SMED30002159

Overview
NameSMED30002159
Smed IDSMED30002159
Length (bp)319
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



SMED30002159

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
prepharyngeal regionSMED30002159h1SMcG0009026 SmedASXL_019138SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30002159h1SMcG0009026 SmedASXL_019138SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30002159h1SMcG0009026 OX_Smed_1.0.09557ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002159 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005196:18897..19370 +1546
Homology
[Close]
BLAST of SMED30002159 vs. TrEMBL
Match: I1ZIC3 (Metalloendopeptidase OS=Schmidtea mediterranea OX=79327 GN=Ast3 PE=2 SV=1)

HSP 1 Score: 138.272 bits (347), Expect = 2.006e-38
Identity = 65/80 (81.25%), Postives = 69/80 (86.25%), Query Frame = -1 
Query:    2 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG 241
            ASQCGC+KKKL+TRAT  L VGDM+LSK DIAIINGFKHHQ +AR WPGG V FAF NDFP DKRNLVKQCL ELQSDLG
Sbjct:   21 ASQCGCNKKKLMTRATENLHVGDMLLSKADIAIINGFKHHQREARAWPGGKVSFAFANDFPADKRNLVKQCLNELQSDLG 100
[Close]
BLAST of SMED30002159 vs. TrEMBL
Match: A0A060Q785 (Metalloendopeptidase OS=Schmidtea mediterranea OX=79327 GN=Ast1 PE=2 SV=1)

HSP 1 Score: 97.0561 bits (240), Expect = 1.932e-22
Identity = 41/80 (51.25%), Postives = 60/80 (75.00%), Query Frame = -1 
Query:    2 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG 241
            + QCGC ++KLL R+ + +++GDM+L K DIA+INGFK+H  + + WP  NV+++F  +FP DK  +V+QCL ELQ DLG
Sbjct:   18 SGQCGCPRQKLLKRSVDSMKMGDMLLDKSDIALINGFKNHYANTKKWPNNNVVYSFAGNFPRDKIPVVRQCLGELQRDLG 97
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BLAST of SMED30002159 vs. TrEMBL
Match: A0A060Q786 (Metalloendopeptidase OS=Schmidtea mediterranea OX=79327 GN=Ast6 PE=2 SV=1)

HSP 1 Score: 95.9005 bits (237), Expect = 5.621e-22
Identity = 42/80 (52.50%), Postives = 57/80 (71.25%), Query Frame = -1 
Query:    2 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG 241
            + QCGC ++KLL R  + +++GDMVL K DIA+INGFK H  + + WP   VLF+F   FP DK+ +V++CL ELQ DLG
Sbjct:   18 SGQCGCPRQKLLKRGLDSMQMGDMVLDKSDIALINGFKAHYSNTKRWPNNQVLFSFAPAFPGDKKGIVRECLVELQKDLG 97
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BLAST of SMED30002159 vs. TrEMBL
Match: A0A060Q714 (Metalloendopeptidase OS=Schmidtea mediterranea OX=79327 GN=Ast2 PE=2 SV=1)

HSP 1 Score: 77.7962 bits (190), Expect = 5.571e-15
Identity = 37/79 (46.84%), Postives = 51/79 (64.56%), Query Frame = -1 
Query:    5 QCGCSKK--KLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDL 235
            QCGC ++  KL TR  + +++GDM+L   DI IINGFK+H  +++ WP   V + F  +FP DK   V+Q L ELQ DL
Sbjct:   20 QCGCPRQSVKLRTRGLDNVKMGDMLLDSTDIQIINGFKNHYANSKKWPNNIVTYTFAGNFPQDKIQTVRQSLGELQKDL 98
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BLAST of SMED30002159 vs. TrEMBL
Match: A0A060Q750 (Metalloendopeptidase OS=Schmidtea mediterranea OX=79327 GN=Ast5 PE=2 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 7.544e-8
Identity = 30/79 (37.97%), Postives = 47/79 (59.49%), Query Frame = -1 
Query:    5 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDL 241
            A +CGC K KL  RA + L++ DM+L   D+  I GF+ +  +AR W    + + F   FP DK+ +V++ + EL +DL
Sbjct:   21 AGKCGCQKSKL-KRAIS-LKIDDMLLDHVDLMKIEGFRGYDKNARRWTDNTLKYTFHPQFPADKKQIVRESMNELTNDL 97
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BLAST of SMED30002159 vs. Planmine SMEST
Match: SMESG000072806.1 (SMESG000072806.1)

HSP 1 Score: 168.703 bits (426), Expect = 6.198e-54
Identity = 80/80 (100.00%), Postives = 80/80 (100.00%), Query Frame = -1 
Query:    2 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG 241
            ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG
Sbjct:   17 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG 96
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BLAST of SMED30002159 vs. Planmine SMEST
Match: SMESG000072804.1 (SMESG000072804.1)

HSP 1 Score: 138.272 bits (347), Expect = 4.975e-42
Identity = 65/80 (81.25%), Postives = 69/80 (86.25%), Query Frame = -1 
Query:    2 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG 241
            ASQCGC+KKKL+TRAT  L VGDM+LSK DIAIINGFKHHQ +AR WPGG V FAF NDFP DKRNLVKQCL ELQSDLG
Sbjct:   17 ASQCGCNKKKLMTRATENLHVGDMLLSKADIAIINGFKHHQREARAWPGGKVSFAFANDFPADKRNLVKQCLNELQSDLG 96
[Close]
BLAST of SMED30002159 vs. Planmine SMEST
Match: SMESG000072804.1 (SMESG000072804.1)

HSP 1 Score: 138.272 bits (347), Expect = 5.579e-42
Identity = 65/80 (81.25%), Postives = 69/80 (86.25%), Query Frame = -1 
Query:    2 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG 241
            ASQCGC+KKKL+TRAT  L VGDM+LSK DIAIINGFKHHQ +AR WPGG V FAF NDFP DKRNLVKQCL ELQSDLG
Sbjct:   21 ASQCGCNKKKLMTRATENLHVGDMLLSKADIAIINGFKHHQREARAWPGGKVSFAFANDFPADKRNLVKQCLNELQSDLG 100
[Close]
BLAST of SMED30002159 vs. Planmine SMEST
Match: SMESG000072804.1 (SMESG000072804.1)

HSP 1 Score: 138.272 bits (347), Expect = 9.477e-42
Identity = 65/80 (81.25%), Postives = 69/80 (86.25%), Query Frame = -1 
Query:    2 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG 241
            ASQCGC+KKKL+TRAT  L VGDM+LSK DIAIINGFKHHQ +AR WPGG V FAF NDFP DKRNLVKQCL ELQSDLG
Sbjct:   35 ASQCGCNKKKLMTRATENLHVGDMLLSKADIAIINGFKHHQREARAWPGGKVSFAFANDFPADKRNLVKQCLNELQSDLG 114
[Close]
BLAST of SMED30002159 vs. Planmine SMEST
Match: SMESG000015174.1 (SMESG000015174.1)

HSP 1 Score: 97.0561 bits (240), Expect = 4.716e-26
Identity = 41/80 (51.25%), Postives = 60/80 (75.00%), Query Frame = -1 
Query:    2 ASQCGCSKKKLLTRATNGLRVGDMVLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYELQSDLG 241
            + QCGC ++KLL R+ + +++GDM+L K DIA+INGFK+H  + + WP  NV+++F  +FP DK  +V+QCL ELQ DLG
Sbjct:   12 SGQCGCPRQKLLKRSVDSMKMGDMLLDKSDIALINGFKNHYANTKKWPNNNVVYSFAGNFPRDKIPVVRQCLGELQRDLG 91
The following BLAST results are available for this feature:
BLAST of SMED30002159 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 SMED30002159 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 SMED30002159 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 SMED30002159 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 SMED30002159 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 SMED30002159 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 SMED30002159 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 SMED30002159 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
I1ZIC32.006e-3881.25Metalloendopeptidase OS=Schmidtea mediterranea OX=... [more]
A0A060Q7851.932e-2251.25Metalloendopeptidase OS=Schmidtea mediterranea OX=... [more]
A0A060Q7865.621e-2252.50Metalloendopeptidase OS=Schmidtea mediterranea OX=... [more]
A0A060Q7145.571e-1546.84Metalloendopeptidase OS=Schmidtea mediterranea OX=... [more]
A0A060Q7507.544e-837.97Metalloendopeptidase OS=Schmidtea mediterranea OX=... [more]
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BLAST of SMED30002159 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 SMED30002159 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 SMED30002159 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 SMED30002159 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 SMED30002159 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 SMED30002159 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000072806.16.198e-54100.00SMESG000072806.1[more]
SMESG000072804.14.975e-4281.25SMESG000072804.1[more]
SMESG000072804.15.579e-4281.25SMESG000072804.1[more]
SMESG000072804.19.477e-4281.25SMESG000072804.1[more]
SMESG000015174.14.716e-2651.25SMESG000015174.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002159 ID=SMED30002159|Name=SMED30002159|organism=Schmidtea mediterranea sexual|type=transcript|length=319bp
TACCCAAGTCAGATTGCAGTTCATACAAACATTGCTTGACCAGATTTCGT
TTGTCATAAGGGAAATCATTTCCAAAAGCAAACAAAACGTTTCCGCCTGG
CCATATACGAGCATCCATTTGATGGTGCTTAAACCCATTGATTATAGCGA
TATCCCCCTTACTCAACACCATATCTCCAACTCGAAGGCCATTCGTGGCT
CTGGTCAACAATTTCTTCTTGCTGCAGCCGCATTGACTGGCCACCTCATT
GACAATCACCAATACGAGAAGGAATAGTAACTTTTTCATGACGACCTCAA
GTTCCTGACACGAACTCGG
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protein sequence of SMED30002159-orf-1

>SMED30002159-orf-1 ID=SMED30002159-orf-1|Name=SMED30002159-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
PSSCQELEVVMKKLLFLLVLVIVNEVASQCGCSKKKLLTRATNGLRVGDM
VLSKGDIAIINGFKHHQMDARIWPGGNVLFAFGNDFPYDKRNLVKQCLYE
LQSDLG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..28
score: 0.729