Tumour necrosis receptor-associated factor

Overview
NameTumour necrosis receptor-associated factor
Smed IDSMED30008444
Length (bp)360
Neoblast Clusters

Zeng et. al., 2018



 

 

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



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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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



SMED30008444

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30008444SMESG000014712.1 Contig14561newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008444SMESG000014712.1 Contig14561uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Tumour necrosis receptor-associated factor vs. Ensembl Cavefish
Match: traf2a (TNF receptor-associated factor 2-like [Source:NCBI gene;Acc:103036375])

HSP 1 Score: 44.669 bits (104), Expect = 5.379e-6
Identity = 28/83 (33.73%), Postives = 41/83 (49.40%), Query Frame = 1 
Query:  133 GKIKKETRLINTGICWKFEWKIENLSQQE------RRKRIHSKPFYTGPNGYKMCLSVYF---GNIWDKEISVNFHLMRGDSD 354
            GK+++ +     G+   F WKI + S++       R   + S  FYT   GYKMCL +Y    G      +S+ F +MRG SD
Sbjct:  298 GKMREMSAATYDGV---FVWKISDFSKKRQDAVAGRAPAMFSPAFYTSKYGYKMCLRIYLNGDGTGRGTHLSLFFVVMRGHSD 377
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BLAST of Tumour necrosis receptor-associated factor vs. Ensembl Sea Lamprey
Match: ENSPMAT00000002130.1 (pep scaffold:Pmarinus_7.0:GL484662:8457:12718:-1 gene:ENSPMAG00000001936.1 transcript:ENSPMAT00000002130.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.8246 bits (107), Expect = 3.710e-7
Identity = 29/90 (32.22%), Postives = 47/90 (52.22%), Query Frame = 1 
Query:  115 MNDLELGKIKKETRLINT-GICWKFEWKIENLSQQE------RRKRIHSKPFYTGPNGYKMCLSVYF---GNIWDKEISVNFHLMRGDSD 354
            M+D  L   ++  +++ T G   K  WKI + ++++      R   ++S+PFYT P GYKMC   Y    G      +S+ F +MRG+ D
Sbjct:  246 MHDGLLDTAERRLQVLETAGYSGKLVWKIRDYARRKQEAASGRTLSLYSQPFYTSPFGYKMCARAYLNGDGVGRGTHLSLFFVVMRGEYD 335
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BLAST of Tumour necrosis receptor-associated factor vs. Ensembl Sea Lamprey
Match: ENSPMAT00000000074.1 (pep scaffold:Pmarinus_7.0:GL482142:165593:173010:-1 gene:ENSPMAG00000000066.1 transcript:ENSPMAT00000000074.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 42.743 bits (99), Expect = 4.332e-6
Identity = 23/67 (34.33%), Postives = 36/67 (53.73%), Query Frame = 1 
Query:  181 KFEWKIENLSQQE------RRKRIHSKPFYTGPNGYKMCLSVYF---GNIWDKEISVNFHLMRGDSD 354
            K  WKI + ++++      R   ++S+PFYT P GY+MC   Y    G      +S+ F +MRG+ D
Sbjct:  326 KLVWKIRDYARRKQDAVSGRTLSLYSQPFYTSPFGYRMCARAYLNGDGVGRGTHLSLFFVVMRGEYD 392
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BLAST of Tumour necrosis receptor-associated factor vs. Ensembl Nematostella
Match: EDO48773 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RI91])

HSP 1 Score: 46.9802 bits (110), Expect = 2.912e-7
Identity = 31/90 (34.44%), Postives = 44/90 (48.89%), Query Frame = 1 
Query:  112 KMNDLELGKIKKETRLINTGICWKFEWKIENLSQQER------RKRIHSKPFYTGPNGYKMCLSVYFGNI---WDKEISVNFHLMRGDSD 354
            K+  LE  +I+ E R+ N      F WK++N  Q            IHS PFYT   GYKMCL +    +     + +S+  H+M+GD D
Sbjct:  314 KLMRLETREIELEGRVCN----GTFIWKLDNFRQCREGSIAGLTAAIHSPPFYTSMYGYKMCLRMNLNGVDGGLGEHVSLFIHMMQGDWD 399
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BLAST of Tumour necrosis receptor-associated factor vs. Ensembl Nematostella
Match: EDO38873 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SBN4])

HSP 1 Score: 43.1282 bits (100), Expect = 5.514e-6
Identity = 23/64 (35.94%), Postives = 35/64 (54.69%), Query Frame = 1 
Query:  190 WKIENLSQQE------RRKRIHSKPFYTGPNGYKMCLSVYF---GNIWDKEISVNFHLMRGDSD 354
            WKI N++ +       R    +S  F+TGP+GYKMC  +Y    G   +  +S+ F +MRG+ D
Sbjct:  337 WKITNVANKRSEATSGRVTSFYSPCFFTGPHGYKMCARIYLNGDGMGRNHHVSLFFVIMRGEFD 400
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BLAST of Tumour necrosis receptor-associated factor vs. Ensembl Medaka
Match: ENSORLT00000020861.2 (TNF receptor-associated factor 2 [Source:NCBI gene;Acc:101167626])

HSP 1 Score: 45.0542 bits (105), Expect = 4.001e-6
Identity = 40/137 (29.20%), Postives = 58/137 (42.34%), Query Frame = 1 
Query:   10 LNNEMEMLCRKIDKMSEQKADNNDGETFTWIIDGKMNDLEL-------------GKIKKETRLINTGICWKFEWKIENLSQQE------RRKRIHSKPFYTGPNGYKMCLSVYF---GNIWDKEISVNFHLMRGDSD 354
            LN E+E  C  ++  + Q   + D      I+  K+  LE              GK+K  +     GI   F WKI + +++       R   + S  FYT   GYKMCL +Y    G      +S+ F +MRG SD
Sbjct:  357 LNRELERSCATMEAYNRQHRLDQDK---IEILSNKVRQLERTVSLRDLSIVEMEGKMKDMSAATYDGI---FIWKISDFTKKRQDAMAGRAPAMFSPAFYTSKYGYKMCLRIYLNGDGTGRGTHLSLFFVVMRGHSD 487
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BLAST of Tumour necrosis receptor-associated factor vs. Planmine SMEST
Match: SMESG000014712.1 (SMESG000014712.1)

HSP 1 Score: 206.453 bits (524), Expect = 7.124e-66
Identity = 104/120 (86.67%), Postives = 106/120 (88.33%), Query Frame = 1 
Query:   19 EMEMLCRKIDKMSEQKAD------NNDGETFTWIIDGKMNDLELGKIKKETRLINTGICWKFEWKIENLSQQERRKRIHSKPFYTGPNGYKMCLSVYFGNIWDKEISVNFHLMRGDSDDK 360
            EMEMLCRKIDKMSEQKAD      NNDGETFTWIIDGKMNDLELGKIKKETRLINTGICWKFEWKIENLSQQERRKRIHSKPFYTGPNGYKMCLSV   NI D  I V FHLM+GDSDD+
Sbjct:  271 EMEMLCRKIDKMSEQKADGASRVDNNDGETFTWIIDGKMNDLELGKIKKETRLINTGICWKFEWKIENLSQQERRKRIHSKPFYTGPNGYKMCLSV---NITDCRIFVGFHLMQGDSDDR 387
[Close]
BLAST of Tumour necrosis receptor-associated factor vs. Planmine SMEST
Match: SMESG000070286.1 (SMESG000070286.1)

HSP 1 Score: 149.058 bits (375), Expect = 5.972e-44
Identity = 80/120 (66.67%), Postives = 95/120 (79.17%), Query Frame = 1 
Query:   19 EMEMLCRKIDKMSEQKA------DNNDGETFTWIIDGKMNDLELGKIKKETRLINTGICWKFEWKIENLSQQERRKRIHSKPFYTGPNGYKMCLSVYFGNIWDKEISVNFHLMRGDSDDK 360
            E+EML ++I+K+SEQ A      DNN+ ETF WIIDGK NDLEL  I+ ET LI  GICW+FEWKIENL++Q+  K+I+SKPFY+GPNGYKMCLSVY   IW   ISV+FHLMRGDSDDK
Sbjct:  264 EVEMLRKEINKVSEQNANGASRVDNNNRETFKWIIDGKTNDLELRIIEIETILITAGICWEFEWKIENLAKQKSGKQIYSKPFYSGPNGYKMCLSVYI--IWSFAISVSFHLMRGDSDDK 381
[Close]
BLAST of Tumour necrosis receptor-associated factor vs. Planmine SMEST
Match: SMESG000070286.1 (SMESG000070286.1)

HSP 1 Score: 149.058 bits (375), Expect = 7.164e-44
Identity = 80/120 (66.67%), Postives = 95/120 (79.17%), Query Frame = 1 
Query:   19 EMEMLCRKIDKMSEQKA------DNNDGETFTWIIDGKMNDLELGKIKKETRLINTGICWKFEWKIENLSQQERRKRIHSKPFYTGPNGYKMCLSVYFGNIWDKEISVNFHLMRGDSDDK 360
            E+EML ++I+K+SEQ A      DNN+ ETF WIIDGK NDLEL  I+ ET LI  GICW+FEWKIENL++Q+  K+I+SKPFY+GPNGYKMCLSVY   IW   ISV+FHLMRGDSDDK
Sbjct:  272 EVEMLRKEINKVSEQNANGASRVDNNNRETFKWIIDGKTNDLELRIIEIETILITAGICWEFEWKIENLAKQKSGKQIYSKPFYSGPNGYKMCLSVYI--IWSFAISVSFHLMRGDSDDK 389
[Close]
BLAST of Tumour necrosis receptor-associated factor vs. Planmine SMEST
Match: SMESG000067250.1 (SMESG000067250.1)

HSP 1 Score: 144.821 bits (364), Expect = 4.735e-43
Identity = 80/121 (66.12%), Postives = 91/121 (75.21%), Query Frame = 1 
Query:   19 EMEMLCRKIDKMSEQ------KADNNDGETFTWIIDGKMNDLELGKIKKETRLINTGICWKFEWKIENLSQQERRKRIHSKPFYTGPNGYKMCLSVYFGNIWDK-EISVNFHLMRGDSDDK 360
            E+EML R+I+K+SEQ      + DNNDGETF  II G+MNDL+LG  +KETRLIN  +    EWKIENLSQQER KRIHSKPFY+GP+GYKMCLSV   NI D   I   FHLMRGDSDDK
Sbjct:  177 EVEMLRREINKLSEQIVNCASRVDNNDGETFKQIIGGEMNDLKLGLTEKETRLINAEVYKGLEWKIENLSQQERGKRIHSKPFYSGPDGYKMCLSV---NINDNLGIFAGFHLMRGDSDDK 294
[Close]
BLAST of Tumour necrosis receptor-associated factor vs. Planmine SMEST
Match: SMESG000070140.1 (SMESG000070140.1)

HSP 1 Score: 132.88 bits (333), Expect = 9.416e-38
Identity = 72/126 (57.14%), Postives = 90/126 (71.43%), Query Frame = 1 
Query:    1 QQQLNNEMEMLCRKIDKMSEQKA------DNNDGETFTWIIDGKMNDLELGKIKKETRLINTGICWKFEWKIENLSQQERRKRIHSKPFYTGPNGYKMCLSVYFGNIWDKEISVNFHLMRGDSDDK 360
            Q+QLN ++EML R+IDK+SE+ A      DNND + F   ID KM+DLELG  + ETRLIN   C +FEWKIENLSQ +R K I+SKPFY+GP+GYK+CLSV   ++    I + FHLMRG  DDK
Sbjct:  272 QKQLNKKLEML-REIDKLSEENANCASRVDNNDEKIFKQSIDEKMSDLELGMTEMETRLINARHCEEFEWKIENLSQLKRDKCIYSKPFYSGPSGYKLCLSVTISDV----IRIYFHLMRGKFDDK 392
The following BLAST results are available for this feature:
BLAST of Tumour necrosis receptor-associated 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 Tumour necrosis receptor-associated 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 Tumour necrosis receptor-associated 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 Tumour necrosis receptor-associated factor 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 Tumour necrosis receptor-associated factor 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 Tumour necrosis receptor-associated 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 Tumour necrosis receptor-associated 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 Tumour necrosis receptor-associated factor vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Tumour necrosis receptor-associated factor vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
traf2a5.379e-633.73TNF receptor-associated factor 2-like [Source:NCBI... [more]
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BLAST of Tumour necrosis receptor-associated factor vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 2
Match NameE-valueIdentityDescription
ENSPMAT00000002130.13.710e-732.22pep scaffold:Pmarinus_7.0:GL484662:8457:12718:-1 g... [more]
ENSPMAT00000000074.14.332e-634.33pep scaffold:Pmarinus_7.0:GL482142:165593:173010:-... [more]
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BLAST of Tumour necrosis receptor-associated 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 Tumour necrosis receptor-associated factor vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 2
Match NameE-valueIdentityDescription
EDO487732.912e-734.44Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO388735.514e-635.94Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of Tumour necrosis receptor-associated factor vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSORLT00000020861.24.001e-629.20TNF receptor-associated factor 2 [Source:NCBI gene... [more]
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BLAST of Tumour necrosis receptor-associated factor vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014712.17.124e-6686.67SMESG000014712.1[more]
SMESG000070286.15.972e-4466.67SMESG000070286.1[more]
SMESG000070286.17.164e-4466.67SMESG000070286.1[more]
SMESG000067250.14.735e-4366.12SMESG000067250.1[more]
SMESG000070140.19.416e-3857.14SMESG000070140.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008444 ID=SMED30008444|Name=Tumour necrosis receptor-associated factor|organism=Schmidtea mediterranea sexual|type=transcript|length=360bp
CAGCAGCAACTGAATAATGAAATGGAAATGCTGTGCAGAAAAATCGATAA
AATGAGTGAGCAAAAGGCTGATAATAATGACGGGGAGACATTCACGTGGA
TTATTGATGGGAAAATGAATGATTTGGAATTGGGAAAGATCAAGAAGGAA
ACGAGATTAATAAATACAGGAATTTGCTGGAAATTCGAATGGAAAATCGA
GAATTTATCCCAACAGGAGAGACGCAAACGGATACACAGCAAGCCGTTTT
ATACCGGTCCAAATGGATACAAAATGTGCTTGAGTGTTTATTTTGGGAAT
ATTTGGGATAAGGAAATATCTGTTAATTTCCATCTGATGCGAGGCGATTC
GGATGATAAA
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protein sequence of SMED30008444-orf-1

>SMED30008444-orf-1 ID=SMED30008444-orf-1|Name=SMED30008444-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
QQQLNNEMEMLCRKIDKMSEQKADNNDGETFTWIIDGKMNDLELGKIKKE
TRLINTGICWKFEWKIENLSQQERRKRIHSKPFYTGPNGYKMCLSVYFGN
IWDKEISVNFHLMRGDSDDK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0046872metal ion binding
GO:0005515protein binding
GO:0004842ubiquitin-protein transferase activity
Vocabulary: biological process
TermDefinition
GO:0042981regulation of apoptotic process
GO:0006955immune response
GO:0007165signal transduction
GO:0016567protein ubiquitination
Vocabulary: INTERPRO
TermDefinition
IPR008974TRAF-like
IPR002083MATH/TRAF_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 1..21
IPR008974TRAF-likeGENE3DG3DSA:2.60.210.10coord: 44..122
e-value: 2.1E-13
score: 52.1
IPR008974TRAF-likeSUPERFAMILYSSF49599TRAF domain-likecoord: 65..119
IPR002083MATH/TRAF domainPROSITEPS50144MATHcoord: 65..122
score: 8.578