SMED30018606

Overview
NameSMED30018606
Smed IDSMED30018606
Length (bp)1421
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



SMED30018606

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 regionSMED30018606 SmedASXL_077810SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30018606 dd_Smed_v4_12455_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018606 dd_Smed_v4_12455_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30018606 dd_Smed_v4_12455_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
Homology
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BLAST of SMED30018606 vs. Planmine SMEST
Match: SMESG000017693.1 (SMESG000017693.1)

HSP 1 Score: 102.064 bits (253), Expect = 1.269e-28
Identity = 53/74 (71.62%), Postives = 61/74 (82.43%), Query Frame = 2 
Query: 1139 CKKYQLDKTLYTLPEDKN--LEFKN*SKT*TPPFIIYEYFESILPKENIYFQ*HLPISAGYLLINNFTGISNYY 1354
            CKK QL  TLYTLP+DK+  L+FKN SKT TPPF+IY  FESILPK++IYFQ HLPISAG LLINNFTG++  Y
Sbjct:  483 CKKNQLGTTLYTLPKDKDKYLQFKNWSKTITPPFVIYADFESILPKDDIYFQKHLPISAGLLLINNFTGMTMNY 556

HSP 2 Score: 102.064 bits (253), Expect = 1.269e-28
Identity = 53/74 (71.62%), Postives = 61/74 (82.43%), Query Frame = 2 
Query: 1139 CKKYQLDKTLYTLPEDKN--LEFKN*SKT*TPPFIIYEYFESILPKENIYFQ*HLPISAGYLLINNFTGISNYY 1354
            CKK QL  TLYTLP+DK+  L+FKN SKT TPPF+IY  FESILPK++IYFQ HLPISAG LLINNFTG++  Y
Sbjct: 1104 CKKNQLGTTLYTLPKDKDKYLQFKNWSKTITPPFVIYADFESILPKDDIYFQKHLPISAGLLLINNFTGMTMNY 1177

HSP 3 Score: 43.8986 bits (102), Expect = 1.269e-28
Identity = 20/28 (71.43%), Postives = 22/28 (78.57%), Query Frame = 1 
Query: 1048 NCNVRIRSIWC*NCLNGFRKPNTF*EPH 1131
            +CNVRIR  WC NCLNGFRKP +F E H
Sbjct:  453 DCNVRIRCKWCENCLNGFRKPKSF-EKH 479

HSP 4 Score: 43.8986 bits (102), Expect = 1.269e-28
Identity = 20/28 (71.43%), Postives = 22/28 (78.57%), Query Frame = 1 
Query: 1048 NCNVRIRSIWC*NCLNGFRKPNTF*EPH 1131
            +CNVRIR  WC NCLNGFRKP +F E H
Sbjct: 1074 DCNVRIRCKWCENCLNGFRKPKSF-EKH 1100
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BLAST of SMED30018606 vs. Planmine SMEST
Match: SMESG000017693.1 (SMESG000017693.1)

HSP 1 Score: 102.064 bits (253), Expect = 1.345e-28
Identity = 53/74 (71.62%), Postives = 61/74 (82.43%), Query Frame = 2 
Query: 1139 CKKYQLDKTLYTLPEDKN--LEFKN*SKT*TPPFIIYEYFESILPKENIYFQ*HLPISAGYLLINNFTGISNYY 1354
            CKK QL  TLYTLP+DK+  L+FKN SKT TPPF+IY  FESILPK++IYFQ HLPISAG LLINNFTG++  Y
Sbjct:  483 CKKNQLGTTLYTLPKDKDKYLQFKNWSKTITPPFVIYADFESILPKDDIYFQKHLPISAGLLLINNFTGMTMNY 556

HSP 2 Score: 43.8986 bits (102), Expect = 1.345e-28
Identity = 20/28 (71.43%), Postives = 22/28 (78.57%), Query Frame = 1 
Query: 1048 NCNVRIRSIWC*NCLNGFRKPNTF*EPH 1131
            +CNVRIR  WC NCLNGFRKP +F E H
Sbjct:  453 DCNVRIRCKWCENCLNGFRKPKSF-EKH 479

