870.1 SMESG000046087.1 SMESG000046084.1 dd_Smed_v4_2768_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30018451SMESG000020870.1 SMESG000046087.1 SMESG000046084.1 dd_Smed_v4_2768_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30018451SMESG000020870.1 SMESG000046087.1 SMESG000046084.1 dd_Smed_v4_2768_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Zebrafish
Match: si:ch211-202h22.8 (si:ch211-202h22.8 [Source:ZFIN;Acc:ZDB-GENE-090313-78])

HSP 1 Score: 57.7658 bits (138), Expect = 2.486e-10
Identity = 41/126 (32.54%), Postives = 57/126 (45.24%), Query Frame = 2 
Query:  194 PPPIGFAVPQSQNQNYPMAYNP-------PANHTTVIIQSAAAN-----------------GSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            PP  G  V Q+Q   YP+ Y P       P +     +QS+ A                  G T+C  C   +I++  Y  G  T  IC  + I     CCLIPFCV++CK+  +RCPNC H + +
Sbjct:    8 PPYSGPEVNQTQFTPYPVQYQPQPVYPPHPKDGFAPAVQSSPAPVVVTQVVMMPPSLSDVPGQTKCPHCQQQIITETRYVNGLLTWLICGGLGILLIWPCCLIPFCVSACKDVEHRCPNCKHVVFL 133
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Zebrafish
Match: si:ch211-202h22.8 (si:ch211-202h22.8 [Source:ZFIN;Acc:ZDB-GENE-090313-78])

HSP 1 Score: 57.7658 bits (138), Expect = 2.486e-10
Identity = 41/126 (32.54%), Postives = 57/126 (45.24%), Query Frame = 2 
Query:  194 PPPIGFAVPQSQNQNYPMAYNP-------PANHTTVIIQSAAAN-----------------GSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            PP  G  V Q+Q   YP+ Y P       P +     +QS+ A                  G T+C  C   +I++  Y  G  T  IC  + I     CCLIPFCV++CK+  +RCPNC H + +
Sbjct:    8 PPYSGPEVNQTQFTPYPVQYQPQPVYPPHPKDGFAPAVQSSPAPVVVTQVVMMPPSLSDVPGQTKCPHCQQQIITETRYVNGLLTWLICGGLGILLIWPCCLIPFCVSACKDVEHRCPNCKHVVFL 133
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Zebrafish
Match: si:ch211-202h22.7 (si:ch211-202h22.7 [Source:ZFIN;Acc:ZDB-GENE-090313-77])

HSP 1 Score: 55.4546 bits (132), Expect = 2.043e-9
Identity = 34/91 (37.36%), Postives = 44/91 (48.35%), Query Frame = 2 
Query:  233 QNYPMAYNPPANHTTVIIQSAAAN--GSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            Q    A  PPA  T V++ S      G   C  C   V+++  Y  G     IC  + IF    CCLIPFCV+SCK+  +RCP C   + V
Sbjct:   52 QTVQTAAPPPAQTTVVLMPSRLGECPGQMRCPHCQQQVVTETTYVNGLLVWGICIGLGIFGIWPCCLIPFCVDSCKDVQHRCPGCKSLVYV 142
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Zebrafish
Match: si:ch211-202h22.7 (si:ch211-202h22.7 [Source:ZFIN;Acc:ZDB-GENE-090313-77])

HSP 1 Score: 50.8322 bits (120), Expect = 5.330e-8
Identity = 34/99 (34.34%), Postives = 46/99 (46.46%), Query Frame = 2 
Query:  233 QNYPMAYNPPANH-------TTVIIQSAAAN---GSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            Q  P+ Y P A         TTV++  +      G   C  C   V+++  Y  G     IC  + IF    CCLIPFCV+SCK+  +RCP C   + V
Sbjct:   23 QQPPVTYQPQAGQLNKALKLTTVVLMPSRLGECPGQMRCPHCQQQVVTETTYVNGLLVWGICIGLGIFGIWPCCLIPFCVDSCKDVQHRCPGCKSLVYV 121
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Zebrafish
Match: si:ch211-157c3.4 (si:ch211-157c3.4 [Source:ZFIN;Acc:ZDB-GENE-030131-8454])

HSP 1 Score: 45.4394 bits (106), Expect = 7.655e-6
Identity = 42/152 (27.63%), Postives = 62/152 (40.79%), Query Frame = 2 
Query:   74 SGNAPPPPYTAVVRQPVGTNDK--------TASAPVYPAQHYSSIQQEPPPIGFAVPQSQNQNYPMAYNPPANHTTVIIQSAAANGSTECQRCHSHVISDVEYRCGCFT-VXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISVK 502
             G   PPPYT  V    G+N K        T  +  Y A H       P        QSQ+     A N   ++ +  +    A  +  C  C   V+++V Y+ G +  +    I F    LGCCLIPF +   K+ ++ CP C   + V+
Sbjct:    4 DGTGTPPPYTIPVEDGKGSNVKVYHVHTPFTPQSSTYGASHAQVASSRPV-------QSQSTE---ARNKYVSYESYELGRKPAMAT--CTSCQQQVLTNVTYKVGVYAWLMCILIFFCGFVLGCCLIPFFMKFFKDAYHSCPRCNKILHVE 143
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Xenopus
Match: ENSXETT00000031517.1 (LITAF domain containing [Source:NCBI gene;Acc:100498168])

HSP 1 Score: 55.0694 bits (131), Expect = 2.963e-9
Identity = 26/63 (41.27%), Postives = 37/63 (58.73%), Query Frame = 2 
Query:  308 STECQRCHSHVISDVEYRCGCFT-VXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTI 493
            ST C  C  ++I+++ Y  G  T +    +      LGCCLIPFCV+SCK+  + CPNC H +
Sbjct:   73 STTCPSCRQNIITNIHYNIGLLTWLLFGILFIFGCWLGCCLIPFCVDSCKDVDHYCPNCNHHL 135
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Xenopus
Match: ENSXETT00000016678.1 (lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [Source:NCBI gene;Acc:100498592])

HSP 1 Score: 46.9802 bits (110), Expect = 4.504e-6
Identity = 28/62 (45.16%), Postives = 34/62 (54.84%), Query Frame = 2 
Query:  311 TECQRCHSHVISDVEYRCGCFTVXXXXXXXXXA-PLGCCLIPFCVNSCKNTHYRCPNCGHTI 493
            T C  C S V +  EY  G  TV +  II +F    GCCLIPF V  CK+ ++ CPNC   I
Sbjct:  125 TTCSFCQSQVRTRTEYTIGSLTVILFLIIILFGCWFGCCLIPFFVQHCKDVNHFCPNCNRLI 186
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Xenopus
Match: ENSXETT00000016660.1 (lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [Source:NCBI gene;Acc:100498592])

HSP 1 Score: 46.595 bits (109), Expect = 4.713e-6
Identity = 28/62 (45.16%), Postives = 34/62 (54.84%), Query Frame = 2 
Query:  311 TECQRCHSHVISDVEYRCGCFTVXXXXXXXXXA-PLGCCLIPFCVNSCKNTHYRCPNCGHTI 493
            T C  C S V +  EY  G  TV +  II +F    GCCLIPF V  CK+ ++ CPNC   I
Sbjct:  102 TTCSFCQSQVRTRTEYTIGSLTVILFLIIILFGCWFGCCLIPFFVQHCKDVNHFCPNCNRLI 163
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. TrEMBL
Match: A0A210QGT7 (Lipopolysaccharide-induced tumor necrosis factor-alpha factor-like OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT17959 PE=4 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 4.179e-8
Identity = 45/128 (35.16%), Postives = 63/128 (49.22%), Query Frame = 2 
Query:  152 PVYPAQHYSSIQQEPPPIGFAVPQSQNQNYPMA--YNPPAN-----HTTVIIQSAAANGS----TECQRCHSHVISDVEYRCGCFTVXXXXXXXXXA-PLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            P Y A   S  QQ P P G+  PQ    +YP A  YN          TT+++Q     G      +CQ CH+++ + +EY  G  T     ++ IF   LGCCLIPFC+N   +  ++CPNC   + V
Sbjct:   29 PKYEAGPQSGYQQAPQPQGYP-PQG---SYPQAPGYNAQGQPVYMAQTTLVVQPQIGFGPNPTPMQCQHCHANISTALEYEAGALTWLSAGVLCIFGCWLGCCLIPFCINDLSDVQHKCPNCNKLVGV 152
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. TrEMBL
Match: G3FF69 (LPS-induced TNF-alpha factor OS=Mizuhopecten yessoensis OX=6573 GN=LITAF PE=2 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 4.533e-8
Identity = 45/128 (35.16%), Postives = 63/128 (49.22%), Query Frame = 2 
Query:  152 PVYPAQHYSSIQQEPPPIGFAVPQSQNQNYPMA--YNPPAN-----HTTVIIQSAAANGS----TECQRCHSHVISDVEYRCGCFTVXXXXXXXXXA-PLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            P Y A   S  QQ P P G+  PQ    +YP A  YN          TT+++Q     G      +CQ CH+++ + +EY  G  T     ++ IF   LGCCLIPFC+N   +  ++CPNC   + V
Sbjct:   29 PKYEAGPQSGYQQAPQPQGYP-PQG---SYPQAPGYNAQGQPVYMAQTTLVVQPQIGFGPNPRPMQCQHCHANISTALEYEAGALTWLSAGVLCIFGCWLGCCLIPFCINDLSDVQHKCPNCNKLVGV 152
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. TrEMBL
Match: A0A094ZX34 (Lipopolysaccharide-induced tumor necrosis factor-alpha factor-like protein (Fragment) OS=Schistosoma haematobium OX=6185 GN=MS3_07296 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 1.761e-7
Identity = 37/107 (34.58%), Postives = 53/107 (49.53%), Query Frame = 2 
Query:  179 SIQQEPPPIGFAVPQSQNQNYPMAYNPPANHTTVIIQSAAANGSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPL-GCCLIPFCVNSCKNTHYRCPNCGHTIS 496
             +QQEP   G      QN+  P+  + P      II       + +C  CH  +++ ++YR G  T   C  + I     GCCLIPFCV +CK+  ++CP CGH I 
Sbjct:    2 GLQQEPMLSG---KTDQNKETPVVTSQPVT----IIPLQDHPITLKCPNCHQEIVTKIKYRNGMLTYAACTGLCIVGCFCGCCLIPFCVKACKDVDHKCPECGHHIG 101
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. TrEMBL
Match: F1BZ88 (LPS-induced TNF-a factor OS=Ruditapes philippinarum OX=129788 PE=2 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.773e-7
Identity = 37/108 (34.26%), Postives = 54/108 (50.00%), Query Frame = 2 
Query:  188 QEPPPIGFAVPQSQNQNYPMAYNPPANHTTVIIQSAA---------ANGSTECQRCHSHVISDVEYRCGCFT-VXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNC 481
            + PPP   A PQ Q   Y   Y  P N +TV++   A         +    +CQ C + V++   Y  G  T V    I  +   +GCCLIPFC+++CK+  ++CPNC
Sbjct:   13 KGPPPPNAAYPQQQPAQYNTPYGQPQNTSTVVVTQPAYTVVQHFRESPVRIKCQFCQADVVTSTFYETGTLTWVACFVIAIVGCWIGCCLIPFCMDACKDVVHQCPNC 120
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. TrEMBL
Match: A0A3Q2D6A7 (LITAF domain-containing protein OS=Cyprinodon variegatus OX=28743 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 2.176e-7
Identity = 38/114 (33.33%), Postives = 56/114 (49.12%), Query Frame = 2 
Query:  158 YPAQHYSSIQQEPPPIGFAVPQSQNQNYPMAYNPPANHTTVIIQSAAANGSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            YP Q+  + QQ  P + +   Q+Q         P    T V  +   A GS  C  C + V++ +EY+ G  T  I   +FI     CCLIPFCVN+CK+  + CP C + + +
Sbjct:  104 YPQQYLKNDQQ--PVVQYMAQQNQ------VAQPVKQVTVVQPRPTDAPGSMLCPHCQTTVVTSIEYKLGLLTWLIVGSLFIIGVWPCCLIPFCVNACKDVQHSCPQCNNVLHI 209
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Cavefish
Match: si:ch211-157c3.4 (lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [Source:NCBI gene;Acc:103024010])

HSP 1 Score: 45.8246 bits (107), Expect = 3.854e-6
Identity = 23/68 (33.82%), Postives = 35/68 (51.47%), Query Frame = 2 
Query:  305 GSTECQRCHSHVISDVEYRCGCFT-VXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISVKS 505
            G+T C  C   V+++V Y+ G F  +     I     +GCCLIPF V   K+ ++ CP C   + V+ 
Sbjct:   72 GTTTCTSCREQVLTNVTYKVGAFAWLMCILFILCGLVIGCCLIPFFVKYFKDAYHTCPRCNRILHVEK 139
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Nematostella
Match: EDO37753 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SES1])

HSP 1 Score: 48.521 bits (114), Expect = 3.756e-8
Identity = 24/62 (38.71%), Postives = 35/62 (56.45%), Query Frame = 2 
Query:  317 CQRCHSHVISDVEYRCGCFT-VXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            C  C +H+++   YR G  T +    I  +   LGCCLIPFC++ CK+  + CPNC   + V
Sbjct:    3 CSFCQTHIVTATTYRYGALTWLLSGGICLLGGWLGCCLIPFCLDGCKDVIHTCPNCQAQLGV 64
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Nematostella
Match: EDO33373 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SSF9])

HSP 1 Score: 45.0542 bits (105), Expect = 1.240e-6
Identity = 24/65 (36.92%), Postives = 35/65 (53.85%), Query Frame = 2 
Query:  308 STECQRCHSHVISDVEYRCGCFT-VXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            S  C  CH+ +++  +Y  G  T +    +  I   LGCC IPFCV+S K+  + CPNC   + V
Sbjct:   35 SMNCPTCHATIVTATDYVTGTLTWLACFGLCIIGCDLGCCFIPFCVDSMKDVVHTCPNCRSQVGV 99
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Medaka
Match: si:ch211-202h22.9 (si:ch211-202h22.9 [Source:ZFIN;Acc:ZDB-GENE-030131-1143])

HSP 1 Score: 50.0618 bits (118), Expect = 2.678e-7
Identity = 25/65 (38.46%), Postives = 37/65 (56.92%), Query Frame = 2 
Query:  305 GSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            G   C  C + V++  E++ G  T  I  ++ I     CCLIPFCVNSCK+  + CP+C + + V
Sbjct:  120 GQMLCPHCQNTVVTKTEHKVGMQTWLIFGVLGIIGCWPCCLIPFCVNSCKDVQHSCPSCNNVLHV 184
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Medaka
Match: ENSORLT00000037533.1 (pep primary_assembly:ASM223467v1:1:23682164:23683902:-1 gene:ENSORLG00000026577.1 transcript:ENSORLT00000037533.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 44.669 bits (104), Expect = 6.322e-6
Identity = 24/62 (38.71%), Postives = 35/62 (56.45%), Query Frame = 2 
Query:  317 CQRCHSHVISDVEYRCGCFT-VXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISV 499
            C +CH  V+S V++  G  T +    + F    LGCCLIPFCV+  K+  + CP+C   + V
Sbjct:   41 CPKCHRTVLSKVDHSAGLLTYLLCGGLFFCGFVLGCCLIPFCVDRVKDAKHSCPSCKTILGV 102
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Planmine SMEST
Match: SMESG000020870.1 (SMESG000020870.1)

HSP 1 Score: 277.715 bits (709), Expect = 3.119e-96
Identity = 147/150 (98.00%), Postives = 149/150 (99.33%), Query Frame = 2 
Query:   62 MKRDSGNAPPPPYTAVVRQPVGTNDKTASAPVYPAQHYSSIQQEPPPIGFAVPQSQNQNYPMAYNPPANHTTVIIQSAAANGSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISVKSPC 511
            MKRDSGNAPPPPYTAVVRQPVGT+DKT SAPVYPAQ+YSSIQQEPPPIGFAVPQSQNQNYPMAYNPPANHTTVIIQSAAANGSTECQRCHSHVISDVEYRCGCFTVFICFIIFIFAPLGCCLIPFCVNSCKNTHYRCPNCGHTISVKSPC
Sbjct:    1 MKRDSGNAPPPPYTAVVRQPVGTDDKTPSAPVYPAQNYSSIQQEPPPIGFAVPQSQNQNYPMAYNPPANHTTVIIQSAAANGSTECQRCHSHVISDVEYRCGCFTVFICFIIFIFAPLGCCLIPFCVNSCKNTHYRCPNCGHTISVKSPC 150
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Planmine SMEST
Match: SMESG000020865.1 (SMESG000020865.1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.161e-11
Identity = 34/91 (37.36%), Postives = 50/91 (54.95%), Query Frame = 2 
Query:  239 YPMAYNPPANHTTVIIQSAAANGSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISVKSPC 511
            +P  +  PA     + +    +    C +C + V   + Y+ G FT  +CFIIF+FAP+GCCLIPFC+N  K+  Y+CP C H +     C
Sbjct:   49 HPHQHQNPAPSVVHVTKINYGSSKVRCDKCENEVFPAISYKSGGFTWLMCFIIFLFAPIGCCLIPFCINGFKDEKYKCPICDHKLYELRRC 139
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Planmine SMEST
Match: SMESG000033033.1 (SMESG000033033.1)

HSP 1 Score: 55.4546 bits (132), Expect = 4.291e-10
Identity = 31/77 (40.26%), Postives = 42/77 (54.55%), Query Frame = 2 
Query:  281 IIQSAAANGSTECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAPLGCCLIPFCVNSCKNTHYRCPNCGHTISVKSPC 511
            II       S  C +C   +++ V+++ GC T   CF I IF PLGCCLIPFC+  CK+ H+ CP C   +     C
Sbjct:   17 IIGFGTEEKSIVCPKCLEEILTVVKFKVGCQTWLFCFGIGIFCPLGCCLIPFCLRECKDAHHFCPKCDRYLGRYKRC 93
[Close]
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Planmine SMEST
Match: SMESG000020853.1 (SMESG000020853.1)

HSP 1 Score: 45.4394 bits (106), Expect = 2.857e-6
Identity = 22/64 (34.38%), Postives = 36/64 (56.25%), Query Frame = 2 
Query:  308 STECQRCHSHVISDVEYRCGCFTVXXXXXXXXXAP-LGCCLIPFCVNSCKNTHYRCPNCGHTIS 496
            +T C  C + +++ + Y  G  T  +C  + +    LGCCLIPFCV+ CK+  + CP+C   + 
Sbjct:   60 NTVCPHCQAQIVTGIRYDNGLLTWLLCGGLALLGCWLGCCLIPFCVDDCKDVIHVCPSCNMKVG 123
The following BLAST results are available for this feature:
BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 5
Match NameE-valueIdentityDescription
si:ch211-202h22.82.486e-1032.54si:ch211-202h22.8 [Source:ZFIN;Acc:ZDB-GENE-090313... [more]
si:ch211-202h22.82.486e-1032.54si:ch211-202h22.8 [Source:ZFIN;Acc:ZDB-GENE-090313... [more]
si:ch211-202h22.72.043e-937.36si:ch211-202h22.7 [Source:ZFIN;Acc:ZDB-GENE-090313... [more]
si:ch211-202h22.75.330e-834.34si:ch211-202h22.7 [Source:ZFIN;Acc:ZDB-GENE-090313... [more]
si:ch211-157c3.47.655e-627.63si:ch211-157c3.4 [Source:ZFIN;Acc:ZDB-GENE-030131-... [more]
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 3
Match NameE-valueIdentityDescription
ENSXETT00000031517.12.963e-941.27LITAF domain containing [Source:NCBI gene;Acc:1004... [more]
ENSXETT00000016678.14.504e-645.16lipopolysaccharide-induced tumor necrosis factor-a... [more]
ENSXETT00000016660.14.713e-645.16lipopolysaccharide-induced tumor necrosis factor-a... [more]
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A210QGT74.179e-835.16Lipopolysaccharide-induced tumor necrosis factor-a... [more]
G3FF694.533e-835.16LPS-induced TNF-alpha factor OS=Mizuhopecten yesso... [more]
A0A094ZX341.761e-734.58Lipopolysaccharide-induced tumor necrosis factor-a... [more]
F1BZ881.773e-734.26LPS-induced TNF-a factor OS=Ruditapes philippinaru... [more]
A0A3Q2D6A72.176e-733.33LITAF domain-containing protein OS=Cyprinodon vari... [more]
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
si:ch211-157c3.43.854e-633.82lipopolysaccharide-induced tumor necrosis factor-a... [more]
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 2
Match NameE-valueIdentityDescription
EDO377533.756e-838.71Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO333731.240e-636.92Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 2
Match NameE-valueIdentityDescription
si:ch211-202h22.92.678e-738.46si:ch211-202h22.9 [Source:ZFIN;Acc:ZDB-GENE-030131... [more]
ENSORLT00000037533.16.322e-638.71pep primary_assembly:ASM223467v1:1:23682164:236839... [more]
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BLAST of Lipopolysaccharide-induced TNF-alpha factor vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000020870.13.119e-9698.00SMESG000020870.1[more]
SMESG000020865.11.161e-1137.36SMESG000020865.1[more]
SMESG000033033.14.291e-1040.26SMESG000033033.1[more]
SMESG000020853.12.857e-634.38SMESG000020853.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018451 ID=SMED30018451|Name=Lipopolysaccharide-induced TNF-alpha factor|organism=Schmidtea mediterranea sexual|type=transcript|length=679bp
TATTGATAAACCTTAAATTCAAATTGTTTACTAATATTTCATAAAACTTT
CGTTTTTAAATATGAAAAGAGATTCAGGAAATGCCCCACCTCCTCCATAT
ACAGCGGTAGTACGCCAGCCGGTGGGCACGAATGATAAAACAGCAAGTGC
TCCGGTTTATCCTGCGCAACATTATTCATCTATCCAACAGGAACCTCCAC
CAATAGGATTCGCTGTGCCACAGTCGCAAAATCAAAACTATCCAATGGCT
TATAACCCACCGGCGAACCATACGACAGTGATAATTCAATCGGCTGCAGC
TAACGGTAGCACGGAGTGCCAACGTTGTCACAGCCACGTCATTTCAGATG
TGGAATACAGATGTGGATGCTTTACAGTCTTTATTTGTTTTATTATCTTT
ATTTTTGCTCCATTAGGCTGTTGCTTAATTCCATTCTGTGTAAATAGCTG
CAAGAATACCCATTATCGCTGTCCGAATTGCGGCCATACAATATCAGTGA
AATCTCCATGTTAAAGCATATTCGACCATATTCATTAATATTTTTACGTC
ATTTTAGTTATAAACATTTGACTAATTTTTTTAATGAATTTTATTCATTC
TGTTCTGAATTATATAATTAACAAATAATAATATAATTTTCTTTAATTGA
AAACATAATGAAATAGGTGGAATTCAAAG
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protein sequence of SMED30018451-orf-1

>SMED30018451-orf-1 ID=SMED30018451-orf-1|Name=SMED30018451-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=151bp
MKRDSGNAPPPPYTAVVRQPVGTNDKTASAPVYPAQHYSSIQQEPPPIGF
AVPQSQNQNYPMAYNPPANHTTVIIQSAAANGSTECQRCHSHVISDVEYR
CGCFTVFICFIIFIFAPLGCCLIPFCVNSCKNTHYRCPNCGHTISVKSPC
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000018Category 4 cell
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR037519LITAF_fam
IPR006629LITAF
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR006629LPS-induced tumour necrosis factor alpha factorSMARTSM00714litafcoord: 81..149
e-value: 1.5E-15
score: 67.6
IPR006629LPS-induced tumour necrosis factor alpha factorPFAMPF10601zf-LITAF-likecoord: 84..146
e-value: 4.2E-16
score: 59.0
IPR006629LPS-induced tumour necrosis factor alpha factorPROSITEPS51837LITAFcoord: 66..149
score: 14.944
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..36
NoneNo IPR availablePANTHERPTHR23292:SF6FI16602P1-RELATEDcoord: 31..146
NoneNo IPR availableTMHMMTMhelixcoord: 104..126
IPR037519LITAF domain containing proteinPANTHERPTHR23292LIPOPOLYSACCHARIDE-INDUCED TRANSCRIPTION FACTOR REGULATING TUMOR NECROSIS FACTOR ALPHAcoord: 31..146