SMED30033184

Overview
NameSMED30033184
Smed IDSMED30033184
Length (bp)614
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



SMED30033184

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 3 cellSMED30033184 dd_Smed_v4_16881_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033184 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000478:135503..136094 -2889
Homology
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BLAST of SMED30033184 vs. Planmine SMEST
Match: SMESG000042773.1 (SMESG000042773.1)

HSP 1 Score: 186.422 bits (472), Expect = 7.100e-60
Identity = 100/140 (71.43%), Postives = 109/140 (77.86%), Query Frame = -3 
Query:  193 AENALLQVNLRGSEDMEL*ELSNLMMTESTTSRNDDELSVIYAPRQPDFTHPVHTPAQITITTTSHSAEAPIIIQISILSRTTPDPKIPSIRRSSPQIVFVVKPTTVRNLRANNSHQSGLIPTSRPPKRRYLPVDIDGED 612
            AENAL Q NLR  EDMEL E S+++  EST   N+DELSV YAPRQPDFTHPV TPAQITITT SHSAEAPI IQIS  SRTTPD + PS  RSSPQI+ VV+PT  RN R NNS+Q+   P SR PKRRYLPVDIDGED
Sbjct:   56 AENAL-QANLRRGEDMELIEFSDMIRAESTNFGNEDELSVTYAPRQPDFTHPVPTPAQITITTNSHSAEAPINIQISTSSRTTPDQEFPSSGRSSPQIISVVEPTITRNQRVNNSNQTDPNPISRSPKRRYLPVDIDGED 194
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BLAST of SMED30033184 vs. Planmine SMEST
Match: SMESG000056978.1 (SMESG000056978.1)

HSP 1 Score: 180.644 bits (457), Expect = 1.297e-57
Identity = 97/140 (69.29%), Postives = 106/140 (75.71%), Query Frame = -3 
Query:  193 AENALLQVNLRGSEDMEL*ELSNLMMTESTTSRNDDELSVIYAPRQPDFTHPVHTPAQITITTTSHSAEAPIIIQISILSRTTPDPKIPSIRRSSPQIVFVVKPTTVRNLRANNSHQSGLIPTSRPPKRRYLPVDIDGED 612
            AEN LL+ NLRGS+  EL E S++M  ESTT RNDDELSVIYA RQPDFTHPV TPAQITI T SHS E  I IQIS  SRTT D +IPS  RSSPQI+ VV+P   RN R +NSHQ+G  P SR PK RYLPVDIDGED
Sbjct:   56 AENTLLKANLRGSDGPELIEFSDIMTAESTTFRNDDELSVIYASRQPDFTHPVPTPAQITIATNSHSVEVLINIQISTSSRTTLDREIPSSGRSSPQIISVVEPRITRNQRVSNSHQTGPNPASRSPKCRYLPVDIDGED 195
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BLAST of SMED30033184 vs. Planmine SMEST
Match: SMESG000057066.1 (SMESG000057066.1)

HSP 1 Score: 174.096 bits (440), Expect = 4.306e-55
Identity = 92/139 (66.19%), Postives = 105/139 (75.54%), Query Frame = -3 
Query:  193 ENALLQVNLRGSEDMEL*ELSNLMMTESTTSRNDDELSVIYAPRQPDFTHPVHTPAQITITTTSHSAEAPIIIQISILSRTTPDPKIPSIRRSSPQIVFVVKPTTVRNLRANNSHQSGLIPTSRPPKRRYLPVDIDGED 609
            +NALLQ NL GS+  +L  +  +MMTEST  RNDDEL+VIYA RQPDFTH V T AQITITT+SHSAE PI I IS  SRTTPD  +PS  R  PQI+ VV+PT  RN  A+N HQ+G  PT+RP KRRYLPVDIDGED
Sbjct:   57 KNALLQANLGGSDGTDLMGICEIMMTESTAFRNDDELNVIYARRQPDFTHSVPTLAQITITTSSHSAEVPINIHISTSSRTTPDRDVPSSGRFLPQIISVVEPTVSRNQMASNFHQTGSNPTTRPSKRRYLPVDIDGED 195
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BLAST of SMED30033184 vs. Planmine SMEST
Match: SMESG000068296.1 (SMESG000068296.1)

HSP 1 Score: 161.77 bits (408), Expect = 3.271e-50
Identity = 87/139 (62.59%), Postives = 99/139 (71.22%), Query Frame = -3 
Query:  193 ENALLQVNLRGSEDMEL*ELSNLMMTESTTSRNDDELSVIYAPRQPDFTHPVHTPAQITITTTSHSAEAPIIIQISILSRTTPDPKIPSIRRSSPQIVFVVKPTTVRNLRANNSHQSGLIPTSRPPKRRYLPVDIDGED 609
            ENALLQ NL GS+   L  +  +MMTEST  RNDDEL+VIYA RQP FTH V T  QITITT+SHSAE PI I I   SR TPD  +P+   S PQI+ VV+PT  RN  A+N HQ+G  P +RP KRRYLPVDIDGED
Sbjct:   57 ENALLQANLGGSDGTNLIGICEIMMTESTAFRNDDELNVIYARRQPGFTHSVPTMVQITITTSSHSAEVPINIHIPTSSRKTPDRDVPTSGLSLPQIISVVEPTVSRNQMASNFHQTGPNPATRPSKRRYLPVDIDGED 195
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BLAST of SMED30033184 vs. Planmine SMEST
Match: SMESG000026554.1 (SMESG000026554.1)

HSP 1 Score: 149.828 bits (377), Expect = 3.344e-46
Identity = 77/128 (60.16%), Postives = 95/128 (74.22%), Query Frame = -3 
Query:  229 AENALLQVNLRGSEDMEL*ELSNLMMTESTTSRNDDELSVIYAPRQPDFTHPVHTPAQITITTTSHSAEAPIIIQISILSRTTPDPKIPSIRRSSPQIVFVVKPTTVRNLRANNSHQSGLIPTSRPPK 612
            A+NALLQ NL GSED EL  ++ +M  E    RND++L++IYAPRQPDF+ PV +PAQITITT SHSAE PI IQIS  SRTTPD   PS  R SPQI+ V++PT  RN RANN H++G   +++PPK
Sbjct:   19 AKNALLQANLGGSEDTELMRITEIMTAEPIVLRNDEDLNIIYAPRQPDFSQPVPSPAQITITTGSHSAEIPISIQISTSSRTTPDRNAPSSGRYSPQIISVIEPTVSRNQRANNLHRTGSSSSTKPPK 146
The following BLAST results are available for this feature:
BLAST of SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 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 SMED30033184 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000042773.17.100e-6071.43SMESG000042773.1[more]
SMESG000056978.11.297e-5769.29SMESG000056978.1[more]
SMESG000057066.14.306e-5566.19SMESG000057066.1[more]
SMESG000068296.13.271e-5062.59SMESG000068296.1[more]
SMESG000026554.13.344e-4660.16SMESG000026554.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033184 ID=SMED30033184|Name=SMED30033184|organism=Schmidtea mediterranea sexual|type=transcript|length=614bp
TGAAGATAGCCTAGGCTATCTTCACCAATCATGCATAAATGTTTAACTAC
AAAAACAACAAAAAAAATTTTATCGATTGACAGTTAGATTTTCACAATAA
AACGTAAATTTTATTGCGGTCACTATATTATTTATTATCAAATTCATTTT
GGTGAAGATAGCCTTATTATAAATTGTGGAAATTTCGCTTCAGTCCTCTC
CATCAATGTCCACTGGAAGGTACCGACGTTTGGGTGGCCTTGATGTTGGA
ATTAAACCACTTTGATGGGAATTGTTCGCTCTCAGATTTCGCACCGTTGT
CGGTTTAACGACAAAGACGATCTGTGGCGAAGATCGCCGGATAGAAGGAA
TTTTTGGGTCTGGAGTTGTTCGGGATAAGATGGATATTTGGATAATAATT
GGTGCCTCGGCAGAGTGACTAGTTGTGGTGATTGTAATTTGTGCCGGGGT
GTGGACGGGATGAGTGAAATCCGGTTGTCGAGGAGCATAAATGACGCTTA
GCTCGTCATCATTTCTGGAAGTTGTAGATTCGGTCATCATCAGGTTTGAG
AGCTCTCACAATTCCATGTCCTCACTGCCTCTCAAATTGACCTGTAGCAG
GGCGTTTTCGGCTC
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protein sequence of SMED30033184-orf-1

>SMED30033184-orf-1 ID=SMED30033184-orf-1|Name=SMED30033184-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=117bp
MMTESTTSRNDDELSVIYAPRQPDFTHPVHTPAQITITTTSHSAEAPIII
QISILSRTTPDPKIPSIRRSSPQIVFVVKPTTVRNLRANNSHQSGLIPTS
RPPKRRYLPVDIDGED*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell