SMED30006688

Overview
NameSMED30006688
Smed IDSMED30006688
Length (bp)502
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




SMED30006688

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
nervous systemSMED30006688SMESG000034453.1 dd_Smed_v4_59562_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30006688SMESG000034453.1 dd_Smed_v4_59562_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30006688SMESG000034453.1 dd_Smed_v4_59562_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30006688SMESG000034453.1 dd_Smed_v4_59562_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
SMED30006688 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011250:12060..12561 +2420
v31.011250:16128..16628 -2053
Homology
BLAST of SMED30006688 vs. Planmine SMEST
Match: SMESG000034453.1 (SMESG000034453.1)

HSP 1 Score: 331.643 bits (849), Expect = 7.295e-117
Identity = 160/167 (95.81%), Postives = 163/167 (97.60%), Query Frame = 2
Query:    2 TRCGIKAFNKYLKYFVMVNDSCHIPTAISAKSTLTPTRHIFEKISNIFTLLRIVNGSGVDPFEYLSNTSNPSSYGVTDKENNYTENYRSILLDEWDILQPINMNVTIRDFNDTVVAWLNFTVYSHDNISSWFNVGNLMDSFPWKKTSLIKKSYRFFSILGDKFRAIS 502
            TRCGIKAFNKY+KYFVMVNDSCHIPTAISAKSTLTPTRHIFEKISNIFTLLRIVNGSGVDPFEYLSNTSNPSSYGVTDKENNYTENYRSILLDEWD LQPINMNV IRDFNDTVVAWL+FTV +HDNISSWFN GNLMDSFPWKKTSLIKKSYRFFSILGDKFRAIS
Sbjct:   23 TRCGIKAFNKYVKYFVMVNDSCHIPTAISAKSTLTPTRHIFEKISNIFTLLRIVNGSGVDPFEYLSNTSNPSSYGVTDKENNYTENYRSILLDEWDTLQPINMNVIIRDFNDTVVAWLDFTVNNHDNISSWFNAGNLMDSFPWKKTSLIKKSYRFFSILGDKFRAIS 189          
BLAST of SMED30006688 vs. Planmine SMEST
Match: SMESG000076267.1 (SMESG000076267.1)

HSP 1 Score: 196.052 bits (497), Expect = 2.626e-63
Identity = 92/162 (56.79%), Postives = 120/162 (74.07%), Query Frame = 2
Query:    5 RCGIKAFNKYLKYFVMVNDSCHIPTAISAKSTLT-PTRHIFEKISNIFTLLRIVNGSGVDPFEYLSNTSNPSSYGVTDKENNYTENYRSILLDEWDILQPINMNVTIRDFNDTVVAWLNFTVYSHDNISSWFNVGNLMDSFPWKKTSLIKKSYRFFSILGDK 487
            RCG+KAF++ + YF MVN SC+IP AISA+ T + PT+ I+++I N  T+LRIVNGSGV P ++LS  SNPS+Y V D +NNY+EN+RS++LDEW  L+P  MNVTIR  N  +V WLNF V + DNI SWF +GNL+DSFPW    L    Y+FFS+ GD+
Sbjct:   25 RCGLKAFDRNIIYFAMVNKSCYIPKAISAQPTQSSPTKIIYQRIENTITVLRIVNGSGVYPPDFLSKLSNPSTYKVKDIQNNYSENFRSVILDEWSTLRPSGMNVTIRAVNKAIVGWLNFRVSAQDNIISWFTLGNLLDSFPWDINVLKNSLYKFFSVTGDR 186          
BLAST of SMED30006688 vs. Planmine SMEST
Match: SMESG000034379.1 (SMESG000034379.1)

HSP 1 Score: 172.17 bits (435), Expect = 1.907e-54
Identity = 85/151 (56.29%), Postives = 109/151 (72.19%), Query Frame = 2
Query:   50 MVNDSCHIPTAISAKSTLTPTRHIFEKISNIFTLLRIVNGSGVDPFEYLSNTSNPSSYGVTDKENNYTENYRSILLDEWDILQPINMNVTIRDFNDTVVAWLNFTVYSHDNISSWFNVGNLMDSFPWKKTSLIKKSYRFFSILGDK--FRA 496
            MVN+ C+ PTA SA+STL    +I+ ++SNI TLLRIVNGSGV P  YLSN   P  Y V +++ NY+ N+RSILLDEW  L+P  MNVTI+D +D +V WL F V + DNISSWF +GNL++SFPW    L  K+Y FFSI+GD+  FR+
Sbjct:    1 MVNNICYTPTAASAQSTLISNENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNASDNISSWFILGNLLNSFPWDTNMLKTKTYNFFSIVGDRTLFRS 151          
BLAST of SMED30006688 vs. Planmine SMEST
Match: SMESG000034462.1 (SMESG000034462.1)

HSP 1 Score: 169.474 bits (428), Expect = 2.044e-53
Identity = 85/151 (56.29%), Postives = 108/151 (71.52%), Query Frame = 2
Query:   50 MVNDSCHIPTAISAKSTLTPTRHIFEKISNIFTLLRIVNGSGVDPFEYLSNTSNPSSYGVTDKENNYTENYRSILLDEWDILQPINMNVTIRDFNDTVVAWLNFTVYSHDNISSWFNVGNLMDSFPWKKTSLIKKSYRFFSILGDK--FRA 496
            MVN+ C+ PTA SA+STL    +I+ ++SNI TLLRIVNGSGV P  YLSN   P  Y V +++ NY+ N+RSILLDEW  L+P  MNVTI+D +D +V WL F V S DNISSWF + NL++SFPW    L  K+Y FFSI+GD+  FR+
Sbjct:    1 MVNNICYTPTAASAQSTLISNENIYRRVSNILTLLRIVNGSGVYPPGYLSNMIYPPQYEVKERKGNYSMNFRSILLDEWSTLRPSYMNVTIKDVDDVIVGWLYFVVNSSDNISSWFILDNLLNSFPWDTNMLKTKTYNFFSIVGDRTLFRS 151          
BLAST of SMED30006688 vs. Planmine SMEST
Match: SMESG000076443.1 (SMESG000076443.1)

HSP 1 Score: 154.451 bits (389), Expect = 7.909e-47
Identity = 83/177 (46.89%), Postives = 109/177 (61.58%), Query Frame = 2
Query:    8 CGIKAFNKYLKYFVMVNDSCHIPTAISAKS-----------------TLTPTRHIFEKISNIFTLLRIVNGSGVDPFEYLSNTSNPSSYGVTDKENNYTENYRSILLDEWDILQPINMNVTIRDFNDTVVAWLNFTVYSHDNISSWFNVGNLMDSFPWKKTSLIKKSYRFFSILGDK 487
            C ++ F K L YF +V++ C  PT  +  +                 T T T+ ++ K+ N   LLRIVNGSGV P +YL+NT+NPS YGV D + N++EN+RSILLD+W   QP N+NVTIRD +D  V WL F+V+  DNI SWF   NL+DSFPW    L   +Y +FSI GDK
Sbjct:   25 CILQTFQKKLTYFSIVDNLCFTPTQPTQPTKSTQPTQSTQTTQSTQSTFTTTKAVYRKMGNTLILLRIVNGSGVYPPDYLANTTNPSPYGVKDYKRNFSENFRSILLDDWKRYQPSNLNVTIRDVSDVEVGWLYFSVFPKDNILSWFASTNLIDSFPWNINVLKNSTYNYFSINGDK 201          
The following BLAST results are available for this feature:
BLAST of SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 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 SMED30006688 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000034453.17.295e-11795.81SMESG000034453.1[more]
SMESG000076267.12.626e-6356.79SMESG000076267.1[more]
SMESG000034379.11.907e-5456.29SMESG000034379.1[more]
SMESG000034462.12.044e-5356.29SMESG000034462.1[more]
SMESG000076443.17.909e-4746.89SMESG000076443.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006688 ID=SMED30006688|Name=SMED30006688|organism=Schmidtea mediterranea sexual|type=transcript|length=502bp
CACCAGATGTGGAATAAAGGCTTTCAACAAGTACCTGAAATATTTTGTCA
TGGTCAATGATTCGTGTCACATTCCAACTGCAATATCCGCAAAATCAACG
CTCACACCCACACGGCATATTTTTGAGAAAATAAGCAACATTTTTACCTT
GCTTAGAATTGTGAATGGCAGCGGTGTAGACCCCTTTGAGTATCTCTCGA
ATACGTCAAATCCATCCTCATACGGAGTGACAGACAAGGAAAATAACTAC
ACAGAGAACTACCGAAGCATTCTTTTAGATGAGTGGGATATCTTGCAACC
TATTAATATGAATGTCACTATAAGAGACTTTAATGATACGGTTGTTGCTT
GGCTGAACTTTACGGTGTACAGCCACGACAATATCTCCTCTTGGTTCAAT
GTCGGCAATTTAATGGATTCCTTTCCTTGGAAGAAAACAAGTTTGATAAA
AAAGAGTTATCGGTTTTTTAGTATTTTAGGAGACAAATTTCGAGCTATAT
CG
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protein sequence of SMED30006688-orf-1

>SMED30006688-orf-1 ID=SMED30006688-orf-1|Name=SMED30006688-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=167bp
TRCGIKAFNKYLKYFVMVNDSCHIPTAISAKSTLTPTRHIFEKISNIFTL
LRIVNGSGVDPFEYLSNTSNPSSYGVTDKENNYTENYRSILLDEWDILQP
INMNVTIRDFNDTVVAWLNFTVYSHDNISSWFNVGNLMDSFPWKKTSLIK
KSYRFFSILGDKFRAIS
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