Hmctn

Overview
NameHmctn
Smed IDSMED30004914
Length (bp)196
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



SMED30004914

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30004914SMESG000006452.1 SmedASXL_010562SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30004914SMESG000006452.1 dd_Smed_v6_31887_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
serotonergic neuronSMED30004914SMESG000006452.1 KF134119.1smed_ncbi_20200123PMID:24131630
März et al., 2013		whole organism asexual adult colorimetric in situ hybridization evidence
secretory cellSMED30004914SMESG000006452.1 KF134119smed_ncbi_20200123PMID:23903188
Currie et al., 2013		whole organism asexual adult fluorescence in situ hybridization evidence
ventral region of the whole animalSMED30004914SMESG000006452.1 KF134119smed_ncbi_20200123PMID:23903188
Currie et al., 2013		whole organism asexual adult fluorescence in situ hybridization evidence
parapharyngeal regionSMED30004914SMESG000006452.1 KF134119smed_ncbi_20200123PMID:23903188
Currie et al., 2013		whole organism asexual adult fluorescence in situ hybridization evidence
serotonergic neuronSMED30004914SMESG000006452.1 KF134119smed_ncbi_20200123PMID:23903188
Currie et al., 2013		whole organism asexual adult fluorescence in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Hmctn vs. TrEMBL
Match: S5WES3 (Hmctn (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 131.339 bits (329), Expect = 6.061e-36
Identity = 63/65 (96.92%), Postives = 64/65 (98.46%), Query Frame = 1 
Query:    1 YNTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIWCEPSIKMGNDVIEQSQGRETMIQAIIN 195
            YNTVTIFN+SRIHNGSYTCIVDNKVEGKQSKSFKLEIW EPSIKMGNDVIEQSQGRETMIQAIIN
Sbjct:   61 YNTVTIFNISRIHNGSYTCIVDNKVEGKQSKSFKLEIWYEPSIKMGNDVIEQSQGRETMIQAIIN 125
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BLAST of Hmctn vs. TrEMBL
Match: H2KUX2 (Opioid-binding protein/cell adhesion molecule homolog OS=Clonorchis sinensis OX=79923 GN=CLF_110631 PE=4 SV=1)

HSP 1 Score: 52.7582 bits (125), Expect = 2.631e-6
Identity = 25/63 (39.68%), Postives = 38/63 (60.32%), Query Frame = 1 
Query:    4 NTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIWCEPSIKMGNDVIEQSQGRETMIQAII 192
            N + IFNV+R  NG Y C+  N +E   S+  +L++   P+I+M N  I Q   R TM++A+I
Sbjct:  250 NHLQIFNVTRTMNGLYKCVAQNGLERMASRVIELDVHFPPTIRMANTKIGQLLYRTTMVRALI 312
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BLAST of Hmctn vs. TrEMBL
Match: A0A419Q306 (Opioid-binding protein/cell adhesion molecule-like protein (Fragment) OS=Clonorchis sinensis OX=79923 GN=OPCML PE=4 SV=1)

HSP 1 Score: 52.7582 bits (125), Expect = 2.896e-6
Identity = 25/63 (39.68%), Postives = 38/63 (60.32%), Query Frame = 1 
Query:    4 NTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIWCEPSIKMGNDVIEQSQGRETMIQAII 192
            N + IFNV+R  NG Y C+  N +E   S+  +L++   P+I+M N  I Q   R TM++A+I
Sbjct:  223 NHLQIFNVTRTMNGLYKCVAQNGLERMASRVIELDVHFPPTIRMANTKIGQLLYRTTMVRALI 285
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BLAST of Hmctn vs. TrEMBL
Match: A0A1S8X8Q7 (Immunoglobulin I-set domain protein (Fragment) OS=Opisthorchis viverrini OX=6198 GN=X801_00983 PE=4 SV=1)

HSP 1 Score: 51.9878 bits (123), Expect = 3.405e-6
Identity = 25/63 (39.68%), Postives = 38/63 (60.32%), Query Frame = 1 
Query:    4 NTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIWCEPSIKMGNDVIEQSQGRETMIQAII 192
            N + IFNV+R  NG Y C+  N +E   S+  +L++   P+I+M N  I Q   R TM++A+I
Sbjct:   64 NHLQIFNVTRTMNGLYKCVAQNGLERMASRVIELDVHFPPTIRMANTKIGQLLYRTTMVRALI 126
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BLAST of Hmctn vs. TrEMBL
Match: A0A4S2LSS5 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_005101 PE=4 SV=1)

