SMED30024409

Overview
NameSMED30024409
Smed IDSMED30024409
Length (bp)588
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




SMED30024409

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 4 cellSMED30024409SMESG000074943.1 dd_Smed_v4_17460_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30024409SMESG000074943.1 dd_Smed_v4_17460_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30024409SMESG000074943.1 dd_Smed_v4_17460_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
Homology
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074943.1 (SMESG000074943.1)

HSP 1 Score: 235.728 bits (600), Expect = 2.271e-75
Identity = 144/147 (97.96%), Postives = 146/147 (99.32%), Query Frame = 1
Query:   82 MNKXXXXXXXXXXXDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYTXXXXXXXXXXXXXXXSVDVRFRFLSKY 522
            MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYTFFWIIIILLIFLALISVDVRFRFL+ +
Sbjct:    1 MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYTFFWIIIILLIFLALISVDVRFRFLTNF 147          
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074943.1 (SMESG000074943.1)

HSP 1 Score: 213.386 bits (542), Expect = 9.450e-67
Identity = 134/147 (91.16%), Postives = 136/147 (92.52%), Query Frame = 1
Query:   82 MNKXXXXXXXXXXXDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYTXXXXXXXXXXXXXXXSVDVRFRFLSKY 522
            MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQ          IIILLIFLALISVDVRFRFL+ +
Sbjct:    1 MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQ----------IIILLIFLALISVDVRFRFLTNF 137          
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074941.1 (SMESG000074941.1)

HSP 1 Score: 105.531 bits (262), Expect = 2.158e-26
Identity = 50/103 (48.54%), Postives = 74/103 (71.84%), Query Frame = 1
Query:  136 NEDPKFSC-VKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYT 441
            +E P+  C + + FKT++  C  F+  C+K  D++C+NFQ +C QCPPSNYS+LM +DL+ VK EL +TK QLEA+K QS++ +N+ S +L KQN QI  ++T
Sbjct:   18 HEIPRSHCPIGSPFKTKDNLCKDFYEVCVKQNDLECLNFQTICKQCPPSNYSVLMFMDLLTVKNELIKTKDQLEALKTQSELCQNKTSGTLMKQNQQIKKIFT 120          
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074941.1 (SMESG000074941.1)

HSP 1 Score: 105.531 bits (262), Expect = 2.325e-26
Identity = 50/103 (48.54%), Postives = 74/103 (71.84%), Query Frame = 1
Query:  136 NEDPKFSC-VKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYT 441
            +E P+  C + + FKT++  C  F+  C+K  D++C+NFQ +C QCPPSNYS+LM +DL+ VK EL +TK QLEA+K QS++ +N+ S +L KQN QI  ++T
Sbjct:   18 HEIPRSHCPIGSPFKTKDNLCKDFYEVCVKQNDLECLNFQTICKQCPPSNYSVLMFMDLLTVKNELIKTKDQLEALKTQSELCQNKTSGTLMKQNQQIKKIFT 120          
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074945.1 (SMESG000074945.1)

HSP 1 Score: 77.411 bits (189), Expect = 7.426e-17
Identity = 38/82 (46.34%), Postives = 56/82 (68.29%), Query Frame = 1
Query:  136 NEDPKFSCV-KNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAI--KVQS 372
             E P+F C     F+T + SCA +++ C+K  D DC NFQ  CNQCPPSNYSI+M ID++N+K ++  +K Q++ +  KV+S
Sbjct:   18 GEKPRFICQNPKSFRTNDNSCADYNDVCIKTGDPDCANFQTACNQCPPSNYSIMMYIDMMNMKNQIIISKSQMKNLTDKVES 99          
The following BLAST results are available for this feature:
BLAST of SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 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 SMED30024409 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074943.12.271e-7597.96SMESG000074943.1[more]
SMESG000074943.19.450e-6791.16SMESG000074943.1[more]
SMESG000074941.12.158e-2648.54SMESG000074941.1[more]
SMESG000074941.12.325e-2648.54SMESG000074941.1[more]
SMESG000074945.17.426e-1746.34SMESG000074945.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024409 ID=SMED30024409|Name=SMED30024409|organism=Schmidtea mediterranea sexual|type=transcript|length=588bp
AATATGTGTGCTATATAGAATTTTATTGGACAACAAAAACTCAACATAAT
TTCTAGTACAGTTTTAAGAAAGGATGTTAGAATGAATAAATTTGTGTTCA
TTATTCTAATAATAATATTCATTGACAAATGTCGAAACGAAGATCCGAAA
TTTTCTTGTGTTAAAAACCTTTTCAAAACCCAAAATGCTTCCTGCGCTGG
TTTCCACAATTTCTGTATGAAAAATGAAGACGTTGATTGCATAAACTTTC
AAAATGTTTGCAATCAATGCCCGCCATCAAATTACAGTATCTTGATGTTG
ATTGATTTAATTAATGTCAAAACTGAGTTAAATCAAACAAAACATCAACT
TGAAGCTATAAAAGTTCAATCACAAATTTATGAAAATCAAATTTCTGAGA
GTTTGAAAAAACAAAATCTTCAAATTAATAATTTATACACATTTTTTTGG
ATAATTATTATTCTGTTAATCTTTCTGGCTCTGATTAGTGTCGACGTCCG
GTTCAGATTTTTGAGTAAGTATAAAAGTTATTTATTTTAAAAAACCAACA
AAAAATTAAATTTTATTTTCAGATAATTTTTAATTTTG
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protein sequence of SMED30024409-orf-1

>SMED30024409-orf-1 ID=SMED30024409-orf-1|Name=SMED30024409-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=153bp
MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNED
VDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIY
ENQISESLKKQNLQINNLYTFFWIIIILLIFLALISVDVRFRFLSKYKSY
LF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 76..103
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.708
NoneNo IPR availableTMHMMTMhelixcoord: 115..137