SMED30013765

Overview
NameSMED30013765
Smed IDSMED30013765
Length (bp)628
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



SMED30013765

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
parapharyngeal regionSMED30013765h1SMcG0001187 SmedASXL_017378SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30013765h1SMcG0001187 SmedASXL_004927SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013765 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004817:23224..23849 -2987
Homology
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BLAST of SMED30013765 vs. Planmine SMEST
Match: SMESG000018709.1 (SMESG000018709.1)

HSP 1 Score: 407.527 bits (1046), Expect = 1.125e-137
Identity = 199/199 (100.00%), Postives = 199/199 (100.00%), Query Frame = -2 
Query:    1 FLGLQLIPANSLNRSVIFTGPVHVIENQMEQFICSLNTREDFQNISVKHSNSEILFWTNLNEKCSVSKDFKNYLSNCTKDSGMLSYEMAFIQAFEGKITCQIEINNERYDRNINVFVNASSPIFNSTERLIYYENETFSFSCQSVNKKTNVMIINYIVYANGIQEDLNYASTNSSLITITQLNLNQTLHDASIGCGIQY 597
            FLGLQLIPANSLNRSVIFTGPVHVIENQMEQFICSLNTREDFQNISVKHSNSEILFWTNLNEKCSVSKDFKNYLSNCTKDSGMLSYEMAFIQAFEGKITCQIEINNERYDRNINVFVNASSPIFNSTERLIYYENETFSFSCQSVNKKTNVMIINYIVYANGIQEDLNYASTNSSLITITQLNLNQTLHDASIGCGIQY
Sbjct:    7 FLGLQLIPANSLNRSVIFTGPVHVIENQMEQFICSLNTREDFQNISVKHSNSEILFWTNLNEKCSVSKDFKNYLSNCTKDSGMLSYEMAFIQAFEGKITCQIEINNERYDRNINVFVNASSPIFNSTERLIYYENETFSFSCQSVNKKTNVMIINYIVYANGIQEDLNYASTNSSLITITQLNLNQTLHDASIGCGIQY 205
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BLAST of SMED30013765 vs. Planmine SMEST
Match: SMESG000018945.1 (SMESG000018945.1)

HSP 1 Score: 264.618 bits (675), Expect = 1.368e-81
Identity = 136/209 (65.07%), Postives = 169/209 (80.86%), Query Frame = -2 
Query:    1 LTAIFFLGLQLIPANSLNRSVIFTGPVHVIENQMEQFICSLNTREDFQNISVKHSNSEILFW--TNLNEKCSV-SKDFKNYLSNCTKDSGMLSYEMAFIQAFEGKITCQIEINNERYDRNINVFVNASSPIFNSTERLIYYENETFSFSCQSV-NKKTNV-MIINYIVYANGIQEDLNYASTNSSLITITQLNLNQTLHDASIGCGIQY 612
            L   + + +  + +++ NRS++F GPVHVIENQ+ QFICSLNTRE+FQNISVK+  +EI+ W  +N +EKC V  ++++ Y+SNC+ D+G+LSYEMAF+ AFEG  TCQI I NE Y+R+INV VNA SP+FNST+RLIYYENETFSFSC SV N  TN+ MIINYIVYANGIQEDL+Y    SSLIT TQLNLNQT++DASIGCGIQY
Sbjct:    3 LYVFWLIYISHVTSSNGNRSIVFRGPVHVIENQIGQFICSLNTREEFQNISVKNLKTEIISWFESNGDEKCVVFQREYRKYISNCSIDNGVLSYEMAFLAAFEGPFTCQIGIKNELYNRSINVLVNAPSPVFNSTDRLIYYENETFSFSCHSVNNNNTNILMIINYIVYANGIQEDLDY----SSLITTTQLNLNQTMNDASIGCGIQY 207
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BLAST of SMED30013765 vs. Planmine SMEST
Match: SMESG000018952.1 (SMESG000018952.1)

