SMED30013218

Overview
NameSMED30013218
Smed IDSMED30013218
Length (bp)272
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



SMED30013218

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30013218 SmedASXL_037403SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30013218 SmedASXL_037403SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30013218 GU295178smed_ncbi_20240424PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
reproductive organSMED30013218 Contig10632newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013218 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002395:32822..33184 +1159
Homology
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BLAST of SMED30013218 vs. TrEMBL
Match: E3T7U0 (Secreted peptide prohormone 7 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 114.39 bits (285), Expect = 1.135e-31
Identity = 56/57 (98.25%), Postives = 56/57 (98.25%), Query Frame = -3 
Query:   97 MKFIISLFVVLFLCVVMAMSEIDKRTVGFGFNRNLHLYKRMLEKRLIDPMTFGSGFV 267
            MKFIISLFVVLFLCVVMAMSEIDKRTVGFGFNRNLHLYKRMLEKRLIDPMTFGSGF 
Sbjct:    1 MKFIISLFVVLFLCVVMAMSEIDKRTVGFGFNRNLHLYKRMLEKRLIDPMTFGSGFA 57
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BLAST of SMED30013218 vs. TrEMBL
Match: E3T7U3 (Secreted peptide prohormone 8 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 82.8037 bits (203), Expect = 4.552e-19
Identity = 39/57 (68.42%), Postives = 46/57 (80.70%), Query Frame = -3 
Query:   97 MKFIISLFVVLFLCVVMAMSEIDKRTVGFGFNRNLHLYKRMLEKRLIDPMTFGSGFV 267
            MK II L + L +C   A+ E++KRT+GFGFNRN+ LYKRMLEKRLIDPMTFGSGF 
Sbjct:    1 MKIIILLAIFLAVCAFEALGEVEKRTMGFGFNRNMLLYKRMLEKRLIDPMTFGSGFA 57
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BLAST of SMED30013218 vs. TrEMBL
Match: E3T7T9 (Secreted peptide prohormone 6 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 4.542e-15
Identity = 31/57 (54.39%), Postives = 43/57 (75.44%), Query Frame = -3 
Query:  100 NMKFIISLFVVLFLCVVMAMSEIDKRTVGFGFNRNLHLYKRMLEKRLIDPMTFGSGF 270
             ++ ++S+ + + +C+   ++EIDKR  G GFNRN  +YKRMLEKRLIDPMTFG GF
Sbjct:    3 KIRILMSVLLFMAICLAAGLAEIDKRIPGIGFNRNFAIYKRMLEKRLIDPMTFGYGF 59
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BLAST of SMED30013218 vs. TrEMBL
Match: A0A193PE78 (Neuropeptide-42 (Fragment) OS=Dugesia japonica OX=6161 GN=DjNp42 PE=2 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 4.647e-13
Identity = 29/42 (69.05%), Postives = 35/42 (83.33%), Query Frame = -3 
Query:  103 CVVMAMSEIDKRTVGFGFNRNLHLYKRMLEKRLIDPMTFGSG 228
            C + A+ E++KRT+GFG N N  LYKR+LEKRLIDPMTFGSG
Sbjct:    2 CAMGALCELEKRTMGFGLNSNYRLYKRLLEKRLIDPMTFGSG 43
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BLAST of SMED30013218 vs. TrEMBL
Match: E3CTK1 (Secreted peptide prohormone-9 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 51.9878 bits (123), Expect = 6.275e-7
Identity = 25/56 (44.64%), Postives = 35/56 (62.50%), Query Frame = -3 
Query:  100 MKFIISLFVVLFLCVVMAMSEIDKRTVGFGFNRNLHLYKRMLEKRLIDPMTFGSGF 267
            M  +I L +V  +C+      + KR++ +  N    LYKR +EKRLIDP+TFGSGF
Sbjct:    1 MNSLIILLIVALVCLANVCCGVQKRSLPY--NPEYELYKRFVEKRLIDPLTFGSGF 54
The following BLAST results are available for this feature:
BLAST of SMED30013218 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 SMED30013218 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 SMED30013218 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 SMED30013218 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 SMED30013218 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 SMED30013218 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 SMED30013218 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 SMED30013218 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
E3T7U01.135e-3198.25Secreted peptide prohormone 7 OS=Schmidtea mediter... [more]
E3T7U34.552e-1968.42Secreted peptide prohormone 8 OS=Schmidtea mediter... [more]
E3T7T94.542e-1554.39Secreted peptide prohormone 6 OS=Schmidtea mediter... [more]
A0A193PE784.647e-1369.05Neuropeptide-42 (Fragment) OS=Dugesia japonica OX=... [more]
E3CTK16.275e-744.64Secreted peptide prohormone-9 OS=Schmidtea mediter... [more]
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BLAST of SMED30013218 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 SMED30013218 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 SMED30013218 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 SMED30013218 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 SMED30013218 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 SMED30013218 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013218 ID=SMED30013218|Name=SMED30013218|organism=Schmidtea mediterranea sexual|type=transcript|length=272bp
TTTTTTTNTTTTTTTTTTNTTTTTTTTTTAGTTTTGAGAAATGATTTATT
CATCAATATTTAACAAAAATTAATGAAAAATCATCATTTAAGATTTGACG
AATCCTGATCCGAAAGTCATTGGGTCGATGAGGCGTTTTTCCAGCATCCT
TTTGTAAAGATGGAGATTCCTATTGAACCCGAATCCCACAGTCCGTTTGT
CTATTTCCGACATGGCCATCACGACGCAGAGAAACAAGACGACAAATAAG
GAAATGATAAATTTCATATTTC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.881
NoneNo IPR availableTMHMMTMhelixcoord: 4..23