Cadmium metallothionein (MT-Cd) (Cd-MT)

Overview
NameCadmium metallothionein (MT-Cd) (Cd-MT)
Smed IDSMED30028521
Length (bp)573
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 Cadmium metallothionein (MT-Cd) (Cd-MT) (SMED30028521) t-SNE clustered cells

Violin plots show distribution of expression levels for Cadmium metallothionein (MT-Cd) (Cd-MT) (SMED30028521) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) (SMED30028521) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Cadmium metallothionein (MT-Cd) (Cd-MT) (SMED30028521) 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




SMED30028521

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



PAGE Curations: 18

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30028521SMESG000008013.1 Contig394GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30028521SMESG000013781.1 PL04025A1H09ncbi_smed_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30028521SMESG000013781.1 Contig394GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30028521SMESG000013781.1 dd_Smed_v4_3412_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30028521SMESG000013781.1 dd_Smed_v4_3412_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30028521SMESG000013781.1 dd_Smed_v4_3412_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30028521SMESG000013781.1 dd_Smed_v4_3412_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30028521SMESG000013781.1 dd_Smed_v4_3412_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30028521SMESG000013781.1 dd_Smed_v4_3412_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30028521SMESG000013781.1 dd_Smed_v4_3412_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30028521SMESG000044505.1 SMESG000039936.1 SMESG000026760.1 SMESG000017179.1 SMESG000013786.1 SMESG000013783.1 SMESG000013781.1 SMESG000013251.1 Contig44456newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30028521SMESG000044505.1 SMESG000039936.1 SMESG000026760.1 SMESG000017179.1 SMESG000013786.1 SMESG000013783.1 SMESG000013781.1 SMESG000013251.1 Contig44456uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
oocyteSMED30028521SMESG000008013.1 Contig394GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30028521SMESG000008013.1 Contig394GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30028521SMESG000013781.1 Contig394GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30028521SMESG000013781.1 Contig394GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Category 4 cellSMED30028521SMESG000013781.1 dd_Smed_v4_3412_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30028521SMESG000013781.1 dd_Smed_v4_3412_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 Cadmium metallothionein (MT-Cd) (Cd-MT) vs. Ensembl Fly
Match: crok (gene:FBgn0032421 transcript:FBtr0080342)

HSP 1 Score: 66.6254 bits (161), Expect = 5.293e-14
Identity = 41/108 (37.96%), Postives = 60/108 (55.56%), Query Frame = 2
Query:   98 KELECYQCNSLTQPHCSDFFDNQTVILERC---PD----DGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAE-EGRWCTDRMGTLRVKVRYCHCNNKQGCNGA 397
            + ++C+ C S   P C D FDN T+ +  C   P+     G   +MCRKI Q+++  G W  RY+R CA  G  G E + R+C  R G+  + + +C CN+K GCN A
Sbjct:   22 QAIKCWDCRSDNDPKCGDPFDNSTLAITDCQQAPELEHLKGVRPTMCRKIRQKVH--GEW--RYFRSCAYMGEPGIEGDERFCLMRTGSYNIFMEFCTCNSKDGCNSA 125          
BLAST of Cadmium metallothionein (MT-Cd) (Cd-MT) vs. TrEMBL
Match: A0A4Z2DUF1 (Uncharacterized protein (Fragment) OS=Schistosoma japonicum OX=6182 GN=EWB00_004880 PE=4 SV=1)

HSP 1 Score: 158.303 bits (399), Expect = 1.146e-46
Identity = 72/96 (75.00%), Postives = 82/96 (85.42%), Query Frame = 2
Query:   98 KELECYQCNSLTQPHCSDFFDNQTVILERCPDDGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAEEGRWCTDRMGTLRVKVRYCHCNNKQG 385
             EL CYQCNSLTQPHC+D+FDN+T  L  CP+DGRNYS C K+IQE+Y DG W RRYYRDCAVTGV+GAE+GRWC DR+GT RVKVRYC+CNNK G
Sbjct:   13 PELRCYQCNSLTQPHCADYFDNRTFPLVACPNDGRNYSRCVKMIQEMYLDGKWTRRYYRDCAVTGVIGAEDGRWCIDRLGTYRVKVRYCNCNNKNG 108          
BLAST of Cadmium metallothionein (MT-Cd) (Cd-MT) vs. TrEMBL
Match: G4VLW4 (Hypothetical Schistosoma spp. protein UPF0506 OS=Schistosoma mansoni OX=6183 GN=Smp_147160 PE=4 SV=1)

HSP 1 Score: 160.614 bits (405), Expect = 4.387e-46
Identity = 73/96 (76.04%), Postives = 83/96 (86.46%), Query Frame = 2
Query:  101 ELECYQCNSLTQPHCSDFFDNQTVILERCPDDGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAEEGRWCTDRMGTLRVKVRYCHCNNKQGC 388
            EL CYQCNSLTQPHC+D+FDN+T  L  CP+DGRNYS C K+IQE+Y DG W RRYYRDCAVTGV+GAE+GRWC DR+GT RVKVRYC+CNNK GC
Sbjct:    7 ELRCYQCNSLTQPHCADYFDNRTFPLVACPNDGRNYSRCVKMIQEMYLDGKWTRRYYRDCAVTGVIGAEDGRWCIDRLGTYRVKVRYCNCNNKNGC 102          
BLAST of Cadmium metallothionein (MT-Cd) (Cd-MT) vs. TrEMBL
Match: A0A430Q7S1 (UPF0506 domain-containing protein OS=Schistosoma bovis OX=6184 GN=DC041_0004473 PE=4 SV=1)

HSP 1 Score: 158.303 bits (399), Expect = 7.273e-46
Identity = 72/95 (75.79%), Postives = 82/95 (86.32%), Query Frame = 2
Query:  101 ELECYQCNSLTQPHCSDFFDNQTVILERCPDDGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAEEGRWCTDRMGTLRVKVRYCHCNNKQG 385
            EL CYQCNSLTQPHC+D+FDN+T  L  CP+DGRNYS C K+IQE+Y DG W RRYYRDCAVTGV+GAE+GRWC DR+GT RVKVRYC+CNNK G
Sbjct:    7 ELRCYQCNSLTQPHCADYFDNRTFPLVACPNDGRNYSRCVKMIQEMYLDGKWTRRYYRDCAVTGVIGAEDGRWCIDRLGTYRVKVRYCNCNNKNG 101          
BLAST of Cadmium metallothionein (MT-Cd) (Cd-MT) vs. TrEMBL
Match: A0A267FNR4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig020458g1 PE=4 SV=1)

HSP 1 Score: 148.288 bits (373), Expect = 4.898e-42
Identity = 66/99 (66.67%), Postives = 78/99 (78.79%), Query Frame = 2
Query:  104 LECYQCNSLTQPHCSDFFDNQTVILERCPDDGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAEEGRWCTDRMGTLRVKVRYCHCNNKQGCNGAK 400
              CY CNS     C+DFFDN+T ++E CP D +NY+MCRKIIQE Y+DG W+RRY RDCAV G +G EEGRWCT+R+GTLRVK+RYCHC NK GCNGA 
Sbjct:   35 FHCYICNSFLDHRCADFFDNRTRLIEPCPGD-KNYTMCRKIIQETYFDGAWDRRYIRDCAVHGEIGQEEGRWCTERLGTLRVKMRYCHCKNKHGCNGAS 132          
BLAST of Cadmium metallothionein (MT-Cd) (Cd-MT) vs. TrEMBL
Match: A0A267G9E9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig017819g1 PE=4 SV=1)

HSP 1 Score: 148.288 bits (373), Expect = 4.952e-42
Identity = 66/99 (66.67%), Postives = 78/99 (78.79%), Query Frame = 2
Query:  104 LECYQCNSLTQPHCSDFFDNQTVILERCPDDGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAEEGRWCTDRMGTLRVKVRYCHCNNKQGCNGAK 400
              CY CNS     C+DFFDN+T ++E CP D +NY+MCRKIIQE Y+DG W+RRY RDCAV G +G EEGRWCT+R+GTLRVK+RYCHC NK GCNGA 
Sbjct:   35 FHCYICNSFLDHRCADFFDNRTRLIEPCPGD-KNYTMCRKIIQETYFDGAWDRRYIRDCAVHGEIGQEEGRWCTERLGTLRVKMRYCHCKNKHGCNGAS 132          
BLAST of Cadmium metallothionein (MT-Cd) (Cd-MT) vs. Planmine SMEST
Match: SMESG000013781.1 (SMESG000013781.1)

HSP 1 Score: 218.394 bits (555), Expect = 2.314e-73
Identity = 122/122 (100.00%), Postives = 122/122 (100.00%), Query Frame = 2
Query:   98 KELECYQCNSLTQPHCSDFFDNQTVILERCPDDGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAEEGRWCTDRMGTLRVKVRYCHCNNKQGCNGAKXXXXXXXXXXXXXXXXXXXPT 463
            KELECYQCNSLTQPHCSDFFDNQTVILERCPDDGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAEEGRWCTDRMGTLRVKVRYCHCNNKQGCNGAKSISFGIILMIFSIIITMLSPT
Sbjct:   26 KELECYQCNSLTQPHCSDFFDNQTVILERCPDDGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAEEGRWCTDRMGTLRVKVRYCHCNNKQGCNGAKSISFGIILMIFSIIITMLSPT 147          
The following BLAST results are available for this feature:
BLAST of Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
crok5.293e-1437.96gene:FBgn0032421 transcript:FBtr0080342[more]
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BLAST of Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4Z2DUF11.146e-4675.00Uncharacterized protein (Fragment) OS=Schistosoma ... [more]
G4VLW44.387e-4676.04Hypothetical Schistosoma spp. protein UPF0506 OS=S... [more]
A0A430Q7S17.273e-4675.79UPF0506 domain-containing protein OS=Schistosoma b... [more]
A0A267FNR44.898e-4266.67Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267G9E94.952e-4266.67Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) 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 Cadmium metallothionein (MT-Cd) (Cd-MT) vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000013781.12.314e-73100.00SMESG000013781.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028521 ID=SMED30028521|Name=Cadmium metallothionein (MT-Cd) (Cd-MT)|organism=Schmidtea mediterranea sexual|type=transcript|length=573bp
TTAAAGTTATAGGAAATTCTTTATGAAGAAGCTTTTATTCGTATTTTTAT
TGGCAGGTTTTATTATATTTGCTATCAATGCATTTCAACAATTTGGTAAA
GAACTAGAATGTTATCAGTGTAATTCATTAACTCAACCACATTGTTCTGA
TTTTTTCGATAATCAGACTGTAATTTTGGAAAGGTGTCCTGACGATGGTA
GAAATTATTCAATGTGTAGAAAAATTATCCAAGAATTATATTATGATGGA
ATTTGGGAACGACGATATTATAGAGATTGTGCAGTTACCGGTGTAGTTGG
TGCTGAAGAAGGTCGGTGGTGCACTGATCGTATGGGCACACTGCGAGTTA
AAGTTAGATATTGTCATTGCAACAACAAACAAGGCTGTAATGGTGCCAAG
TCAATATCATTTGGAATTATTTTGATGATTTTTTCAATAATTATTACTAT
GTTATCTCCTACTTAATTCATCTCACCATTGAATCAATAATTAATATCTT
TTGGCTGTGTAGTTTTTTGTAAATACTTTTTCATTGCATATCAAATGTAT
TTTATTATCTATTGTTAGTAAGG
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protein sequence of SMED30028521-orf-1

>SMED30028521-orf-1 ID=SMED30028521-orf-1|Name=SMED30028521-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=148bp
MKKLLFVFLLAGFIIFAINAFQQFGKELECYQCNSLTQPHCSDFFDNQTV
ILERCPDDGRNYSMCRKIIQELYYDGIWERRYYRDCAVTGVVGAEEGRWC
TDRMGTLRVKVRYCHCNNKQGCNGAKSISFGIILMIFSIIITMLSPT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0030431sleep
GO:0032222regulation of synaptic transmission, cholinergic
GO:1903818positive regulation of voltage-gated potassium channel activity
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000018Category 4 cell
PLANA:0000020protonephridia
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR031424QVR
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR031424Protein quiverPFAMPF17064QVRcoord: 26..125
e-value: 1.9E-6
score: 28.0
NoneNo IPR availablePANTHERPTHR33562:SF2CROOKED-RELATEDcoord: 10..145
NoneNo IPR availablePANTHERPTHR33562FAMILY NOT NAMEDcoord: 10..145
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.875
NoneNo IPR availableTMHMMTMhelixcoord: 4..21
NoneNo IPR availableTMHMMTMhelixcoord: 122..144