TNF receptor associated factor 4

Overview
NameTNF receptor associated factor 4
Smed IDSMED30001813
Length (bp)727
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 TNF receptor associated factor 4 (SMED30001813) t-SNE clustered cells

Violin plots show distribution of expression levels for TNF receptor associated factor 4 (SMED30001813) 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 TNF receptor associated factor 4 (SMED30001813) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for TNF receptor associated factor 4 (SMED30001813) 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




SMED30001813

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
zeta neoblastSMED30001813 dd_Smed_v4_17632_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
BLAST of TNF receptor associated factor 4 vs. TrEMBL
Match: A0A0F7GWW3 (TNF receptor associated factor 4 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 103.605 bits (257), Expect = 9.184e-24
Identity = 72/111 (64.86%), Postives = 89/111 (80.18%), Query Frame = 3
Query:  177 GCEVCIIARNKVEDYLESEILTHTKLLMDFIGNFXXXXXXXXXXXXXXXXXXXXXQTEINELKLNDERRR-EIVDLQKTITDRAGQIELLNEDISELRNADRNVSDGLDGL 506
            GC+ C I+++KV D+L+SEI  HTKLLMDF+ NFNNE+E+LKANNN L   N+LL+ EINELKL+ +RRR EI DLQ+   ++A +IELLNEDI  LRN DRNVSD LDGL
Sbjct:   67 GCDKCNISQDKVTDHLQSEIFVHTKLLMDFVVNFNNEMEMLKANNNGLSPVNELLRNEINELKLDGDRRRVEIGDLQRKCANQAEEIELLNEDIPALRNVDRNVSDRLDGL 177          
BLAST of TNF receptor associated factor 4 vs. Planmine SMEST
Match: SMESG000025934.1 (SMESG000025934.1)

HSP 1 Score: 141.354 bits (355), Expect = 1.268e-45
Identity = 107/191 (56.02%), Postives = 131/191 (68.59%), Query Frame = 3
Query:  177 GCEVCIIARNKVEDYLESEILTHTKLLMDFIGNFXXXXXXXXXXXXXXXXXXXXXQTEINELKLNDERRRE-IVDLQKTITDRAGQIELLNEDISELRNADRNVSDGLDGLKLNIELSQVKY**SC*SIDDESLFLLAIRACENNFQQAK-------NKIFQIENRQIIDLAEMSNIIDKSMKNFAGKLLE 725
            GC+ C I+++KV D+L+SEI  HTKLLMDF+ NF+NE+E+LKANNN L A N+LL+ EINELKL+ ERRRE I +LQ    D+A +IELLNEDI  LRN DRNVSD LDGL+L IE +QV           E+ F   I  C  N QQA+       +KI Q+EN+Q +DL EMSN IDKS  N   KLLE
Sbjct:  133 GCDKCNISQDKVTDHLQSEIFAHTKLLMDFVVNFHNEMEMLKANNNGLSAVNELLRNEINELKLDGERRREEIAELQMKCADQAEEIELLNEDIPALRNVDRNVSDRLDGLQLIIEGNQVAM------RAVENDFQQQIAQCATNCQQAEIKQKELIDKIGQMENKQKVDLTEMSNKIDKSSGNVDRKLLE 317          

HSP 2 Score: 48.1358 bits (113), Expect = 1.268e-45
Identity = 21/31 (67.74%), Postives = 27/31 (87.10%), Query Frame = 1
Query:   19 KICPGNTEECKLEILNLNENIFADQHMHIEI 111
            +ICPGNTE+CK E+L LNENI+ DQ M+I+I
Sbjct:   62 EICPGNTEDCKQEVLYLNENIYVDQPMNIKI 92          

HSP 3 Score: 33.113 bits (74), Expect = 1.268e-45
Identity = 17/32 (53.12%), Postives = 25/32 (78.12%), Query Frame = 2
Query:   86 PINICISRLKVKFPEMSCEY-G*IKKREDYSR 178
            P+NI IS+L+VK  EMSC+Y   ++K E++SR
Sbjct:   87 PMNIKISKLQVKCKEMSCDYVDELRKMEEHSR 118          
BLAST of TNF receptor associated factor 4 vs. Planmine SMEST
Match: SMESG000025980.1 (SMESG000025980.1)

