SMED30003559

Overview
NameSMED30003559
Smed IDSMED30003559
Length (bp)763
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



SMED30003559

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
nervous systemSMED30003559 dd_Smed_v4_9607_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30003559 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
SMED30003559 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000264:183248..184006 +3168
v31.000295:7980..8738 +3156
v31.001736:72955..73708 +3144
v31.002762:42292..43054 +3139
v31.013043:8012..8774 +3112
v31.001915:22984..23746 +3112
v31.000245:162064..162824 -3097
v31.002552:12990..13752 -3085
Homology
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BLAST of SMED30003559 vs. Planmine SMEST
Match: SMESG000011446.1 (SMESG000011446.1)

HSP 1 Score: 173.711 bits (439), Expect = 9.143e-55
Identity = 83/109 (76.15%), Postives = 100/109 (91.74%), Query Frame = -2 
Query:    1 MSVNSNSTASDLPRIPRLSPSVVALRHRYQELKQQHTALRIKYERVKGTWATPETVKELRQKISRLTRARDELVAESRSQRLLIREQSTALRRAFTDVELRPHVPGSVR 327
            M+ +++S  S+LPRIPRLSPSVVA+RH+Y++LK++H  LR KYERVKGTWA PETV+ELRQKI+R+T+ARDEL+AESRSQRLLIREQ+TALRRAFTDVE R HVPGSVR
Sbjct:    1 MNTSTSSKTSELPRIPRLSPSVVAVRHKYEKLKREHEELRTKYERVKGTWAPPETVRELRQKIARITQARDELIAESRSQRLLIREQATALRRAFTDVEFRTHVPGSVR 109
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BLAST of SMED30003559 vs. Planmine SMEST
Match: SMESG000015007.1 (SMESG000015007.1)

HSP 1 Score: 168.703 bits (426), Expect = 5.460e-51
Identity = 82/109 (75.23%), Postives = 97/109 (88.99%), Query Frame = -2 
Query:    1 MSVNSNSTASDLPRIPRLSPSVVALRHRYQELKQQHTALRIKYERVKGTWATPETVKELRQKISRLTRARDELVAESRSQRLLIREQSTALRRAFTDVELRPHVPGSVR 327
            M+  SNS+ +DLPRIPRLSPSVVA+R +Y+ELK QH ALR KYERVKGTWA PETV+ L Q+I+RLT AR+EL+AESRSQRLLI+EQ+TALR+AFTDVEL+ HVPGSVR
Sbjct:    1 MNSPSNSSTNDLPRIPRLSPSVVAMRQKYEELKLQHAALRAKYERVKGTWAPPETVRGLLQEIARLTEAREELIAESRSQRLLIKEQATALRQAFTDVELQTHVPGSVR 109
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BLAST of SMED30003559 vs. Planmine SMEST
Match: SMESG000063980.1 (SMESG000063980.1)

HSP 1 Score: 175.637 bits (444), Expect = 7.403e-50
Identity = 77/109 (70.64%), Postives = 95/109 (87.16%), Query Frame = -2 
Query:    1 MSVNSNSTASDLPRIPRLSPSVVALRHRYQELKQQHTALRIKYERVKGTWATPETVKELRQKISRLTRARDELVAESRSQRLLIREQSTALRRAFTDVELRPHVPGSVR 327
            M+ N+    +DLPRIPRL PS++A+R +Y+ELKQ H+ L++KYERVKGTWA P+TVK LRQKI RLTRARDEL++ESR+QRLLI+EQS ALRRAFTDVEL+ HVPGS+R
Sbjct:    1 MNANNQDNLNDLPRIPRLPPSIIAIRRQYEELKQAHSELKVKYERVKGTWAPPDTVKVLRQKIERLTRARDELISESRAQRLLIKEQSIALRRAFTDVELQAHVPGSIR 109
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BLAST of SMED30003559 vs. Planmine SMEST
Match: SMESG000068757.1 (SMESG000068757.1)

