SMED30004187

Overview
NameSMED30004187
Smed IDSMED30004187
Length (bp)357
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



SMED30004187

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



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30004187SMESG000043423.1 Contig1792newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30004187SMESG000043423.1 Contig1792uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30004187SMESG000043423.1 Contig1792newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30004187SMESG000043423.1 Contig1792uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30004187SMESG000043423.1 Contig1792newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004187SMESG000043423.1 Contig1792uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30004187SMESG000072544.1 Contig1792newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30004187SMESG000072544.1 Contig1792uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30004187SMESG000072544.1 Contig1792newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30004187SMESG000072544.1 Contig1792uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30004187SMESG000072544.1 Contig1792newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004187SMESG000072544.1 Contig1792uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
prepharyngeal regionSMED30004187SMESG000043423.1 SmedASXL_018913SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30004187SMESG000043423.1 tr5_10443mu_Smed_v1PMID:25558068
Reuter et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30004187SMESG000043423.1 dd_Smed_v4_1028_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004187SMESG000043423.1 Contig1792newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004187SMESG000043423.1 Contig1792uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004187SMESG000072544.1 Contig1792newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004187SMESG000072544.1 Contig1792uc_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
Alignments
SMED30004187 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.018650:5916..6340 -1760
Homology
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BLAST of SMED30004187 vs. Planmine SMEST
Match: SMESG000043423.1 (SMESG000043423.1)

HSP 1 Score: 175.252 bits (443), Expect = 2.231e-58
Identity = 83/83 (100.00%), Postives = 83/83 (100.00%), Query Frame = 3 
Query:   54 IVPIFCDLETYQDSEDEAEVTEKELDHYNDEKLENGAKKVLRYRYCTSRFCRFYWNRWFSCFILFYAPIGIRSRCGPKKIYCL 302
            IVPIFCDLETYQDSEDEAEVTEKELDHYNDEKLENGAKKVLRYRYCTSRFCRFYWNRWFSCFILFYAPIGIRSRCGPKKIYCL
Sbjct:   13 IVPIFCDLETYQDSEDEAEVTEKELDHYNDEKLENGAKKVLRYRYCTSRFCRFYWNRWFSCFILFYAPIGIRSRCGPKKIYCL 95
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BLAST of SMED30004187 vs. Planmine SMEST
Match: SMESG000043393.1 (SMESG000043393.1)

HSP 1 Score: 50.447 bits (119), Expect = 4.199e-9
Identity = 27/75 (36.00%), Postives = 43/75 (57.33%), Query Frame = 3 
Query:   81 TYQDSEDEAEVTEKELDHYNDEKLENGAKKVLRYRYCTSRFCRFYWN-RWFSCFILFYAPIGIRSRCGPKKIYCL 302
            T  +S D   + E+E++  ND++ EN  K  +++RYC  R CR Y+  RWF+C + FY    I   C P++  C+
Sbjct:   27 TNDESFDVKSLKEEEIEEGNDKEEENDTKLFIKHRYCGLRTCRLYFGRRWFTCTVRFYR---IGRLCKPRRFACV 98
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BLAST of SMED30004187 vs. Planmine SMEST
Match: SMESG000043388.1 (SMESG000043388.1)

HSP 1 Score: 49.2914 bits (116), Expect = 1.196e-8
Identity = 26/75 (34.67%), Postives = 43/75 (57.33%), Query Frame = 3 
Query:   81 TYQDSEDEAEVTEKELDHYNDEKLENGAKKVLRYRYCTSRFCRFYWN-RWFSCFILFYAPIGIRSRCGPKKIYCL 302
            T  +S D   + E+E++  ND++ EN  K ++++RYC  R CR ++  RWF+C + FY    I   C P +  C+
Sbjct:   27 TNDESFDVKSLKEEEIEEGNDKEEENDTKLLIKHRYCGLRTCRLHFGRRWFTCTVRFYR---IGRLCKPSRFNCV 98
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BLAST of SMED30004187 vs. Planmine SMEST
Match: SMESG000040596.1 (SMESG000040596.1)

HSP 1 Score: 42.743 bits (99), Expect = 3.192e-6
Identity = 29/75 (38.67%), Postives = 42/75 (56.00%), Query Frame = 3 
Query:   81 TYQDSEDEAEVTEKELDHYNDEKLENGAKKVLRYRYCTSRFCRFYWN-RWFSCFILFYAPIGIRSRCGPKKIYCL 302
            T  +S D   + E+EL+  ND++ EN  K   R RYC  R CRF++  RWF+C + FY     R  C P++  C+
Sbjct:   27 TNDESFDVKSLKEEELEEGNDKEEENDTKLFKRRRYCGLRTCRFFFGRRWFTCTVRFYRS---RRLCKPRRFSCV 98
The following BLAST results are available for this feature:
BLAST of SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 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 SMED30004187 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000043423.12.231e-58100.00SMESG000043423.1[more]
SMESG000043393.14.199e-936.00SMESG000043393.1[more]
SMESG000043388.11.196e-834.67SMESG000043388.1[more]
SMESG000040596.13.192e-638.67SMESG000040596.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004187 ID=SMED30004187|Name=SMED30004187|organism=Schmidtea mediterranea sexual|type=transcript|length=357bp
CCGACACGAATTTAATCATGAAGCTTTTCTACTTACTTTTAGGACTATTG
CTGATTGTTCCGATTTTCTGTGATTTGGAAACGTATCAGGATTCCGAGGA
TGAAGCGGAAGTGACAGAAAAAGAATTGGATCATTATAACGATGAGAAAC
TGGAAAATGGAGCTAAAAAAGTACTACGATATCGATATTGTACTTCGAGA
TTCTGTAGGTTTTACTGGAACCGTTGGTTTTCATGCTTCATTCTATTCTA
CGCACCGATTGGCATCAGATCAAGATGTGGCCCAAAGAAAATATATTGTC
TTTAATGGAATTTGACTTTGAAATATAACTGAAGGTTTTGAAAATAAATA
ATAAATT
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protein sequence of SMED30004187-orf-1

>SMED30004187-orf-1 ID=SMED30004187-orf-1|Name=SMED30004187-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
DTNLIMKLFYLLLGLLLIVPIFCDLETYQDSEDEAEVTEKELDHYNDEKL
ENGAKKVLRYRYCTSRFCRFYWNRWFSCFILFYAPIGIRSRCGPKKIYCL
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000044cephalic ganglia
PLANA:0000070intestinal phagocyte
PLANA:0000419prepharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 28..48
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..23
score: 0.823
NoneNo IPR availableTMHMMTMhelixcoord: 4..23
NoneNo IPR availableTMHMMTMhelixcoord: 70..88