HSP 1 Score: 136.346 bits (342), Expect = 5.626e-43
Identity = 106/191 (55.50%), Postives = 130/191 (68.06%), Query Frame = 3
Query:  177 GCEVCIIARNKVEDYLESEILTHTKLLMDFIGNFXXXXXXXXXXXXXXXXXXXXXQTEINELKLNDERRR-EIVDLQKTITDRAGQIELLNEDISELRNADRNVSDGLDGLKLNIELSQVKY**SC*SIDDESLFLLAIRACENNFQQAK-------NKIFQIENRQIIDLAEMSNIIDKSMKNFAGKLLE 725
            GC+ C I+++KV D+L+SEI  HTKLLMDF+ NFNNE+EILKANNN L   N+LL+ EINELKL+ +RRR EI DLQ+   ++A +IELLNEDI  LRN DRNVSD LDGL+L IE +QV           E+ F   I  C  N QQA+       +KI Q+EN+Q +DL EMSN IDK   N   KLLE
Sbjct:  134 GCDKCNISQDKVTDHLQSEIFVHTKLLMDFVVNFNNEMEILKANNNGLSPVNELLRNEINELKLDGDRRRVEIGDLQRKCANQAEEIELLNEDIPALRNVDRNVSDRLDGLQLIIEGNQVAM------RAVENDFQQQIAQCATNCQQAEIKQKELIDKIGQMENKQKVDLTEMSNKIDKLSGNVDRKLLE 318          

HSP 2 Score: 44.2838 bits (103), Expect = 5.626e-43
Identity = 22/37 (59.46%), Postives = 27/37 (72.97%), Query Frame = 1
Query:    1 FLYSGYKICPGNTEECKLEILNLNENIFADQHMHIEI 111
            FL    K CPGNTEECK E+L+LNENI  D  M+++I
Sbjct:   57 FLDHKKKNCPGNTEECKQEMLHLNENICVDYPMNMKI 93          

HSP 3 Score: 32.7278 bits (73), Expect = 5.626e-43
Identity = 16/32 (50.00%), Postives = 25/32 (78.12%), Query Frame = 2
Query:   86 PINICISRLKVKFPEMSCEY-G*IKKREDYSR 178
            P+N+ I++L+VK  EMSC+Y   ++K ED+SR
Sbjct:   88 PMNMKIAKLQVKCKEMSCDYVDELRKMEDHSR 119          
BLAST of TNF receptor associated factor 4 vs. Planmine SMEST
Match: SMESG000026956.1 (SMESG000026956.1)

HSP 1 Score: 122.865 bits (307), Expect = 4.152e-42
Identity = 93/213 (43.66%), Postives = 114/213 (53.52%), Query Frame = 3
Query:  177 GCEVCIIARNKVEDYLESEILTHTKLLMDFIGNFXXXXXXXXXXXXXXXXXXXXXQTEINELKLNDERRR-EIVDLQKTITDRAGQIELLNEDISELRNADRNVSDGLDGLKLNIELSQVKY**SC*SIDDESLFLLAIRACENNFQQ-----AKN------------------------KIFQIENRQIIDLAEMSNIIDKSMKNFAGKLLE 725
            GC+ C I ++KV D+L+SE+LTHTKL MDFIGNF             + A N  L  EIN LKL+ ER + EI DLQ+    +A +I+LLN +I  LRN D NVSD LDGL+LN+E +Q                 LAIRACENN QQ     A N                        KI Q+EN+Q  D+  +SN IDKSM N   KLLE
Sbjct:  107 GCDKCNIFQDKVVDHLQSELLTHTKLFMDFIGNF-------NNEMEMMKANNNGLSAEINGLKLDRERMQVEIGDLQRKCAGQAEEIKLLNGEIPALRNVDMNVSDRLDGLQLNVEGNQ-----------------LAIRACENNLQQQIAQYATNCHQAESKFHSANQMREIKQKELIDKIGQMENKQKTDMTNISNKIDKSMANPDRKLLE 295          

HSP 2 Score: 49.6766 bits (117), Expect = 4.152e-42
Identity = 24/37 (64.86%), Postives = 29/37 (78.38%), Query Frame = 1
Query:    1 FLYSGYKICPGNTEECKLEILNLNENIFADQHMHIEI 111
            FL    KICPGNTE CKLE+LN+N NI  +QHM+I+I
Sbjct:   30 FLDDENKICPGNTEFCKLEMLNMNINICVNQHMNIKI 66          

HSP 3 Score: 38.1206 bits (87), Expect = 4.152e-42
Identity = 21/32 (65.62%), Postives = 26/32 (81.25%), Query Frame = 2
Query:   89 INICISRLKVKFPEMSCEY-G*IKKREDYSRM 181
            +NI ISRLKVK PEMSCEY   ++K ED+SR+
Sbjct:   62 MNIKISRLKVKCPEMSCEYICELRKMEDHSRV 93          
BLAST of TNF receptor associated factor 4 vs. Planmine SMEST
Match: SMESG000025794.1 (SMESG000025794.1)

HSP 1 Score: 129.413 bits (324), Expect = 1.523e-41
Identity = 99/184 (53.80%), Postives = 122/184 (66.30%), Query Frame = 3
Query:  177 GCEVCIIARNKVEDYLESEILTHTKLLMDFIGNFXXXXXXXXXXXXXXXXXXXXXQTEINELKLNDERRR-EIVDLQKTITDRAGQIELLNEDISELRNADRNVSDGLDGLKLNIELSQVKY**SC*SIDDESLFLLAIRACENNFQQAKNKIFQIENRQIIDLAEMSNIIDKSMKNFAGKLLE 725
            GC+ C I+++KV D+L+SEI  HTKLLMDF+ NFNNE+E+LKANNN L A N+LL+ EINELKL+ ERRR EI DLQ+   D+A +IELLNEDI  LRN DRNVSD LDGL+L IE +Q                           ++  +KI Q+EN+Q +DL EMSN IDK   N   KLLE
Sbjct:  134 GCDKCNISQDKVTDHLQSEIFAHTKLLMDFVVNFNNEMEMLKANNNGLSAVNELLRNEINELKLDGERRRVEIADLQRKCADQAEEIELLNEDIPALRNVDRNVSDRLDGLQLIIEGNQ---------------------------KELIDKIGQMENKQKVDLTEMSNKIDKLSGNVDRKLLE 290          

HSP 2 Score: 46.2098 bits (108), Expect = 1.523e-41
Identity = 23/37 (62.16%), Postives = 28/37 (75.68%), Query Frame = 1
Query:    1 FLYSGYKICPGNTEECKLEILNLNENIFADQHMHIEI 111
            FL    KICPG+TEECK E+L+LNENI  D  M+I+I
Sbjct:   57 FLDHKEKICPGDTEECKQEMLHLNENICVDYPMNIKI 93          

HSP 3 Score: 33.113 bits (74), Expect = 1.523e-41
Identity = 18/32 (56.25%), Postives = 24/32 (75.00%), Query Frame = 2
Query:   86 PINICISRLKVKFPEMSCEY-G*IKKREDYSR 178
            P+NI IS+L+VK  EMSC Y   ++K ED+SR
Sbjct:   88 PMNIKISKLQVKCKEMSCVYVDELRKMEDHSR 119          
BLAST of TNF receptor associated factor 4 vs. Planmine SMEST
Match: SMESG000026954.1 (SMESG000026954.1)

HSP 1 Score: 119.783 bits (299), Expect = 5.324e-41
Identity = 91/213 (42.72%), Postives = 113/213 (53.05%), Query Frame = 3
Query:  177 GCEVCIIARNKVEDYLESEILTHTKLLMDFIGNFXXXXXXXXXXXXXXXXXXXXXQTEINELKLNDERRR-EIVDLQKTITDRAGQIELLNEDISELRNADRNVSDGLDGLKLNIELSQVKY**SC*SIDDESLFLLAIRACENNFQQ-----AKN------------------------KIFQIENRQIIDLAEMSNIIDKSMKNFAGKLLE 725
            GC+ C I+++KV D+L+SEILTHTKL MDFIGNF             + A N  L  EIN LKL+ ER + EI DLQ+    +A +I+LLN +I  LRN + NVSD LD L+LN+E +Q                 LAIR CENN QQ     A N                        KI Q+EN+Q  D+  +SN IDKSM N   KLLE
Sbjct:  107 GCDKCNISQDKVADHLQSEILTHTKLFMDFIGNF-------NNEMEMMKANNNGLSAEINGLKLDRERMQVEIADLQRKCAGQAEEIKLLNGEIPALRNVNMNVSDRLDELQLNVEGNQ-----------------LAIRTCENNLQQQIAQCATNCQQAESKFYNANQMREIKQKELIDKIGQMENKQKTDMTNISNKIDKSMANPDRKLLE 295          

HSP 2 Score: 48.521 bits (114), Expect = 5.324e-41
Identity = 23/37 (62.16%), Postives = 29/37 (78.38%), Query Frame = 1
Query:    1 FLYSGYKICPGNTEECKLEILNLNENIFADQHMHIEI 111
            FL    KICPGNTE CKLE+L++N NI  +QHM+I+I
Sbjct:   30 FLDDENKICPGNTEFCKLEMLDMNINICVNQHMNIKI 66          

HSP 3 Score: 38.1206 bits (87), Expect = 5.324e-41
Identity = 21/32 (65.62%), Postives = 26/32 (81.25%), Query Frame = 2
Query:   89 INICISRLKVKFPEMSCEY-G*IKKREDYSRM 181
            +NI ISRLKVK PEMSCEY   ++K ED+SR+
Sbjct:   62 MNIKISRLKVKCPEMSCEYICELRKMEDHSRV 93          
The following BLAST results are available for this feature:
BLAST of TNF receptor associated factor 4 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 TNF receptor associated factor 4 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 TNF receptor associated factor 4 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 TNF receptor associated factor 4 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of TNF receptor associated factor 4 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 TNF receptor associated factor 4 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of TNF receptor associated factor 4 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of TNF receptor associated factor 4 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A0F7GWW39.184e-2464.86TNF receptor associated factor 4 (Fragment) OS=Sch... [more]
back to top
BLAST of TNF receptor associated factor 4 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of TNF receptor associated factor 4 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 TNF receptor associated factor 4 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 TNF receptor associated factor 4 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 TNF receptor associated factor 4 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of TNF receptor associated factor 4 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000025934.11.268e-4556.02SMESG000025934.1[more]
SMESG000025980.15.626e-4355.50SMESG000025980.1[more]
SMESG000026956.14.152e-4243.66SMESG000026956.1[more]
SMESG000025794.11.523e-4153.80SMESG000025794.1[more]
SMESG000026954.15.324e-4142.72SMESG000026954.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001813 ID=SMED30001813|Name=TNF receptor associated factor 4|organism=Schmidtea mediterranea sexual|type=transcript|length=727bp
TTTCTATATAGTGGATATAAAATTTGTCCTGGCAATACCGAGGAATGCAA
ACTGGAAATCCTCAATTTGAATGAAAATATTTTTGCCGATCAACATATGC
ATATCGAGATTAAAAGTAAAATTTCCAGAAATGTCTTGTGAATATGGATG
AATTAAGAAAAGGGAAGATTATTCACGGATGTGAGGTATGCATAATAGCC
CGAAATAAAGTTGAGGATTATTTGGAATCTGAAATATTGACTCACACAAA
ACTATTGATGGATTTCATTGGGAATTTCAACAATGAAATAGAGATATTAA
AGGCCAATAATAACGAATTGTTAGCTGAGAATAAATTATTGCAAACTGAA
ATAAACGAATTGAAATTGAATGACGAAAGAAGACGAGAAATTGTAGACTT
GCAGAAGACAATCACTGATCGAGCTGGGCAAATCGAATTATTGAATGAAG
ATATATCGGAATTGAGGAACGCAGACAGAAATGTGAGTGATGGATTGGAC
GGATTGAAATTGAATATCGAGCTCAGCCAGGTGAAATATTGATGAAGTTG
TTAATCAATTGATGATGAGTCATTATTTCTGCTGGCTATTCGGGCATGTG
AGAACAATTTCCAGCAAGCCAAAAATAAGATATTTCAAATTGAAAATAGA
CAAATAATTGATCTGGCGGAAATGTCAAATATAATCGATAAATCAATGAA
AAATTTCGCCGGGAAATTATTGGAAAT
back to top

protein sequence of SMED30001813-orf-1

>SMED30001813-orf-1 ID=SMED30001813-orf-1|Name=SMED30001813-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=133bp
MDELRKGKIIHGCEVCIIARNKVEDYLESEILTHTKLLMDFIGNFNNEIE
ILKANNNELLAENKLLQTEINELKLNDERRREIVDLQKTITDRAGQIELL
NEDISELRNADRNVSDGLDGLKLNIELSQVKY*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
Vocabulary: molecular function
TermDefinition
GO:0004842ubiquitin-protein transferase activity
GO:0008270zinc ion binding
GO:0046872metal ion binding
Vocabulary: biological process
TermDefinition
GO:0016567protein ubiquitination
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 4..38