HSP 1 Score: 52.373 bits (124), Expect = 3.635e-6
Identity = 25/63 (39.68%), Postives = 38/63 (60.32%), Query Frame = 1 
Query:    4 NTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIWCEPSIKMGNDVIEQSQGRETMIQAII 192
            N + IFNV+R  NG Y C+  N +E   S+  +L++   P+I+M N  I Q   R TM++A+I
Sbjct:  250 NHLQIFNVTRTMNGLYKCMAQNGLERMASRVIELDVHFPPTIRMANTKIGQLLYRTTMVRALI 312
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BLAST of Hmctn vs. Planmine SMEST
Match: SMESG000006452.1 (SMESG000006452.1)

HSP 1 Score: 132.88 bits (333), Expect = 1.366e-38
Identity = 64/65 (98.46%), Postives = 64/65 (98.46%), Query Frame = 1 
Query:    1 YNTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIWCEPSIKMGNDVIEQSQGRETMIQAIIN 195
            YNTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIW EPSIKMGNDVIEQSQGRETMIQAIIN
Sbjct:  259 YNTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIWYEPSIKMGNDVIEQSQGRETMIQAIIN 323
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BLAST of Hmctn vs. Planmine SMEST
Match: SMESG000006452.1 (SMESG000006452.1)

HSP 1 Score: 132.494 bits (332), Expect = 1.604e-38
Identity = 64/65 (98.46%), Postives = 64/65 (98.46%), Query Frame = 1 
Query:    1 YNTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIWCEPSIKMGNDVIEQSQGRETMIQAIIN 195
            YNTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIW EPSIKMGNDVIEQSQGRETMIQAIIN
Sbjct:  253 YNTVTIFNVSRIHNGSYTCIVDNKVEGKQSKSFKLEIWYEPSIKMGNDVIEQSQGRETMIQAIIN 317
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BLAST of Hmctn vs. Planmine SMEST
Match: SMESG000067482.1 (SMESG000067482.1)

HSP 1 Score: 41.2022 bits (95), Expect = 9.330e-6
Identity = 20/62 (32.26%), Postives = 34/62 (54.84%), Query Frame = 1 
Query:   16 IFNVSRIH---NGSYTCIVDNKVEGKQSKSFKLEIWCEPSIKMGNDVIEQSQGRETMIQAII 192
            +  +SR+H    G Y C+ +NKVE +    F+L +  +P I M N  I Q    +T+I+ ++
Sbjct:  194 MLQISRVHRDMTGFYACVANNKVEPEARSKFQLIVKFKPEIVMTNSEIHQRLKGDTVIECVV 255
The following BLAST results are available for this feature:
BLAST of Hmctn 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 Hmctn 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 Hmctn 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 Hmctn 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 Hmctn 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 Hmctn 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 Hmctn 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 Hmctn vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
S5WES36.061e-3696.92Hmctn (Fragment) OS=Schmidtea mediterranea OX=7932... [more]
H2KUX22.631e-639.68Opioid-binding protein/cell adhesion molecule homo... [more]
A0A419Q3062.896e-639.68Opioid-binding protein/cell adhesion molecule-like... [more]
A0A1S8X8Q73.405e-639.68Immunoglobulin I-set domain protein (Fragment) OS=... [more]
A0A4S2LSS53.635e-639.68Uncharacterized protein OS=Opisthorchis felineus O... [more]
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BLAST of Hmctn 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 Hmctn 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 Hmctn 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 Hmctn 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 Hmctn 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 Hmctn vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000006452.11.366e-3898.46SMESG000006452.1[more]
SMESG000006452.11.604e-3898.46SMESG000006452.1[more]
SMESG000067482.19.330e-632.26SMESG000067482.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004914 ID=SMED30004914|Name=Hmctn|organism=Schmidtea mediterranea sexual|type=transcript|length=196bp
TATAACACAGTTACAATTTTTAACGTTTCCCGAATTCATAACGGTTCATA
CACTTGCATCGTTGACAACAAAGTTGAGGGTAAGCAGTCAAAATCTTTCA
AATTAGAAATATGGTGTGAACCCTCTATCAAAATGGGCAATGATGTCATT
GAACAGTCCCAAGGACGCGAAACCATGATTCAGGCAATAATAAACG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000105secretory cell
PLANA:0000143ventral region of the whole animal
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0000481serotonergic neuron
Vocabulary: INTERPRO
TermDefinition
IPR036179Ig-like_dom_sf
IPR013783Ig-like_fold
IPR007110Ig-like_dom
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
IPR013783Immunoglobulin-like foldGENE3DG3DSA:2.60.40.10coord: 1..51
e-value: 8.7E-8
score: 34.1
NoneNo IPR availableCDDcd00096Igcoord: 3..34
e-value: 0.00176174
score: 31.0585
IPR036179Immunoglobulin-like domain superfamilySUPERFAMILYSSF48726Immunoglobulincoord: 3..44