SMED30007237

Overview
NameSMED30007237
Smed IDSMED30007237
Length (bp)890
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



SMED30007237

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30007237 SmedASXL_072405SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30007237 dd_Smed_v4_9607_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007237 dd_Smed_v4_9607_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30007237 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003526:4949..5841 +3552
v31.000752:69322..70213 -3550
v31.000709:35292..36150 -3326
v31.000785:28251..29112 -3269
Homology
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BLAST of SMED30007237 vs. Planmine SMEST
Match: SMESG000015007.1 (SMESG000015007.1)

HSP 1 Score: 209.534 bits (532), Expect = 2.882e-66
Identity = 106/145 (73.10%), Postives = 117/145 (80.69%), Query Frame = -1 
Query:   33 MSSYSNPTTSDLPRIPRLSPSVVALRHRYEELKQQHTALRTKYERVKGTWASPETVKELHQKIARLTRTREEFIAESHSQRLLIKEQAISLRQAFSDVEFQTHVAGSFRALHLNIIPEHHLPIAGLPSIPSTSAPPLMESPQVPV 467
            M+S SN +T+DLPRIPRLSPSVVA+R +YEELK QH ALR KYERVKGTWA PETV+ L Q+IARLT  REE IAES SQRLLIKEQA +LRQAF+DVE QTHV GS RA  LNIIP HHLPI  LP  P+ S  P MESPQ+PV
Sbjct:    1 MNSPSNSSTNDLPRIPRLSPSVVAMRQKYEELKLQHAALRAKYERVKGTWAPPETVRGLLQEIARLTEAREELIAESRSQRLLIKEQATALRQAFTDVELQTHVPGSVRAHQLNIIPAHHLPITKLPPTPTASTLPSMESPQIPV 145
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BLAST of SMED30007237 vs. Planmine SMEST
Match: SMESG000079367.1 (SMESG000079367.1)

HSP 1 Score: 190.66 bits (483), Expect = 1.145e-60
Identity = 93/155 (60.00%), Postives = 117/155 (75.48%), Query Frame = -1 
Query:    3 MSSYSNPTTSDLPRIPRLSPSVVALRHRYEELKQQHTALRTKYERVKGTWASPETVKELHQKIARLTRTREEFIAESHSQRLLIKEQAISLRQAFSDVEFQTHVAGSFRALHLNIIPEHHLPIAGLPSIPSTSAPPLMESPQVPVA*PSVNTAHR 467
            M++  N   + L RI RLSPSV+ALR R E+L+ ++ ++R KYER+KGTW+SP+  + LHQKI RL RTRE+ +AES SQRLLIKEQA +L QAF+DVE QT V G  R   LNIIP+HHLP+AG PSIP+ SAPP +ESP++PVA    N AHR
Sbjct:    1 MNTNVNSEVNSLSRISRLSPSVIALRQRLEDLETKYNSVRIKYERIKGTWSSPKATQGLHQKIERLARTREDLVAESRSQRLLIKEQATALLQAFTDVELQTLVPGCVRDRQLNIIPKHHLPLAGFPSIPTFSAPPPIESPRIPVAATPTNPAHR 155
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BLAST of SMED30007237 vs. Planmine SMEST
Match: SMESG000011446.1 (SMESG000011446.1)

HSP 1 Score: 187.193 bits (474), Expect = 1.491e-59
Identity = 89/131 (67.94%), Postives = 111/131 (84.73%), Query Frame = -1 
Query:   75 MSSYSNPTTSDLPRIPRLSPSVVALRHRYEELKQQHTALRTKYERVKGTWASPETVKELHQKIARLTRTREEFIAESHSQRLLIKEQAISLRQAFSDVEFQTHVAGSFRALHLNIIPEHHLPIAGLPSIPS 467
            M++ ++  TS+LPRIPRLSPSVVA+RH+YE+LK++H  LRTKYERVKGTWA PETV+EL QKIAR+T+ R+E IAES SQRLLI+EQA +LR+AF+DVEF+THV GS RA  LN+IP HHLP+  +P  PS
Sbjct:    1 MNTSTSSKTSELPRIPRLSPSVVAVRHKYEKLKREHEELRTKYERVKGTWAPPETVRELRQKIARITQARDELIAESRSQRLLIREQATALRRAFTDVEFRTHVPGSVRASQLNLIPAHHLPVDEVPPTPS 131
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BLAST of SMED30007237 vs. Planmine SMEST
Match: SMESG000071407.1 (SMESG000071407.1)

HSP 1 Score: 179.874 bits (455), Expect = 6.077e-56
Identity = 90/154 (58.44%), Postives = 111/154 (72.08%), Query Frame = -1 
Query:    6 MSSYSNPTTSDLPRIPRLSPSVVALRHRYEELKQQHTALRTKYERVKGTWASPETVKELHQKIARLTRTREEFIAESHSQRLLIKEQAISLRQAFSDVEFQTHVAGSFRALHLNIIPEHHLPIAGLPSIPSTSAPPLMESPQVPVA*PSVNTAH 467
            M++ S    ++LPRIPRLSPSVVALR + EEL+ +H  L+TKY+RVKGTW SPE  K LHQKI RL+R R+E IAES SQR+LIKEQ+ +LRQ F+D E +  + GS  A HLNIIPE HLP+  +   PSTSAP +ME PQ+ VA P    A 
Sbjct:    1 MNTNSRTDLNNLPRIPRLSPSVVALRQKLEELEGKHETLKTKYDRVKGTWTSPEAAKGLHQKIIRLSRARDELIAESRSQRVLIKEQSTTLRQIFTDAELRARIPGSVWARHLNIIPEQHLPMDTINPTPSTSAPQIMEPPQILVAEPRARAAQ 154
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BLAST of SMED30007237 vs. Planmine SMEST
Match: SMESG000038040.1 (SMESG000038040.1)

HSP 1 Score: 177.178 bits (448), Expect = 5.609e-54
Identity = 93/154 (60.39%), Postives = 113/154 (73.38%), Query Frame = -1 
Query:    6 MSSYSNPTTSDLPRIPRLSPSVVALRHRYEELKQQHTALRTKYERVKGTWASPETVKELHQKIARLTRTREEFIAESHSQRLLIKEQAISLRQAFSDVEFQTHVAGSFRALHLNIIPEHHLPIAGLPSIPSTSAPPLMESPQVPVA*PSVNTAH 467
            M++ S    ++L RIPRLSPSV+ALR R +E++ ++ +LRTKYER+KGTW+SPE  + LH+K+ RLTRTRE+ IAES SQRLLIKEQA +LRQAF+D   +THV GS RA  LNIIPEHHL IA  P IPST AP     P   VA  SVN  H
Sbjct:    1 MNTNSESAVNNLSRIPRLSPSVIALRQRLKEMEAKYNSLRTKYERIKGTWSSPEVTQALHRKVERLTRTREDLIAESRSQRLLIKEQATALRQAFTDEALRTHVPGSVRARQLNIIPEHHLRIAERPPIPSTLAP----LPAATVAVTSVNPVH 150
The following BLAST results are available for this feature:
BLAST of SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 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 SMED30007237 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000015007.12.882e-6673.10SMESG000015007.1[more]
SMESG000079367.11.145e-6060.00SMESG000079367.1[more]
SMESG000011446.11.491e-5967.94SMESG000011446.1[more]
SMESG000071407.16.077e-5658.44SMESG000071407.1[more]
SMESG000038040.15.609e-5460.39SMESG000038040.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007237 ID=SMED30007237|Name=SMED30007237|organism=Schmidtea mediterranea sexual|type=transcript|length=890bp
CGTCGATGGGCGGTGTTGACGCTTGGTCAGGCCACCGGAACTTGGGGCGA
CTCCATGAGTGGAGGAGCCGAGGTGGATGGAATCGATGGGAGTCCGGCGA
TCGGTAAATGATGTTCTGGGATTATGTTCAAGTGGAGAGCTCGAAAACTC
CCAGCGACATGAGTCTGAAATTCCACGTCCGAGAACGCCTGACGCAGGGA
AATGGCTTGCTCTTTAATTAGCAGCCGTTGGCTGTGGGACTCTGCTATAA
ACTCCTCCCGAGTCCGAGTTAGCCTTGCAATTTTCTGATGCAATTCTTTG
ACTGTTTCCGGCGAGGCCCAGGTGCCTTTTACTCGCTCATATTTGGTTCG
GAGCGCGGTATGTTGCTGTTTCAACTCCTCGTATCTGTGTCTGAGGGCCA
CCACTGACGGGGATAATCGTGGGATCCGCGGAAGATCGCTTGTCGTTGGG
TTGGAATAGGAACTCATGTCTAGAGATAGAAAAGGAATTCAAGAAATGGA
GAGTTAACGAGAGAAAATGAGGGAAAATCGACGGGAAAATTAGCAGAAGG
ACTTTATGAATATTAATTAGGCAGGCGGTTCACCAATTTACATTATCCCT
AGCTAGGGTTTGCAATTATTCGGGTTTCTATCATTGATTATTGGGCATTT
TGGACACCTAAACATCATCATGAGTTATTTTAATTCTATTACTGCAGTTA
ACGTTGACGGGATTAAACGCCATATAATTCGTTATATGGTCGTATTACTA
CTTTTCTGTCCTAATCGTTACTACAAATTTAACGTTGTCCTCATTAATGA
CTATTTCGGAATATAGAATCAGTGTAACTGATTATATACTCGCCCTACTA
GTATTCCCGTTTAATATTATAACGAATTACATTAATTCCT
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protein sequence of SMED30007237-orf-1

>SMED30007237-orf-1 ID=SMED30007237-orf-1|Name=SMED30007237-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=147bp
MSSYSNPTTSDLPRIPRLSPSVVALRHRYEELKQQHTALRTKYERVKGTW
ASPETVKELHQKIARLTRTREEFIAESHSQRLLIKEQAISLRQAFSDVEF
QTHVAGSFRALHLNIIPEHHLPIAGLPSIPSTSAPPLMESPQVPVA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head