HSP 3 Score: 97.8265 bits (242), Expect = 2.403e-27
Identity = 51/68 (75.00%), Postives = 57/68 (83.82%), Query Frame = 2 
Query: 1139 CKKYQLDKTLYTLPEDKN--LEFKN*SKT*TPPFIIYEYFESILPKENIYFQ*HLPISAGYLLINNFT 1336
            CKK QL  TLYTLP+DK+  L+FKN SKT TPPF+IY  FESILPK++IYFQ HLPISAG LLINNFT
Sbjct: 1104 CKKNQLGTTLYTLPKDKDKYLQFKNWSKTITPPFVIYADFESILPKDDIYFQKHLPISAGLLLINNFT 1171

HSP 4 Score: 43.8986 bits (102), Expect = 2.403e-27
Identity = 20/28 (71.43%), Postives = 22/28 (78.57%), Query Frame = 1 
Query: 1048 NCNVRIRSIWC*NCLNGFRKPNTF*EPH 1131
            +CNVRIR  WC NCLNGFRKP +F E H
Sbjct: 1074 DCNVRIRCKWCENCLNGFRKPKSF-EKH 1100
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BLAST of SMED30018606 vs. Planmine SMEST
Match: SMESG000071708.1 (SMESG000071708.1)

HSP 1 Score: 97.4413 bits (241), Expect = 3.897e-24
Identity = 49/84 (58.33%), Postives = 60/84 (71.43%), Query Frame = 2 
Query: 1100 FESQIHFKNLTNYCKKYQLDKTLYTLPEDKNLEFKN*SKT*TPPFIIYEYFESILPKENIYFQ*HLPISAGYLLINNFTGISNY 1351
            F + I        C K QL  TLYTLP +KNLEFKN +KT TPPF++Y  FE+ILP ++I+FQ H+PISAG LLINNFTG  +Y
Sbjct: 1492 FRNIISLNKHKGLCDKNQLGTTLYTLPLNKNLEFKNWAKTVTPPFVLYADFEAILPSDDIHFQIHMPISAGLLLINNFTGEKSY 1575

HSP 2 Score: 33.113 bits (74), Expect = 3.897e-24
Identity = 11/17 (64.71%), Postives = 14/17 (82.35%), Query Frame = 1 
Query: 1054 NVRIRSIWC*NCLNGFR 1104
            + R++SIWC  CLNGFR
Sbjct: 1477 DTRVQSIWCHRCLNGFR 1493

HSP 3 Score: 20.0162 bits (40), Expect = 3.897e-24
Identity = 7/16 (43.75%), Postives = 12/16 (75.00%), Query Frame = 3 
Query:  888 LVQMQNHSFTDRKFRT 935
            L+  +NHSFTD + ++
Sbjct: 1467 LLNYRNHSFTDTRVQS 1482
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BLAST of SMED30018606 vs. Planmine SMEST
Match: SMESG000076702.1 (SMESG000076702.1)

HSP 1 Score: 106.301 bits (264), Expect = 5.460e-24
Identity = 54/75 (72.00%), Postives = 63/75 (84.00%), Query Frame = 2 
Query: 1139 CKKYQLDKTLYTLPEDKN--LEFKN*SKT*TPPFIIYEYFESILPKENIYFQ*HLPISAGYLLINNFTGISNYYQ 1357
            CKK QL  TLYTLP+DK+  LEFKN SKT TPPF+IY  FESILPK++IYFQ HLPISAG LLINNFTG+++Y+ 
Sbjct:  423 CKKNQLGTTLYTLPKDKDKYLEFKNWSKTITPPFVIYADFESILPKDDIYFQKHLPISAGLLLINNFTGMTSYHH 497
[Close]
BLAST of SMED30018606 vs. Planmine SMEST
Match: SMESG000076702.1 (SMESG000076702.1)

