tr5_12233

Overview
Nametr5_12233 (AIZ98418.1)
Smed IDSMED30022285
Length (bp)1219
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 tr5_12233 (SMED30022285) t-SNE clustered cells

Violin plots show distribution of expression levels for tr5_12233 (SMED30022285) 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 tr5_12233 (SMED30022285) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for tr5_12233 (SMED30022285) 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



SMED30022285

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



PAGE Curations: 17

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
posterior region of the whole animalSMED30022285SMESG000029156.1 dd_Smed_v4_13065_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
posterior region of the whole animalSMED30022285SMESG000029156.1 dd_Smed_v4_13065_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30022285SMESG000029156.1 dd_Smed_v4_13065_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30022285SMESG000029156.1 SmedASXL_010139SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
posterior region of the whole animalSMED30022285SMESG000029156.1 tr5_12233smed_ncbi_20200123PMID:25558068
Reuter et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30022285SMESG000029156.1 tr5_12233smed_ncbi_20200123PMID:25558068
Reuter et al., 2015		whole organism asexual adult fluorescence in situ hybridization evidence
posterior region of the whole animalSMED30022285SMESG000003359.1 tr5_12233smed_ncbi_20200123PMID:25558068
Reuter et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30022285SMESG000003359.1 tr5_12233smed_ncbi_20200123PMID:25558068
Reuter et al., 2015		whole organism asexual adult fluorescence in situ hybridization evidence
nervous systemSMED30022285SMESG000029156.1 dd_Smed_v4_13065_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022285SMESG000029156.1 dd_Smed_v4_13065_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30022285SMESG000029156.1 dd_Smed_v4_13065_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30022285SMESG000029156.1 dd_Smed_v4_13065_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30022285SMESG000029156.1 dd_Smed_v4_13065_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30022285SMESG000029156.1 dd_Smed_v4_13065_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022285SMESG000029156.1 Contig54978newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022285SMESG000029156.1 Contig54978uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
tail regionSMED30022285SMESG000029156.1 dd_Smed_v6_13065_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of tr5_12233 vs. UniProt/SwissProt
Match: sp|P18519|TNR16_CHICK (Tumor necrosis factor receptor superfamily member 16 OS=Gallus gallus OX=9031 GN=NGFR PE=2 SV=1)

HSP 1 Score: 51.2174 bits (121), Expect = 9.293e-6
Identity = 45/182 (24.73%), Postives = 81/182 (44.51%), Query Frame = 2 
Query:  290 NYINVYCAILGLIILYLVGFVIYKLWEQKSDTLLCTAISSKGSNGNSLRLQKCSPSGKS---------DNKEMVTLVTPTDEMKLPSYE---QVLMSQPLYRLSEDQIEAIVFSLSDESSGVGWLQLALYYNFKQDEIEFIAQNNSKNEAVRTFLRKWSENPNHTLKKLIKSLHEISRPDTA 799
            N I VYC+IL  +++ LV ++ +K W            + +G+N   +  Q  SP G+          D++ +     P    + P+ +    +  S P  +  ++++E ++ S ++E+    W QLA    +K+D I+   +  S     R  L  WS     TL  L+ +L +I R D A
Sbjct:  239 NLIPVYCSILAAVVVGLVAYIAFKRWNSCKQ-------NKQGANNRPVN-QTPSPEGEKLHSDSGISVDSQSLHDQQPPNQSTQGPAPKGDGSLYASLPPSK--QEEVEKLLSSSAEET----WRQLAGELGYKEDLIDCFTREESP---ARALLADWSAKETATLDALLVALRKIQRGDIA 403
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BLAST of tr5_12233 vs. TrEMBL
Match: A0A0A7NXD8 (Quetzal protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 480.33 bits (1235), Expect = 3.873e-168
Identity = 233/233 (100.00%), Postives = 233/233 (100.00%), Query Frame = 2 
Query:  203 TDWRLLIAPYFKNSSNYQTESPRVIDSDFNYINVYCAILGLIILYLVGFVIYKLWEQKSDTLLCTAISSKGSNGNSLRLQKCSPSGKSDNKEMVTLVTPTDEMKLPSYEQVLMSQPLYRLSEDQIEAIVFSLSDESSGVGWLQLALYYNFKQDEIEFIAQNNSKNEAVRTFLRKWSENPNHTLKKLIKSLHEISRPDTAFLIKSAIRKLSHLERNETNNNLMNKEIQKMALKL 901
            TDWRLLIAPYFKNSSNYQTESPRVIDSDFNYINVYCAILGLIILYLVGFVIYKLWEQKSDTLLCTAISSKGSNGNSLRLQKCSPSGKSDNKEMVTLVTPTDEMKLPSYEQVLMSQPLYRLSEDQIEAIVFSLSDESSGVGWLQLALYYNFKQDEIEFIAQNNSKNEAVRTFLRKWSENPNHTLKKLIKSLHEISRPDTAFLIKSAIRKLSHLERNETNNNLMNKEIQKMALKL
Sbjct:   20 TDWRLLIAPYFKNSSNYQTESPRVIDSDFNYINVYCAILGLIILYLVGFVIYKLWEQKSDTLLCTAISSKGSNGNSLRLQKCSPSGKSDNKEMVTLVTPTDEMKLPSYEQVLMSQPLYRLSEDQIEAIVFSLSDESSGVGWLQLALYYNFKQDEIEFIAQNNSKNEAVRTFLRKWSENPNHTLKKLIKSLHEISRPDTAFLIKSAIRKLSHLERNETNNNLMNKEIQKMALKL 252
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BLAST of tr5_12233 vs. TrEMBL
Match: D1LXA8 (p75 neurotrophin receptor-like protein OS=Saccoglossus kowalevskii OX=10224 PE=2 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 1.157e-7
Identity = 60/189 (31.75%), Postives = 90/189 (47.62%), Query Frame = 2 
Query:  272 VIDSDFNYINVYCAILGLIILYLVGFVI---YKLWEQKSDTLLCTAISS-KGSNGNSLRLQKC--SPSGKSDNKEMVTLVTPTDEMKLPSYEQVLMSQPLYR-LSED---QIEAIVFSLSDESSGVGWLQLALYYNFKQDEIEFIAQNNSKNEAVRTFLRKWSENPNHTLKKLIKSLHEISRPDTAFLI 808
            V DS  N + +YC++LG +I+ L+ +V    YK+W+ K      +  S  KG     + + K   S SG   N + V+ V     M L S    L S  L+R ++ED   QIE ++ +   +  G  W  LA   +F  + I   + +  K+  VR  L +WS+  N  L  L+ SLH I R D   LI
Sbjct:  208 VDDSSSNVVPIYCSVLGAVIVGLLVYVACKRYKIWKNKQKHYKASRTSPVKGPPLRDVEMGKGHGSDSGVFTNTDNVSAVNGCARMPLMS----LPSTTLFRDIAEDKKRQIELLLCTTRRD--GRDWRALARELDFSDNSIMEFSNSVGKHSPVRKLLCQWSKRDNACLGLLVTSLHRIQRDDITKLI 390
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BLAST of tr5_12233 vs. Planmine SMEST
Match: SMESG000029156.1 (SMESG000029156.1)

HSP 1 Score: 480.33 bits (1235), Expect = 1.077e-171
Identity = 233/233 (100.00%), Postives = 233/233 (100.00%), Query Frame = 2 
Query:  203 TDWRLLIAPYFKNSSNYQTESPRVIDSDFNYINVYCAILGLIILYLVGFVIYKLWEQKSDTLLCTAISSKGSNGNSLRLQKCSPSGKSDNKEMVTLVTPTDEMKLPSYEQVLMSQPLYRLSEDQIEAIVFSLSDESSGVGWLQLALYYNFKQDEIEFIAQNNSKNEAVRTFLRKWSENPNHTLKKLIKSLHEISRPDTAFLIKSAIRKLSHLERNETNNNLMNKEIQKMALKL 901
            TDWRLLIAPYFKNSSNYQTESPRVIDSDFNYINVYCAILGLIILYLVGFVIYKLWEQKSDTLLCTAISSKGSNGNSLRLQKCSPSGKSDNKEMVTLVTPTDEMKLPSYEQVLMSQPLYRLSEDQIEAIVFSLSDESSGVGWLQLALYYNFKQDEIEFIAQNNSKNEAVRTFLRKWSENPNHTLKKLIKSLHEISRPDTAFLIKSAIRKLSHLERNETNNNLMNKEIQKMALKL
Sbjct:   20 TDWRLLIAPYFKNSSNYQTESPRVIDSDFNYINVYCAILGLIILYLVGFVIYKLWEQKSDTLLCTAISSKGSNGNSLRLQKCSPSGKSDNKEMVTLVTPTDEMKLPSYEQVLMSQPLYRLSEDQIEAIVFSLSDESSGVGWLQLALYYNFKQDEIEFIAQNNSKNEAVRTFLRKWSENPNHTLKKLIKSLHEISRPDTAFLIKSAIRKLSHLERNETNNNLMNKEIQKMALKL 252
The following BLAST results are available for this feature:
BLAST of tr5_12233 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 tr5_12233 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 tr5_12233 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 tr5_12233 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of tr5_12233 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of tr5_12233 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 tr5_12233 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|P18519|TNR16_CHICK9.293e-624.73Tumor necrosis factor receptor superfamily member ... [more]
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BLAST of tr5_12233 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A0A7NXD83.873e-168100.00Quetzal protein (Fragment) OS=Schmidtea mediterran... [more]
D1LXA81.157e-731.75p75 neurotrophin receptor-like protein OS=Saccoglo... [more]
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BLAST of tr5_12233 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of tr5_12233 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 tr5_12233 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 tr5_12233 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of tr5_12233 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of tr5_12233 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000029156.11.077e-171100.00SMESG000029156.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30022285
GenBankAIZ98418.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022285 ID=SMED30022285|Name=tr5_12233|organism=Schmidtea mediterranea sexual|type=transcript|length=1219bp
GTTTTGGTAATAAATCAAAATAAATCAAAACAAATTCTCAAATTTGAAAA
AAAAAGTTCAATCAGCCATATAATCAATTTTTTCTCTTCAATCCATTTGA
TTTGCCTCCGACAAACGAGCGGTTCTATTATAGAAATTTCAATAAATGAA
ACTCATCATCCATTTCAATTCCTCTAATTCCAATTCATTTGGGATCAACA
TTACGGACTGGAGATTATTAATAGCACCATATTTCAAAAATTCCTCCAAT
TATCAAACAGAAAGTCCTCGAGTAATTGATTCAGATTTTAATTACATCAA
TGTATATTGCGCAATACTCGGATTGATTATACTTTATCTCGTTGGTTTTG
TTATTTATAAATTATGGGAACAGAAAAGTGACACCTTGCTCTGTACAGCG
ATTTCATCGAAAGGCAGTAACGGAAATAGTTTAAGATTACAAAAATGTTC
ACCATCCGGAAAATCAGACAATAAAGAAATGGTTACTTTAGTGACCCCTA
CTGATGAAATGAAATTGCCAAGTTACGAGCAAGTTCTAATGAGTCAACCT
TTGTATCGCCTTTCAGAAGATCAAATAGAAGCCATTGTTTTTAGCCTTTC
TGATGAAAGTTCCGGTGTCGGTTGGCTTCAATTGGCATTATACTATAATT
TTAAACAAGATGAAATAGAATTCATAGCACAAAATAATTCAAAAAATGAA
GCAGTTCGAACATTTTTGAGGAAATGGTCAGAAAATCCGAACCATACCCT
GAAAAAACTAATCAAAAGTCTTCATGAAATTTCGAGACCAGATACTGCTT
TTTTGATAAAGTCTGCGATCAGAAAACTGAGCCATTTGGAGCGCAATGAA
ACAAACAATAATCTCATGAATAAAGAAATTCAGAAAATGGCATTAAAATT
ATAGTTTACACATGTATAAACCGAATCACATTTTAATTTTCCTTTTTGAT
CTCACATTGGAATTTTTTTTGTAAATGAAAATGAATGAATATTTGATAAA
AATTCTAGTTTGGAAGACGTTATTAAAACAACTGCAACTCATAGAAAGTG
ATGATGACAATTTGTTGTATTCAAGGATCTTTGAACTTTGCAACATATAA
GAATTTCTGTATATTTTTATTTTTTATTTATTTTACTAAATTGAAAATTT
CACTTTCGACATTAATTAAATGTTCAAATGGTAATTTATTAAGTTCATAT
TTTACATTAGTAAAAAAAG
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protein sequence of SMED30022285-orf-1

>SMED30022285-orf-1 ID=SMED30022285-orf-1|Name=SMED30022285-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=253bp
MKLIIHFNSSNSNSFGINITDWRLLIAPYFKNSSNYQTESPRVIDSDFNY
INVYCAILGLIILYLVGFVIYKLWEQKSDTLLCTAISSKGSNGNSLRLQK
CSPSGKSDNKEMVTLVTPTDEMKLPSYEQVLMSQPLYRLSEDQIEAIVFS
LSDESSGVGWLQLALYYNFKQDEIEFIAQNNSKNEAVRTFLRKWSENPNH
TLKKLIKSLHEISRPDTAFLIKSAIRKLSHLERNETNNNLMNKEIQKMAL
KL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0000421tail
PLANA:0002056medial muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR041448TNFR16_TM
IPR000488Death_domain
IPR011029DEATH-like_dom_sf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
Vocabulary: biological process
TermDefinition
GO:0007165signal transduction
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
IPR000488Death domainSMARTSM00005DEATH_4coord: 134..225
e-value: 0.0021
score: 27.3
IPR000488Death domainPFAMPF00531Deathcoord: 156..223
e-value: 2.6E-10
score: 40.3
IPR000488Death domainPROSITEPS50017DEATH_DOMAINcoord: 145..225
score: 16.385
IPR041448Tumor necrosis factor receptor member 16, transmembrane domainPFAMPF18422TNFR_16_TMcoord: 49..75
e-value: 1.2E-8
score: 34.7
NoneNo IPR availableGENE3DG3DSA:1.10.533.10coord: 137..242
e-value: 3.1E-12
score: 48.2
NoneNo IPR availablePANTHERPTHR46605FAMILY NOT NAMEDcoord: 40..224
NoneNo IPR availableCDDcd01670Deathcoord: 157..218
e-value: 7.22409E-8
score: 46.5061
NoneNo IPR availableTMHMMTMhelixcoord: 48..70
IPR011029Death-like domain superfamilySUPERFAMILYSSF47986DEATH domaincoord: 151..225