HSP 1 Score: 263.077 bits (671), Expect = 5.686e-81
Identity = 135/209 (64.59%), Postives = 169/209 (80.86%), Query Frame = -2 
Query:    1 LTAIFFLGLQLIPANSLNRSVIFTGPVHVIENQMEQFICSLNTREDFQNISVKHSNSEILFW--TNLNEKCSV-SKDFKNYLSNCTKDSGMLSYEMAFIQAFEGKITCQIEINNERYDRNINVFVNASSPIFNSTERLIYYENETFSFSCQSV-NKKTNV-MIINYIVYANGIQEDLNYASTNSSLITITQLNLNQTLHDASIGCGIQY 612
            L   + + +  + +++ NRS++F GPVHVIENQ+ +FICSLNTRE+FQNISVK+  +EI+ W  +N +EKC V  ++++ Y+SNC+ D+G+LSYEMAF+ AFEG  TCQI I NE Y+R+INV VNA SP+FNST+RLIYYENETFSFSC SV N  TN+ MIINYIVYANGIQEDL+Y    SSLIT TQLNLNQT++DASIGCGIQY
Sbjct:    3 LYVFWLIYISHVTSSNGNRSIVFRGPVHVIENQIGKFICSLNTREEFQNISVKNLKTEIISWFESNGDEKCVVFQREYRKYISNCSIDNGVLSYEMAFLAAFEGPFTCQIGIKNELYNRSINVLVNAPSPVFNSTDRLIYYENETFSFSCHSVNNNNTNILMIINYIVYANGIQEDLDY----SSLITTTQLNLNQTMNDASIGCGIQY 207
The following BLAST results are available for this feature:
BLAST of SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 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 SMED30013765 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000018709.11.125e-137100.00SMESG000018709.1[more]
SMESG000018945.11.368e-8165.07SMESG000018945.1[more]
SMESG000018952.15.686e-8164.59SMESG000018952.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013765 ID=SMED30013765|Name=SMED30013765|organism=Schmidtea mediterranea sexual|type=transcript|length=628bp
ATACTGGATTCCGCATCCAATGCTTGCGTCATGCAATGTTTGATTGAGAT
TCAATTGAGTAATCGTAATTAAGGATGAATTGGTGCTTGCATAATTGAGG
TCTTCTTGTATCCCATTTGCATATACGATATAGTTTATAATCATAACATT
CGTCTTCTTATTCACCGACTGACATGAAAAGCTGAAAGTTTCATTTTCAT
AATAAATTAATCGTTCCGTCGAATTGAAAATGGGACTCGAGGCATTAACG
AACACATTGATGTTTCTGTCGTATCTTTCGTTATTAATCTCGATTTGGCA
GGTGATTTTACCTTCGAAGGCCTGTATGAAAGCCATTTCATACGATAGCA
TTCCACTGTCCTTTGTGCAATTGGATAAATAGTTTTTAAAATCTTTGCTA
ACAGAACACTTTTCGTTCAAATTTGTCCAAAAAAGTATTTCACTATTTGA
ATGTTTTACAGAGATATTTTGAAAATCTTCTCGTGTATTTAGTGAACAAA
TAAATTGTTCCATTTGGTTCTCAATGACATGTACAGGGCCCGTGAAAATG
ACAGACCTGTTTAGAGAGTTAGCTGGAATGAGCTGAAGACCAAGAAAAAA
AATCGCAGTCAACACTACGAAACAAGAA
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protein sequence of SMED30013765-orf-1

>SMED30013765-orf-1 ID=SMED30013765-orf-1|Name=SMED30013765-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=209bp
SCFVVLTAIFFLGLQLIPANSLNRSVIFTGPVHVIENQMEQFICSLNTRE
DFQNISVKHSNSEILFWTNLNEKCSVSKDFKNYLSNCTKDSGMLSYEMAF
IQAFEGKITCQIEINNERYDRNINVFVNASSPIFNSTERLIYYENETFSF
SCQSVNKKTNVMIINYIVYANGIQEDLNYASTNSSLITITQLNLNQTLHD
ASIGCGIQY
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region