HSP 1 Score: 156.762 bits (395), Expect = 5.983e-44
Identity = 75/107 (70.09%), Postives = 91/107 (85.05%), Query Frame = -2 
Query:    1 VNSNSTASDLPRIPRLSPSVVALRHRYQELKQQHTALRIKYERVKGTWATPETVKELRQKISRLTRARDELVAESRSQRLLIREQSTALRRAFTDVELRPHVPGSVR 321
            + +N  +++  RIPRL PS+VA+RH+Y++LK QH  L+ KYER+KGTWA PETV+ELRQKI RLTRARDEL+ ESRSQRLLI EQS ALR+AFTDVELR HVPG+VR
Sbjct:    1 MKNNDESTNPSRIPRLHPSIVAIRHKYEDLKLQHGDLQAKYERIKGTWAPPETVRELRQKILRLTRARDELIVESRSQRLLIHEQSKALRQAFTDVELRTHVPGNVR 107
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BLAST of SMED30003559 vs. Planmine SMEST
Match: SMESG000009535.1 (SMESG000009535.1)

HSP 1 Score: 154.451 bits (389), Expect = 1.227e-43
Identity = 79/111 (71.17%), Postives = 96/111 (86.49%), Query Frame = -2 
Query:    1 LDMSVNSNSTASDLPRIPRLSPSVVALRHRYQELKQQHTALRIKYERVKGTWATPETVKELRQKISRLTRARDELVAESRSQRLLIREQSTALRRAFTDVELRPHVPGSVR 333
            +D   ++NS +S LPRIPRLSPS+VA+RH+Y+EL++++ AL  KYERVKGTWA+P+ +K LRQKI RLTRARDELV ESR QRLLIREQSTALRRAFTD+ELR  VPG+VR
Sbjct:   31 IDWMNSNNSNSSGLPRIPRLSPSIVAVRHQYEELQRKYDALHAKYERVKGTWASPDVIKSLRQKIERLTRARDELVTESRIQRLLIREQSTALRRAFTDIELRTLVPGNVR 141
The following BLAST results are available for this feature:
BLAST of SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 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 SMED30003559 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000011446.19.143e-5576.15SMESG000011446.1[more]
SMESG000015007.15.460e-5175.23SMESG000015007.1[more]
SMESG000063980.17.403e-5070.64SMESG000063980.1[more]
SMESG000068757.15.983e-4470.09SMESG000068757.1[more]
SMESG000009535.11.227e-4371.17SMESG000009535.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003559 ID=SMED30003559|Name=SMED30003559|organism=Schmidtea mediterranea sexual|type=transcript|length=763bp
CCGGACACTCCCTGGGACGTGAGGCCGAAGCTCTACGTCCGTGAATGCAC
GACGAAGTGCCGTTGATTGCTCACGTATCAGCAGCCGTTGGCTGCGCGAC
TCTGCGACTAACTCATCTCGAGCCCGAGTCAGCCTTGAAATTTTCTGGCG
TAATTCTTTAACTGTTTCTGGCGTGGCCCAAGTGCCCTTTACTCGCTCAT
ATTTGATTCGGAGCGCGGTATGTTGCTGTTTCAGCTCCTGGTACCTGTGC
CTCAGGGCCACCACCGACGGGGATAGTCGGGGGATCCGTGGAAGATCACT
TGCCGTTGAGTTGGAATTAACACTCATGTCTAGAGATAGAAAAGGGGTTC
AGGAAATGGAGATTAGTTGAGAGAAAATGAGGAAAAAGGAAAATTGACGG
AAAAGTAGCAGAAGGACTTTATGAATGCTGAATTAGCCAGGGGGTTCCAG
ATTTACATTATCCCTCGTTATGGCTTGTAAATATTGAATTCCTATCGTTC
ATTATCGGGTGGATAGGGTCATGTTTTAGTGACCTTAAATTAGGGTTTTT
TTCGTGAGATTGAGTGTCAGTATCAACACGGTAATTCGGTCTTTTAGACG
AATTGACGCCATCATAAATTGTATTATTTCTATTACTACGGTTACCTTTA
ACGGGATTGAACTTAGTAGAATTCGTAATAAGGTCATAATATCATTTTTC
CGAGTTAAGCGTTGCTATGAATTTGACGTTATCCTCATTAGTGACTATTT
CGGAATATAAAAT
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protein sequence of SMED30003559-orf-1

>SMED30003559-orf-1 ID=SMED30003559-orf-1|Name=SMED30003559-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
MSVNSNSTASDLPRIPRLSPSVVALRHRYQELKQQHTALRIKYERVKGTW
ATPETVKELRQKISRLTRARDELVAESRSQRLLIREQSTALRRAFTDVEL
RPHVPGSVR
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..20