HSP 1 Score: 105.916 bits (263), Expect = 6.021e-24
Identity = 54/75 (72.00%), Postives = 63/75 (84.00%), Query Frame = 2 
Query: 1139 CKKYQLDKTLYTLPEDKN--LEFKN*SKT*TPPFIIYEYFESILPKENIYFQ*HLPISAGYLLINNFTGISNYYQ 1357
            CKK QL  TLYTLP+DK+  LEFKN SKT TPPF+IY  FESILPK++IYFQ HLPISAG LLINNFTG+++Y+ 
Sbjct:  423 CKKNQLGTTLYTLPKDKDKYLEFKNWSKTITPPFVIYADFESILPKDDIYFQKHLPISAGLLLINNFTGMTSYHH 497
The following BLAST results are available for this feature:
BLAST of SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 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 SMED30018606 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000017693.11.269e-2871.62SMESG000017693.1[more]
SMESG000017693.11.345e-2871.62SMESG000017693.1[more]
SMESG000071708.13.897e-2458.33SMESG000071708.1[more]
SMESG000076702.15.460e-2472.00SMESG000076702.1[more]
SMESG000076702.16.021e-2472.00SMESG000076702.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018606 ID=SMED30018606|Name=SMED30018606|organism=Schmidtea mediterranea sexual|type=transcript|length=1421bp
AAAACACATTGAAATATTTGTTTTAATTCGACGATTCTCAAAATTTTCCA
GTTGAATTATTTGGATAACCTTGCATTCACATTTTATTTAAAATTTGTTC
AAAAATTTGCGGCAGCATCATATATATATATGTGTGTGTGTGTAAACATT
TATTGAAAAATATGAGAAAAATTCACAATAAATCTCTGTGAACTATATAA
TAATTTTAAGCCTTAACAAATTTACAAAACCTTTAATATAACATTTTGCG
ACGTTTTGCATGGTTGATTCTCACTAGCTTGAATTTATTTTTAATAAATA
TGAAAAACGACATTTTACTTTTATTATGCATTTGTATTCATTTCAATTTA
ACAGTTTTGTCAAAATCTATTTTTTGAAAAAGTACTACATAATTATTTTG
AAATATCTCCAACATGAAGGAATAGTTTTCTCTTGCTCGTTTCTACTGTT
GTTTTCCTTCCTCACTTAACCTACGATCAGAACGTTTTAAGCAATCATCA
TGTATTCCTGTACCAACAAGTTGCAAGATGTGTAGTTTCCCATCAAATTT
CATCATTGTCTGATATTGAAGACTTTCTCTCAGTTCCCTCTTCATGAAAA
TCATCAACTAGTGACATAATTATTATTCGAATAAATTAGACATTGGTTTA
TTGTTTTTATGTTTACAAGCGGTTTTACACAAAATGAAAGAATTTAAGGA
GGAAACTTCAATTCCCCAGAATAAAACCTTTCTTCATCATTTTAATGATT
TTCGTAAAAAAATAATATATTTGATCAACGTGGTCCACTCCGCCAATAAA
TTTATTATAATTCAATACTACTCATGTATAGTATCTGAGGACTTAAAGAT
GAGACCTTTCAGGGTTAGTGATTGATTTGAGCAGGTTCTTGTACAAATGC
AAAATCATTCTTTCACTGACAGAAAGTTCAGGACAAATTCAAGGGATCCA
AAATAGGACAATATTGAATATACGTATCCAGTATTTGAAAATTATCATTC
TACTGCAATGAATAATTTACAAAGTGGATGAATTGTAACAAATTATTAAT
TGTAATGTTCGGATTAGAAGCATATGGTGTTAAAATTGTTTAAATGGATT
TCGAAAGCCAAATACATTTTAAGAACCTCACTAATTATTGCAAGAAATAT
CAATTGGATAAAACTCTATATACTTTGCCCGAAGACAAAAATTTGGAATT
TAAAAATTGATCAAAGACATGAACACCCCCATTTATTATTTATGAATATT
TTGAATCTATATTACCAAAAGAAAACATTTATTTTCAATAGCATTTGCCA
ATTTCTGCTGGATACTTATTGATTAACAATTTTACTGGAATATCAAATTA
TTATCAGAAATTTCCTTTGAAACTTATCGGTTGATTATAGTTTCTATTAG
CTAATTCATTGTTACTGTAGT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000419prepharyngeal region
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell