SMED30015560

Overview
NameSMED30015560
Smed IDSMED30015560
Length (bp)1637
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 SMED30015560 (SMED30015560) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015560 (SMED30015560) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 SMED30015560 (SMED30015560) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015560 (SMED30015560) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top


 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30015560

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30015560h1SMcG0005609 SmedASXL_015852SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30015560h1SMcG0005609 Contig54771newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30015560h1SMcG0005609 Contig54771uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30015560h1SMcG0005609 Contig25635uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30015560h1SMcG0005609 Contig25635newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30015560h1SMcG0005609 dd_Smed_v4_10117_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30015560h1SMcG0005609 dd_Smed_v4_10117_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30015560h1SMcG0005609 dd_Smed_v4_10117_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30015560h1SMcG0005609 dd_Smed_v4_10117_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30015560h1SMcG0005609 dd_Smed_v4_10117_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal ventral margin of the whole animalSMED30015560h1SMcG0005609 dd_Smed_v4_10117_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
Alignments
SMED30015560 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005695:22192..24529 +7905
Homology
BLAST of SMED30015560 vs. Ensembl Zebrafish
Match: unm_sa808 (un-named sa808 [Source:ZFIN;Acc:ZDB-GENE-120727-21])

HSP 1 Score: 51.6026 bits (122), Expect = 9.429e-7
Identity = 50/198 (25.25%), Postives = 86/198 (43.43%), Query Frame = 3
Query:  735 LENSIAGMNADKIRLISKEIKTAMRNGKLLAQKITIFQQTV---NRNVDKI--TGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHIIDGVLMWRIDSTFTR-------LKAPRILFSKHFSSNSHPYKMRLAIRVHS------SRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNME 1274
            L + I GM      L   ++    R  + L  K   F+  V   NR V++   T E + ++  + Q+  E L  K++++  +    D  +           +   DGV +WRI S FT+        +AP  +FS  F ++ + YKM L I ++       +  ++  VV   + D  L WPF   VT+ +++  N E
Sbjct:   26 LLHYIMGMKVSLEGLEKTKVADLGRRCQDLEVKAGTFEDVVCVLNREVERFATTMEASNRQHRLDQDKIEALSNKVRQLERQVGVKDLTVAEMEGRLREMSATTFDGVFIWRI-SDFTKKRQDAIAGRAP-AMFSPAFYTSKYGYKMCLRIYLNGDGTGRGTHLSLFFVVMRGMSDALLKWPFNQKVTLMLLDQSNRE 221          
BLAST of SMED30015560 vs. Ensembl Zebrafish
Match: traf2b (Tnf receptor-associated factor 2b [Source:ZFIN;Acc:ZDB-GENE-030131-5345])

HSP 1 Score: 50.0618 bits (118), Expect = 6.147e-6
Identity = 46/177 (25.99%), Postives = 85/177 (48.02%), Query Frame = 3
Query:  810 NGKLLAQKITIFQQTV---NRNVDK--ITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHI----IDGVLMWRIDSTFTR-------LKAPRILFSKHFSSNSHPYKMRLAIRVHS------SRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNME 1274
             G  + +K+T  +  V   N+ V++  +T E   ++  + QE  E L  K++++       D ++    A +E++L  +     DGV +W+I + F+R        +AP  +FS  F S+ + YKM L + ++       S  ++  VV     D  L WPF   VT+ +++ +N E
Sbjct:  302 GGPGVQKKVTTLENIVCVLNKEVERSALTMEAISRQHRLDQEKIENLSNKVRQLERTLTTRDLQL----AESEQSLRELQFCTYDGVFIWKI-AEFSRRRQDAVAGRAP-AMFSPAFYSSKYGYKMCLRLYLNGDGTGRGSHLSLFFVVMKGKYDALLKWPFSQKVTLMLLDQNNRE 472          
BLAST of SMED30015560 vs. Ensembl Zebrafish
Match: traf2b (Tnf receptor-associated factor 2b [Source:ZFIN;Acc:ZDB-GENE-030131-5345])

HSP 1 Score: 50.0618 bits (118), Expect = 6.147e-6
Identity = 46/177 (25.99%), Postives = 85/177 (48.02%), Query Frame = 3
Query:  810 NGKLLAQKITIFQQTV---NRNVDK--ITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHI----IDGVLMWRIDSTFTR-------LKAPRILFSKHFSSNSHPYKMRLAIRVHS------SRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNME 1274
             G  + +K+T  +  V   N+ V++  +T E   ++  + QE  E L  K++++       D ++    A +E++L  +     DGV +W+I + F+R        +AP  +FS  F S+ + YKM L + ++       S  ++  VV     D  L WPF   VT+ +++ +N E
Sbjct:  302 GGPGVQKKVTTLENIVCVLNKEVERSALTMEAISRQHRLDQEKIENLSNKVRQLERTLTTRDLQL----AESEQSLRELQFCTYDGVFIWKI-AEFSRRRQDAVAGRAP-AMFSPAFYSSKYGYKMCLRLYLNGDGTGRGSHLSLFFVVMKGKYDALLKWPFSQKVTLMLLDQNNRE 472          
BLAST of SMED30015560 vs. Ensembl Zebrafish
Match: traf2b (Tnf receptor-associated factor 2b [Source:ZFIN;Acc:ZDB-GENE-030131-5345])

HSP 1 Score: 49.6766 bits (117), Expect = 7.028e-6
Identity = 46/177 (25.99%), Postives = 85/177 (48.02%), Query Frame = 3
Query:  810 NGKLLAQKITIFQQTV---NRNVDK--ITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHI----IDGVLMWRIDSTFTR-------LKAPRILFSKHFSSNSHPYKMRLAIRVHS------SRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNME 1274
             G  + +K+T  +  V   N+ V++  +T E   ++  + QE  E L  K++++       D ++    A +E++L  +     DGV +W+I + F+R        +AP  +FS  F S+ + YKM L + ++       S  ++  VV     D  L WPF   VT+ +++ +N E
Sbjct:  315 GGPGVQKKVTTLENIVCVLNKEVERSALTMEAISRQHRLDQEKIENLSNKVRQLERTLTTRDLQL----AESEQSLRELQFCTYDGVFIWKI-AEFSRRRQDAVAGRAP-AMFSPAFYSSKYGYKMCLRLYLNGDGTGRGSHLSLFFVVMKGKYDALLKWPFSQKVTLMLLDQNNRE 485          
BLAST of SMED30015560 vs. Ensembl Mouse
Match: Traf2 (TNF receptor-associated factor 2 [Source:MGI Symbol;Acc:MGI:101835])

HSP 1 Score: 52.7582 bits (125), Expect = 9.737e-7
Identity = 48/179 (26.82%), Postives = 85/179 (47.49%), Query Frame = 3
Query:  804 MRNGKLLAQKITIFQQTV---NRNVDKI--TGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHI----IDGVLMWRIDSTFTR-------LKAPRILFSKHFSSNSHPYKMRLAIRVHS------SRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNME 1274
            ++  ++L QKI  F+  V   NR V+++  T E   ++  + Q+  E L  K++++       D      +A  E+ +S +     DGV +W+I S FTR        + P I FS  F ++ + YKM L + ++       +  ++  VV     D  L WPF   VT+ +++ +N E
Sbjct:  276 LQRCQILEQKIATFENIVCVLNREVERVAVTAEACSRQHRLDQDKIEALSNKVQQLERSIGLKD----LAMADLEQKVSELEVSTYDGVFIWKI-SDFTRKRQEAVAGRTPAI-FSPAFYTSRYGYKMCLRVYLNGDGTGRGTHLSLFFVVMKGPNDALLQWPFNQKVTLMLLDHNNRE 448          
BLAST of SMED30015560 vs. Ensembl Mouse
Match: Traf2 (TNF receptor-associated factor 2 [Source:MGI Symbol;Acc:MGI:101835])

HSP 1 Score: 52.373 bits (124), Expect = 9.992e-7
Identity = 48/179 (26.82%), Postives = 85/179 (47.49%), Query Frame = 3
Query:  804 MRNGKLLAQKITIFQQTV---NRNVDKI--TGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHI----IDGVLMWRIDSTFTR-------LKAPRILFSKHFSSNSHPYKMRLAIRVHS------SRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNME 1274
            ++  ++L QKI  F+  V   NR V+++  T E   ++  + Q+  E L  K++++       D      +A  E+ +S +     DGV +W+I S FTR        + P I FS  F ++ + YKM L + ++       +  ++  VV     D  L WPF   VT+ +++ +N E
Sbjct:  269 LQRCQILEQKIATFENIVCVLNREVERVAVTAEACSRQHRLDQDKIEALSNKVQQLERSIGLKD----LAMADLEQKVSELEVSTYDGVFIWKI-SDFTRKRQEAVAGRTPAI-FSPAFYTSRYGYKMCLRVYLNGDGTGRGTHLSLFFVVMKGPNDALLQWPFNQKVTLMLLDHNNRE 441          
BLAST of SMED30015560 vs. UniProt/SwissProt
Match: sp|P39429|TRAF2_MOUSE (TNF receptor-associated factor 2 OS=Mus musculus OX=10090 GN=Traf2 PE=1 SV=1)

HSP 1 Score: 52.373 bits (124), Expect = 6.990e-6
Identity = 48/179 (26.82%), Postives = 85/179 (47.49%), Query Frame = 3
Query:  804 MRNGKLLAQKITIFQQTV---NRNVDKI--TGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHI----IDGVLMWRIDSTFTR-------LKAPRILFSKHFSSNSHPYKMRLAIRVHS------SRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNME 1274
            ++  ++L QKI  F+  V   NR V+++  T E   ++  + Q+  E L  K++++       D      +A  E+ +S +     DGV +W+I S FTR        + P I FS  F ++ + YKM L + ++       +  ++  VV     D  L WPF   VT+ +++ +N E
Sbjct:  269 LQRCQILEQKIATFENIVCVLNREVERVAVTAEACSRQHRLDQDKIEALSNKVQQLERSIGLKD----LAMADLEQKVSELEVSTYDGVFIWKI-SDFTRKRQEAVAGRTPAI-FSPAFYTSRYGYKMCLRVYLNGDGTGRGTHLSLFFVVMKGPNDALLQWPFNQKVTLMLLDHNNRE 441          
BLAST of SMED30015560 vs. TrEMBL
Match: I1ZID7 (TNF receptor associated factor-3 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 72.0182 bits (175), Expect = 1.228e-10
Identity = 47/161 (29.19%), Postives = 80/161 (49.69%), Query Frame = 3
Query:  912 QQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHIID---GVLMWRIDSTFTRLKAPRILFSKHFSSNSHPYKMRLAIRVHSSR------FNVSLVVFHSVKDVPLPWPFKASVTISIINPDNMETFKAMRKFCRISKPIMNSFNISDAFIFMFTE 1367
            +QE  E +  ++ K+   + +  + I  KV   E  L   ID   G+  W ++    + K  + +FS++F +    +K+ L    + S       FNV L +F  +++  L WPF+A+VTI I+N    ++ K + K  RI +P  N +N SD F F + E
Sbjct:   36 KQECAEIVTAEVSKLRRDFQEFQERIELKVQNIESYLKQKIDETSGIFSWNVNGISAKRKENQSMFSEYFYTKVSKHKVSLQFTANVSNDINEIGFNVFLFIFSGIQESKLNWPFQANVTIKIVNRSVPDSSKIVTKCFRIEEPPCN-YNWSDPFYFCYDE 195          
BLAST of SMED30015560 vs. Ensembl Cavefish
Match: traf2b (TNF receptor associated factor 2 [Source:NCBI gene;Acc:103028261])

HSP 1 Score: 52.7582 bits (125), Expect = 7.457e-7
Identity = 44/161 (27.33%), Postives = 78/161 (48.45%), Query Frame = 3
Query:  834 ITIFQQTVNRNVDKITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIM-AKVALTERNLSHIIDGVLMWRIDSTFTR-------LKAPRILFSKHFSSNSHPYKMRLAIRVHS------SRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNME 1274
            + +  + V R V ++  E   ++Q++ QE  E L  K++++       D ++  ++ AL E       DGV +W+I S F+R        +AP  +FS  F S+ + YKM L + ++       S  ++  VV     D  L WPF   VT+ +++ +N E
Sbjct:  316 VCVLNREVERTVLRL--EALTRQQQLDQEKIENLSNKVRQLERTLTMRDLQLAESEQALRELQFC-TYDGVFVWKI-SDFSRRRQDALAGRAP-AMFSPAFYSSKYGYKMCLRLYLNGDGTGRGSHLSLFFVVMRGKYDALLKWPFSQKVTLMLLDQNNRE 471          
BLAST of SMED30015560 vs. Ensembl Medaka
Match: unm_sa808 (TNF receptor-associated factor 2 [Source:NCBI gene;Acc:101155367])

HSP 1 Score: 49.2914 bits (116), Expect = 8.654e-6
Identity = 50/201 (24.88%), Postives = 87/201 (43.28%), Query Frame = 3
Query:  735 LENSIAGMNADKIRLISKEIKTA--MRNGKLLAQKITIFQQTV---NRNVDKITGEMNM--KRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHIIDGVLMWRI--------DSTFTRLKAPRILFSKHFSSNSHPYKMRLAIRVHS------SRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNME 1274
            L +S+    A +++L S++ K A   R    L  K   F+  V   NR V++ T  M    ++ ++ Q+  E L  K++++       D  +           +   DGV +WRI        D+   R  A   +FS  F ++ + YKM L I ++       +  ++  VV   + D  L WPF   VT+ +++  N E
Sbjct:  341 LPSSVGA--ALELQLHSEKTKVAELGRRCTELEVKSGTFENVVCVLNREVERFTTTMEASNRQHKLDQDKIEALSNKVRQLERTVGLKDLTVAEMEGRLREMAATTFDGVFIWRISDFAKKRQDAVAGRAPA---MFSPAFYTSKYGYKMCLRIYLNGDGTGRGTHLSLFFVVMRGLSDALLKWPFNQKVTLMLLDQSNRE 536          
BLAST of SMED30015560 vs. Planmine SMEST
Match: SMESG000024738.1 (SMESG000024738.1)

HSP 1 Score: 811.216 bits (2094), Expect = 0.000e+0
Identity = 431/434 (99.31%), Postives = 433/434 (99.77%), Query Frame = 3
Query:  132 ISKCPFYGIGCDQEYVVFDQMVEHLRLESYTHSKSLIVMLDSIKSSLEEIKKNDEVHKNEIKKLQFNEKLRDQMIDSLNQEIKSIRMENKEQITEKWKKKLETKFDSVRFEIEAKTFDKIRSEMEVKQIENLKTISEIESLKNKIDHLNTCFEVRMEAMNREIKDQAYFMXXXXXXXXXXXXARIKEQEKLTNNVEILRRNLENSIAGMNADKIRLISKEIKTAMRNGKLLAQKITIFQQTVNRNVDKITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHIIDGVLMWRIDSTFTRLKAPRILFSKHFSSNSHPYKMRLAIRVHSSRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNMETFKAMRKFCRISKPIMNSFNISDAFIFMFTEFGXXXXXXXXXXXXXXXXVDEI 1433
            ISKCPFYGIGCDQEYVVFDQMVEHLRLESYTHSKSLIVMLDSIKS+LEEIKKNDEVHKNEIKKLQFNEKLRDQMIDSLNQEIKSIRMENKEQITEKWKK LETKFDSVRFEIEAKTFD+IRSEMEVKQIENLKTISEIESLKNKIDHLNTCFEVRMEAMNREIKDQAYFMKEKNKKDEEELKARIKEQEKLTNNVEILRRNLENSIAGMNADKIRLISKEIKTAMRNGKLLAQKITIFQQTVNRNVDKITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHIIDGVLMWRIDSTFTRLKAPRILFSKHFSSNSHPYKMRLAIRVHSSRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNMETFKAMRKFCRISKPIMNSFNISDAFIFMFTEFGSDRLLERSSSLLLECSVDEI
Sbjct:   11 ISKCPFYGIGCDQEYVVFDQMVEHLRLESYTHSKSLIVMLDSIKSNLEEIKKNDEVHKNEIKKLQFNEKLRDQMIDSLNQEIKSIRMENKEQITEKWKKNLETKFDSVRFEIEAKTFDRIRSEMEVKQIENLKTISEIESLKNKIDHLNTCFEVRMEAMNREIKDQAYFMKEKNKKDEEELKARIKEQEKLTNNVEILRRNLENSIAGMNADKIRLISKEIKTAMRNGKLLAQKITIFQQTVNRNVDKITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHIIDGVLMWRIDSTFTRLKAPRILFSKHFSSNSHPYKMRLAIRVHSSRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNMETFKAMRKFCRISKPIMNSFNISDAFIFMFTEFGSDRLLERSSSLLLECSVDEI 444          
BLAST of SMED30015560 vs. Planmine SMEST
Match: SMESG000070535.1 (SMESG000070535.1)

HSP 1 Score: 105.916 bits (263), Expect = 7.087e-24
Identity = 106/435 (24.37%), Postives = 210/435 (48.28%), Query Frame = 3
Query:  138 KCPFYGIGCDQEYVVFDQMVEHLRLESYTHSKSLIVMLDSIKSSLEEIKKNDEVHKNEIKKLQFNEKLRDQMIDSLNQEIKSIRMENKEQITEKWKKKLETKFDSVRFEIEAKTFDKIRSEMEVKQIENLK-TISEIESLKNKIDHLNTCFEVRMEAMNREIKD------------QAYFMXXXXXXXXXXXXARIKEQEKLTNNVEILRRNLENSIAGM-NADKIRLISKEIKTAMRNGKLLAQKITIFQQTVNRNVDKITGEMNMKRQEIQQEMRETLERKLKKI--NDRYDKHDQE--IMAKVALTERNLSHIIDGVLMWRIDSTFTRLKAPRILFSKHFSSNSHPYKMRLAIRVHSSRFN------VSLVVFHSVKDVPLPWPFKASVTISIINPDNMETFKAMRKFCRISKPIMNSFNISDAFIFMFTEF 1370
            KC FY +GC +  +    + EH  L +Y H+K L  ++++IK+ + E++K++E  +N++K L  N +L +   +S   E++ ++ EN          KLE +  +    +E +  +KI SEME    ++L+  I E +++K+++        + +E + ++I +            + + M ++    + + K+ +++   + NN   + ++ E  ++ + N + +++  +EI          ++KI + Q    R+  K +  M    + + +   +T E K  KI       K DQE    +++   ER L +  +G   W ID+   R K   ++ S++F     PYKMRL +R+++   N      + L ++  ++   L WPF  +VTI + N +     K + K+C I KP  N  + SD F F+ +E 
Sbjct:  127 KCIFYEMGCKETSLTQGTIDEHFILNNYHHNKILTEIIENIKNEIYEMRKSEETSRNQMKSLSENTRLTNVKNESWRLEVQLLKNEN---------SKLENRVST----LEKEFINKI-SEMEANLSKSLEPVIEENKTMKDEVQEFKCRIHIALENIWKKIDEIDSRIDIQCANKETFLMNDEINSIKVDFKSLLEKVNPVENNENKVTKSEEKGLSKIVNINSLQMEIEEI----------SKKIEVLQFNFERHTSKCSKNM----KNVDKSESKTKEIKYYKIMLQQFRQKMDQETNFESRINQLERCLDNKRNGTFEWTIDNLSERKKQSGMIKSEYFYLKMKPYKMRLGMRLNNIEENSDFGLRILLFIYEDIESEWLEWPFSGNVTIKVTNKNKRNISKTVTKYCEIPKPKSNEASSSDRFNFLHSEL 533          
BLAST of SMED30015560 vs. Planmine SMEST
Match: SMESG000070535.1 (SMESG000070535.1)

HSP 1 Score: 105.531 bits (262), Expect = 9.001e-24
Identity = 106/435 (24.37%), Postives = 210/435 (48.28%), Query Frame = 3
Query:  138 KCPFYGIGCDQEYVVFDQMVEHLRLESYTHSKSLIVMLDSIKSSLEEIKKNDEVHKNEIKKLQFNEKLRDQMIDSLNQEIKSIRMENKEQITEKWKKKLETKFDSVRFEIEAKTFDKIRSEMEVKQIENLK-TISEIESLKNKIDHLNTCFEVRMEAMNREIKD------------QAYFMXXXXXXXXXXXXARIKEQEKLTNNVEILRRNLENSIAGM-NADKIRLISKEIKTAMRNGKLLAQKITIFQQTVNRNVDKITGEMNMKRQEIQQEMRETLERKLKKI--NDRYDKHDQE--IMAKVALTERNLSHIIDGVLMWRIDSTFTRLKAPRILFSKHFSSNSHPYKMRLAIRVHSSRFN------VSLVVFHSVKDVPLPWPFKASVTISIINPDNMETFKAMRKFCRISKPIMNSFNISDAFIFMFTEF 1370
            KC FY +GC +  +    + EH  L +Y H+K L  ++++IK+ + E++K++E  +N++K L  N +L +   +S   E++ ++ EN          KLE +  +    +E +  +KI SEME    ++L+  I E +++K+++        + +E + ++I +            + + M ++    + + K+ +++   + NN   + ++ E  ++ + N + +++  +EI          ++KI + Q    R+  K +  M    + + +   +T E K  KI       K DQE    +++   ER L +  +G   W ID+   R K   ++ S++F     PYKMRL +R+++   N      + L ++  ++   L WPF  +VTI + N +     K + K+C I KP  N  + SD F F+ +E 
Sbjct:  145 KCIFYEMGCKETSLTQGTIDEHFILNNYHHNKILTEIIENIKNEIYEMRKSEETSRNQMKSLSENTRLTNVKNESWRLEVQLLKNEN---------SKLENRVST----LEKEFINKI-SEMEANLSKSLEPVIEENKTMKDEVQEFKCRIHIALENIWKKIDEIDSRIDIQCANKETFLMNDEINSIKVDFKSLLEKVNPVENNENKVTKSEEKGLSKIVNINSLQMEIEEI----------SKKIEVLQFNFERHTSKCSKNM----KNVDKSESKTKEIKYYKIMLQQFRQKMDQETNFESRINQLERCLDNKRNGTFEWTIDNLSERKKQSGMIKSEYFYLKMKPYKMRLGMRLNNIEENSDFGLRILLFIYEDIESEWLEWPFSGNVTIKVTNKNKRNISKTVTKYCEIPKPKSNEASSSDRFNFLHSEL 551          
BLAST of SMED30015560 vs. Planmine SMEST
Match: SMESG000072057.1 (SMESG000072057.1)

HSP 1 Score: 102.449 bits (254), Expect = 4.490e-23
Identity = 65/235 (27.66%), Postives = 121/235 (51.49%), Query Frame = 3
Query:  690 EQEKLTNNVEILRRNLENSIAGMNA--------DKIRLISKEIKTAMRNGKLLAQKITIFQQTVNRNVDKITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLSHIIDGVLMWRIDSTFTRLKAPRILFSKHFSSNSHPYKMRLAIRVHSSRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNMETFKAMRKFCRISKPIMNSFNISDAFIFMFTEF 1370
            EQ++L N +E L+  +EN I  ++A        D+I  I  EI      G+ +++   + +  +    +K   EMN K + +Q E+    E K+ K+ +R   +  +   +++  E+NL ++IDG+ MW+I+     +K    ++S++F SN++ Y+ RL +  +     +   ++ S  D+ L WPF+A VT+ + +     + K + K C I KP   S   SD F F +++F
Sbjct:  196 EQQELLNEMENLKPTVENKINEISAELVNLVRDDRIDSIWNEIDLMKAEGQNMSRGFEVIKHDIG---EKFKLEMNGKLKAMQAEIECQSEMKMSKLCEREKVNQYDFEKRLSEVEKNL-NLIDGIFMWKINK-IEEIKKCGYIWSEYFYSNANSYRQRLRLDAYGDHLWIRFCLYSSPVDIDLDWPFQAEVTLKVASKLWPNSGKTITKNCTIDKPPFGSCECSDEFKFSYSDF 425          
BLAST of SMED30015560 vs. Planmine SMEST
Match: SMESG000025120.1 (SMESG000025120.1)

HSP 1 Score: 79.7221 bits (195), Expect = 5.632e-16
Identity = 58/211 (27.49%), Postives = 102/211 (48.34%), Query Frame = 3
Query:  759 NADKIRLISKEIKTAMRNGKLLAQKITIFQQTVNRNVDKITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHDQEIMAKVALTERNLS--HIIDGVLMWRIDSTFTRLKAPRILFSKHFSSNSHPYKMRL-----AIRVHSSRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNMETFKAMRKFCRISKPIMNSFNISDAFIFMFTEF 1370
            NA KI+L+ +EI+      + L   +  ++  ++  ++ +  EM    Q+I+ E+    +RK  + +D  D     I +K  LTE  +S    I G+  W ID    +      ++S+ F + ++ YKMRL           +  ++ L ++ S  +    WPFKA VT+ I+N  N    K + K+C I KP++N F    +F F++ E 
Sbjct:  127 NAAKIKLMDEEIRMLKSVNESLIHMMDHWRTMLDNKLESMNSEMRTTFQDIKLEIEGAAKRKQSQ-SDENDILSTSI-SKTKLTEPRISLERKIAGIYTWNIDRVMEKRGKRGSIWSEFFYTRNNHYKMRLQFHPNGFVCTGTGLSIYLFLYPSETNSKGLWPFKADVTMKIVNKANPSKSKILTKYCHIEKPVINPFKCCASFDFIYQEL 335          
The following BLAST results are available for this feature:
BLAST of SMED30015560 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015560 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015560 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015560 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 4
Match NameE-valueIdentityDescription
unm_sa8089.429e-725.25un-named sa808 [Source:ZFIN;Acc:ZDB-GENE-120727-21... [more]
traf2b6.147e-625.99Tnf receptor-associated factor 2b [Source:ZFIN;Acc... [more]
traf2b6.147e-625.99Tnf receptor-associated factor 2b [Source:ZFIN;Acc... [more]
traf2b7.028e-625.99Tnf receptor-associated factor 2b [Source:ZFIN;Acc... [more]
back to top
BLAST of SMED30015560 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015560 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Traf29.737e-726.82TNF receptor-associated factor 2 [Source:MGI Symbo... [more]
Traf29.992e-726.82TNF receptor-associated factor 2 [Source:MGI Symbo... [more]
back to top
BLAST of SMED30015560 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|P39429|TRAF2_MOUSE6.990e-626.82TNF receptor-associated factor 2 OS=Mus musculus O... [more]
back to top
BLAST of SMED30015560 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZID71.228e-1029.19TNF receptor associated factor-3 (Fragment) OS=Sch... [more]
back to top
BLAST of SMED30015560 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
traf2b7.457e-727.33TNF receptor associated factor 2 [Source:NCBI gene... [more]
back to top
BLAST of SMED30015560 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015560 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015560 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015560 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
unm_sa8088.654e-624.88TNF receptor-associated factor 2 [Source:NCBI gene... [more]
back to top
BLAST of SMED30015560 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000024738.10.000e+099.31SMESG000024738.1[more]
SMESG000070535.17.087e-2424.37SMESG000070535.1[more]
SMESG000070535.19.001e-2424.37SMESG000070535.1[more]
SMESG000072057.14.490e-2327.66SMESG000072057.1[more]
SMESG000025120.15.632e-1627.49SMESG000025120.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015560 ID=SMED30015560|Name=SMED30015560|organism=Schmidtea mediterranea sexual|type=transcript|length=1637bp
AGGGCATTTATATATACAATTCTTCAAATGACATTTTAATTCATTTATAT
TTTCAGATTTTAGTTTTACTTTGGCTTTGAATGAACATATTCAGTTTTAA
AATGTTTGATTTTTTCAAGAAACCGAAAAAAATATCAAAATGTCCGTTTT
ACGGCATTGGGTGTGATCAAGAATACGTTGTGTTTGACCAAATGGTTGAA
CATTTGAGACTGGAAAGTTACACCCACAGCAAATCTCTTATTGTAATGTT
GGACTCGATCAAATCTAGTTTAGAAGAAATAAAAAAGAACGACGAAGTTC
ATAAAAACGAAATAAAAAAATTGCAATTTAATGAAAAATTAAGAGACCAA
ATGATTGATTCATTAAATCAAGAAATTAAATCAATTAGAATGGAAAATAA
AGAGCAAATAACTGAAAAATGGAAAAAGAAATTAGAAACAAAATTTGATA
GCGTGAGATTTGAAATTGAAGCAAAAACCTTTGATAAGATCCGGTCAGAA
ATGGAAGTCAAACAAATTGAAAATTTGAAAACAATATCTGAAATAGAATC
ATTAAAAAACAAAATTGATCATCTTAATACTTGCTTTGAAGTGCGGATGG
AGGCCATGAATCGGGAAATTAAAGATCAAGCCTACTTCATGAAAGAAAAG
AACAAAAAGGATGAAGAAGAACTGAAAGCTAGAATAAAAGAGCAAGAGAA
ATTGACAAATAATGTGGAAATTTTACGTCGCAATTTAGAGAACTCAATTG
CAGGAATGAATGCGGACAAAATTCGTTTGATCAGCAAAGAAATAAAAACA
GCGATGAGAAATGGGAAATTGTTAGCCCAGAAAATAACTATTTTTCAGCA
GACTGTCAATCGCAATGTGGACAAAATCACTGGGGAAATGAATATGAAAC
GCCAAGAAATACAACAAGAAATGAGAGAAACGTTGGAACGAAAGTTAAAG
AAAATCAACGACAGATACGATAAACACGACCAGGAAATTATGGCAAAAGT
TGCTCTCACTGAAAGAAATCTTTCTCATATAATTGATGGAGTTTTGATGT
GGAGAATTGATTCGACATTTACTAGACTTAAAGCACCAAGAATTTTATTC
AGTAAGCATTTTTCATCAAATAGCCATCCTTACAAAATGCGATTGGCGAT
TCGTGTCCATTCCTCTCGATTTAACGTGTCACTGGTTGTCTTCCACAGCG
TTAAAGATGTCCCTTTGCCATGGCCATTCAAAGCCAGTGTAACAATTAGC
ATCATAAATCCAGACAACATGGAAACTTTTAAAGCTATGAGAAAGTTCTG
TCGAATCTCTAAACCTATTATGAATTCTTTCAACATAAGTGATGCGTTTA
TATTTATGTTTACGGAATTCGGAAGTGACAGGCTGCTTGAGAGAAGCTCG
AGCCTTTTGTTAGAATGCTCAGTAGATGAAATTTGATAGTTTTCACATGG
GTGCAATGATTACATGAAAATTCCCAATGCATAACACTGGATAGCTTCCA
TTTTCCTGTGTTCTTTTTATCAACAGATAGCGTAAAATTCTTAATTTCAA
TAATCTCCATCGTGTATTATGTTCCTTATACCCCCCAACTCGTAGGATAT
GCAGAAATTCCTTAATATTTTGTCGATTAATAAATGT
back to top

protein sequence of SMED30015560-orf-1

>SMED30015560-orf-1 ID=SMED30015560-orf-1|Name=SMED30015560-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=452bp
MNIFSFKMFDFFKKPKKISKCPFYGIGCDQEYVVFDQMVEHLRLESYTHS
KSLIVMLDSIKSSLEEIKKNDEVHKNEIKKLQFNEKLRDQMIDSLNQEIK
SIRMENKEQITEKWKKKLETKFDSVRFEIEAKTFDKIRSEMEVKQIENLK
TISEIESLKNKIDHLNTCFEVRMEAMNREIKDQAYFMKEKNKKDEEELKA
RIKEQEKLTNNVEILRRNLENSIAGMNADKIRLISKEIKTAMRNGKLLAQ
KITIFQQTVNRNVDKITGEMNMKRQEIQQEMRETLERKLKKINDRYDKHD
QEIMAKVALTERNLSHIIDGVLMWRIDSTFTRLKAPRILFSKHFSSNSHP
YKMRLAIRVHSSRFNVSLVVFHSVKDVPLPWPFKASVTISIINPDNMETF
KAMRKFCRISKPIMNSFNISDAFIFMFTEFGSDRLLERSSSLLLECSVDE
I*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR008974TRAF-like
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 263..302
NoneNo IPR availableCOILSCoilCoilcoord: 188..222
NoneNo IPR availableCOILSCoilCoilcoord: 57..84
NoneNo IPR availableCOILSCoilCoilcoord: 92..112
IPR008974TRAF-likeGENE3DG3DSA:2.60.210.10coord: 271..439
e-value: 7.7E-13
score: 50.4
IPR008974TRAF-likeSUPERFAMILYSSF49599TRAF domain-likecoord: 319..432