SMED30018670

Overview
NameSMED30018670
Smed IDSMED30018670
Length (bp)373
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



SMED30018670

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30018670 SmedASXL_076292SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30018670 SmedASXL_076292SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30018670 vs. Planmine SMEST
Match: SMESG000059479.1 (SMESG000059479.1)

HSP 1 Score: 105.916 bits (263), Expect = 7.487e-30
Identity = 83/104 (79.81%), Postives = 89/104 (85.58%), Query Frame = -2 
Query:   40 LNRIPANHLPVAELPPTPSALVVPPAEIAVETNANPAHXXXXXXXXXXXXXXXXXXXPIKGPCRIDDLPPPYQEFEIPWLDPDILYAPTVTLPPLAPQIHINLV 351
            +N I A++LPV ELPPT SALVVPPAEI VETNANPA RRPNRNRRR E ELLRETEPI+GPCRIDDLPPPYQEFEIP LDPD+ YAP    PP APQIHI+LV
Sbjct:    1 MNIILAHNLPVTELPPTSSALVVPPAEITVETNANPARRRPNRNRRRWEVELLRETEPIEGPCRIDDLPPPYQEFEIPGLDPDVPYAPMAVFPPRAPQIHIDLV 104
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BLAST of SMED30018670 vs. Planmine SMEST
Match: SMESG000015007.1 (SMESG000015007.1)

HSP 1 Score: 105.916 bits (263), Expect = 9.853e-29
Identity = 71/114 (62.28%), Postives = 82/114 (71.93%), Query Frame = -2 
Query:   40 SVRASQLNRIPANHLPVAELPPTPSALVVPPAEI----AVETNANPAHXXXXXXXXXXXXXXXXXXXPIKGPCRIDDLPPPYQEFEIPWLDPDILYAPTVTLPPLAPQIHINLV 369
            SVRA QLN IPA+HLP+ +LPPTP+A  +P  E      +E+ A+PAHRRPNRNRRR +         I+GPCR+DDLPP YQEFEIP LDPDILYAP VT P  A  IHINLV
Sbjct:  107 SVRAHQLNIIPAHHLPITKLPPTPTASTLPSMESPQIPVMESPAHPAHRRPNRNRRRSDRRRRETEP-IEGPCRVDDLPPHYQEFEIPGLDPDILYAPNVTFPSRASLIHINLV 219
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BLAST of SMED30018670 vs. Planmine SMEST
Match: SMESG000075471.1 (SMESG000075471.1)

HSP 1 Score: 79.337 bits (194), Expect = 3.417e-18
Identity = 50/110 (45.45%), Postives = 58/110 (52.73%), Query Frame = -2 
Query:   40 SVRASQLNRIPANHLPVAELPPTPSALVVPPAEIAVETNANPAHXXXXXXXXXXXXXXXXXXXPIKGPCRIDDLPPPYQEFEIPWLDPDILYAPTVTLPPLAPQIHINLV 369
            SV A QLN IP +HLP+ E PPT SAL   P     ET+ NP+  +                       +    PP   EFEIP LDP+ILYAPT T PPLA QIHINL+
Sbjct:  107 SVGARQLNIIPEHHLPIVEPPPTLSALFSLPQATVAETSVNPSQSKATT-------------------SQGSGAPPGNGEFEIPGLDPNILYAPTATFPPLATQIHINLM 197

HSP 2 Score: 53.5286 bits (127), Expect = 3.138e-9
Identity = 26/43 (60.47%), Postives = 31/43 (72.09%), Query Frame = -2 
Query:   40 PCRIDDLPPPYQEFEIPWLDPDILYAPTVTLPPLAPQIHINLV 168
            P R +DLPPPYQEFE P  DPDI+YAP++     A  I+INLV
Sbjct:  417 PNRENDLPPPYQEFEFPNFDPDIIYAPSMINHSPARSIYINLV 459
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BLAST of SMED30018670 vs. Planmine SMEST
Match: SMESG000034473.1 (SMESG000034473.1)

HSP 1 Score: 72.4034 bits (176), Expect = 9.420e-16
Identity = 54/114 (47.37%), Postives = 60/114 (52.63%), Query Frame = -2 
Query:   40 SVRASQLNRIPANHLPVAELPPTPSALVVPPAEIAVETNANPAHXXXXXXXXXXXXXXXXX----XXPIKGPCRIDDLPPPYQEFEIPWLDPDILYAPTVTLPPLAPQIHINLV 369
            SV A  LN IP  H P+    PTPS    P   IA   +     R     RRR    +  E    TEP   P RIDDL PPYQEF+IP LDPD+LYAP+ T    A  IHINLV
Sbjct:  947 SVWARHLNIIPEQHFPLEAANPTPST-SAPQIPIAKPRSGAARRRPNRNRRRRERRRMEAELLRETEPSSAPYRIDDLLPPYQEFKIPGLDPDVLYAPSATFYSPARSIHINLV 1059
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BLAST of SMED30018670 vs. Planmine SMEST
Match: SMESG000034473.1 (SMESG000034473.1)

HSP 1 Score: 70.4774 bits (171), Expect = 3.903e-15
Identity = 54/114 (47.37%), Postives = 60/114 (52.63%), Query Frame = -2 
Query:   40 SVRASQLNRIPANHLPVAELPPTPSALVVPPAEIAVETNANPAHXXXXXXXXXXXXXXXXX----XXPIKGPCRIDDLPPPYQEFEIPWLDPDILYAPTVTLPPLAPQIHINLV 369
            SV A  LN IP  H P+    PTPS    P   IA   +     R     RRR    +  E    TEP   P RIDDL PPYQEF+IP LDPD+LYAP+ T    A  IHINLV
Sbjct:  639 SVWARHLNIIPEQHFPLEAANPTPST-SAPQIPIAKPRSGAARRRPNRNRRRRERRRMEAELLRETEPSSAPYRIDDLLPPYQEFKIPGLDPDVLYAPSATFYSPARSIHINLV 751
The following BLAST results are available for this feature:
BLAST of SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 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 SMED30018670 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000059479.17.487e-3079.81SMESG000059479.1[more]
SMESG000015007.19.853e-2962.28SMESG000015007.1[more]
SMESG000075471.13.417e-1845.45SMESG000075471.1[more]
SMESG000034473.19.420e-1647.37SMESG000034473.1[more]
SMESG000034473.13.903e-1547.37SMESG000034473.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018670 ID=SMED30018670|Name=SMED30018670|organism=Schmidtea mediterranea sexual|type=transcript|length=373bp
CGAGGGCTTGGGAGACTCCGGGGAGTCTGAGTCTTCATCCACTAGATTTA
TGTGGATTTGGGGAGCTAGTGGTGGTAAGGTCACGGTCGGAGCGTACAGT
ATGTCCGGATCGAGCCACGGAATCTCGAATTCCTGGTATGGGGGCGGTAG
ATCATCGATCCGGCACGGACCTTTGATGGGCTCCGTTTCCCGGAGGAGCT
CCTCTTCCCGGCGGCGCCGGTTCCGATTTGGTCGTCGGTGGGCCGGATTT
GCATTAGTCTCCACCGCGATTTCTGCCGGTGGAACGACAAGAGCGGAAGG
AGTCGGTGGGAGCTCGGCGACAGGGAGATGATTGGCCGGAATTCTATTCA
ATTGGCTGGCTCGAACACTTACG
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protein sequence of SMED30018670-orf-1

>SMED30018670-orf-1 ID=SMED30018670-orf-1|Name=SMED30018670-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=124bp
VSVRASQLNRIPANHLPVAELPPTPSALVVPPAEIAVETNANPAHRRPNR
NRRRREEELLRETEPIKGPCRIDDLPPPYQEFEIPWLDPDILYAPTVTLP
PLAPQIHINLVDEDSDSPESPKPS
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell