SMED30013479

Overview
NameSMED30013479
Smed IDSMED30013479
Length (bp)2070
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



SMED30013479

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30013479h1SMcG0001894 Contig1740uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30013479h1SMcG0001894 Contig1740newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30013479h1SMcG0014605 Contig1740uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30013479h1SMcG0014605 Contig1740newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30013479h1SMcG0014605 SmedASXL_018153SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30013479h1SMcG0014605 dd_Smed_v6_9223_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30013479h1SMcG0014605 dd_Smed_v6_13594_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30013479h1SMcG0014605 OX_Smed_1.0.07834ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30013479h1SMcG0001894 Contig1740uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30013479h1SMcG0001894 Contig1740newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30013479h1SMcG0014607 Contig51118uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30013479h1SMcG0014605 Contig51118uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30013479h1SMcG0014605 Contig1740uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30013479h1SMcG0014605 Contig1740newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30013479 vs. Planmine SMEST
Match: SMESG000009144.1 (SMESG000009144.1)

HSP 1 Score: 905.59 bits (2339), Expect = 0.000e+0
Identity = 567/635 (89.29%), Postives = 570/635 (89.76%), Query Frame = -2 
Query:    3 LDNINMKLNWTLRKYLQCQARFTGALGRLIGLESRKRYLKMRNFLENKINRLFGKRHSINKRKHLRVRKFKNENQLIKKCLRNNLKEIYQIIKRKIINEYHYKLIKKRINFMRRIIRHAKIRNSRIILKQIRNLKIFLTKIKRTNGLKSLKMEHFLKDGKIGHRKRLENYIRHILVTRSKSKQSRSFEYNKYKNWIGKSLSRQRFRVERTRNRFDSDRQYRYSGSKQMKIHKNSYKXXXXXXXXXXXXXXXXSLKFMTKNKDLGDLLESLKRLNKFYSSRREGNNYQSLKRNNKSRVGKKNKS-------KRDXXXXXXXXXLTHQKKNKSRKYRAQFLXXXXXXXXXXKYFAKHFRIXXXXXXXXXXXXXXXXKHKNMKRNRLKKYIEKITSNDKEIQNIKRHISKYKTSKTRKLSMNSKLSGLQFIRSKKFKKQSSRNRNHKIVKKIANKSLLRVKKEKLKPKQSLTNEKHFKTLVKFLWNHRYQLLRRKARINNRRHXXXXXXXXXXXKRIN-------------------------------RRISK-----------------------NHNKKHITKSLRRMKNKGKYHSKLSDSQRNSKQNRILMHGKQKSHRLIKSRKTQNKIKITK 1724
            +DNINMKLNWTLRKYLQCQARFTGALGRLIGLESRKRYLKMRNFLENKINRLFGKRHSINKRKHLRVRKFKNENQLIKKCLRNNLKEIYQIIKRKIINEYHYKLIKKRINFMRRIIRHAKIRNSRIILKQIRNLKIFLTKIKRTNGLKSLKMEHFLKDGKIGHRKRLENYIRHILVTRSKSKQSRSFEYNKYKNWIGKSLSRQRFRVERTR RFDSDRQYRYSGSKQMKIHKNSYKNRFFSRNINKNNKNQNSLKFMTKNKDL DLLESLKRLNKFYSSRREGNNYQSL RNNKSRVGKKNKS       KRDYKLYKLRYKLTHQKKNKSRKYRAQFLNKNKKRRVNKKYFAKHFRILQKLKQLNKYYLKQLQKHKNMKRNRLKKYIEKITSNDKEIQNIKRHISKYKTS+TRKLSMNSKLSGLQFIRSKKFKKQSSRNRNHK VKKIANKSLLRVKKEKLKPKQSLTNEKHFKTLVKFLWNHRYQLLRRKARINNRRHKKSKKQTKNSTKRIN                               R+ISK                       NHNKKHITKSLRRMKNKGKYHSKLSDSQRNSKQNRILMHGKQKSHRLIKSRKTQNKIKITK
Sbjct:   39 IDNINMKLNWTLRKYLQCQARFTGALGRLIGLESRKRYLKMRNFLENKINRLFGKRHSINKRKHLRVRKFKNENQLIKKCLRNNLKEIYQIIKRKIINEYHYKLIKKRINFMRRIIRHAKIRNSRIILKQIRNLKIFLTKIKRTNGLKSLKMEHFLKDGKIGHRKRLENYIRHILVTRSKSKQSRSFEYNKYKNWIGKSLSRQRFRVERTRKRFDSDRQYRYSGSKQMKIHKNSYKNRFFSRNINKNNKNQNSLKFMTKNKDLEDLLESLKRLNKFYSSRREGNNYQSLNRNNKSRVGKKNKSKRLNKGRKRDYKLYKLRYKLTHQKKNKSRKYRAQFLNKNKKRRVNKKYFAKHFRILQKLKQLNKYYLKQLQKHKNMKRNRLKKYIEKITSNDKEIQNIKRHISKYKTSETRKLSMNSKLSGLQFIRSKKFKKQSSRNRNHKTVKKIANKSLLRVKKEKLKPKQSLTNEKHFKTLVKFLWNHRYQLLRRKARINNRRHKKSKKQTKNSTKRINRIEIDNKKSRHIRKHGKQHEHERRQIKWKHRRQISKKSHIGTNKHSGTHQKRNYQRISKNHNKKHITKSLRRMKNKGKYHSKLSDSQRNSKQNRILMHGKQKSHRLIKSRKTQNKIKITK 673
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BLAST of SMED30013479 vs. Planmine SMEST
Match: SMESG000009143.1 (SMESG000009143.1)

HSP 1 Score: 93.9745 bits (232), Expect = 1.068e-19
Identity = 48/48 (100.00%), Postives = 48/48 (100.00%), Query Frame = -2 
Query:    3 MKNKGKYHSKLSDSQRNSKQNRILMHGKQKSHRLIKSRKTQNKIKITK 146
            MKNKGKYHSKLSDSQRNSKQNRILMHGKQKSHRLIKSRKTQNKIKITK
Sbjct:    1 MKNKGKYHSKLSDSQRNSKQNRILMHGKQKSHRLIKSRKTQNKIKITK 48
The following BLAST results are available for this feature:
BLAST of SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 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 SMED30013479 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000009144.10.000e+089.29SMESG000009144.1[more]
SMESG000009143.11.068e-19100.00SMESG000009143.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013479 ID=SMED30013479|Name=SMED30013479|organism=Schmidtea mediterranea sexual|type=transcript|length=2070bp
GATTTTGTAATCTTTATCTTGTTTTGTGTTTTTCGGCTCTTGATTAATCT
ATGAGACTTTTGTTTGCCGTGCATTAATATCCGGTTTTGTTTTGAATTTC
TTTGAGAATCTGATAATTTACTATGATATTTGCCTTTATTTTTCATTCTT
CTTAATGATTTTGTAATATGCTTTTTATTGTGATTTTTACTGATTCTTCG
ATTGATTCTTTTGGTTGAATTTTTGGTTTGTTTTTTACTTTTTTTATGTC
GTCGATTGTTTATTCTCGCTTTCCGGCGTAACAATTGATATCTGTGATTC
CATAGAAATTTCACTAATGTTTTAAAATGCTTTTCATTGGTCAAACTTTG
TTTGGGTTTTAATTTCTCTTTTTTAACCCTTAATAAACTTTTATTTGCTA
TTTTCTTTACAATTTTATGATTTCTATTCCTACTAGATTGTTTTTTAAAT
TTTTTACTGCGAATGAACTGAAGTCCTGAAAGCTTTGAATTCATAGACAA
TTTTCTGGTTTTAGATGTTTTGTATTTCGAAATATGTCTTTTTATGTTTT
GTATTTCTTTATCGTTGCTCGTGATTTTCTCGATGTACTTTTTCAATCGA
TTTCTTTTCATATTTTTATGTTTTTGTAATTGTTTTAAATAATATTTATT
TAATTGTTTTAACTTTTGTAGAATTCGAAAATGTTTTGCAAAGTATTTTT
TATTTACTCGTCTCTTTTTGTTTTTATTTAAAAATTGTGCACGATATTTT
CTTGATTTGTTTTTCTTTTGATGCGTAAGTTTGTATCTAAGTTTATACAA
TTTATAATCTCTTTTACTTTTATTTTTTTTACCAACTCGACTTTTATTGT
TTCTCTTTAATGATTGGTAATTATTTCCTTCTCTTCGACTCGAGTAAAAT
TTATTCAATCTCTTCAAACTTTCCAATAAATCTCCTAAATCTTTATTTTT
TGTCATAAATTTTAATGAATTTTGATTTTTATTATTTTTGTTGATATTTC
GAGAAAAAAATCGATTTTTGTAACTATTTTTGTGTATTTTCATTTGTTTA
GAACCGGAATATCGATATTGTCTGTCACTATCGAATCTATTCCTCGTTCT
TTCTACACGGAATCTTTGTCGACTCAAACTTTTCCCTATCCAATTTTTAT
ATTTATTATATTCGAAGGATCTTGATTGCTTGGACTTGCTCCTAGTTACT
AAAATATGTCTGATATAGTTTTCCAATCTTTTTCTATGGCCAATTTTCCC
GTCTTTAAGAAAATGCTCCATTTTCAATGATTTCAATCCATTTGTTCTCT
TTATTTTTGTAAGGAAAATTTTCAAATTTCTAATTTGCTTCAATATTATT
CTAGAATTTCTGATTTTTGCGTGACGAATAATTCGTCTCATAAAATTAAT
TCGTTTCTTTATCAATTTATAGTGATATTCATTGATGATTTTTCTTTTAA
TTATTTGATAAATTTCTTTGAGATTATTTCTCAAACACTTTTTAATCAGC
TGATTTTCATTTTTAAATTTTCGAACTCGCAAATGCTTTCGTTTGTTTAT
TGAATGTCGTTTCCCAAACAATCGGTTTATTTTGTTTTCGAGGAAATTTC
TCATTTTCAAATACCTCTTCCTGGATTCCAGTCCAATTAACCGACCGAGA
GCCCCAGTGAATCGTGCTTGACATTGAAGGTATTTTCGTAATGTCCAATT
CAATTTCATGTTGATGTTGTCTAAATATTAATATATCAAATTTGTTGACA
AAAATGTGCAGAAAATTCTCACTAACCAATTCCTTGAACATTTCTGTCGG
CTTTTCCCGTTTCCAAATCATAAATTTCAGCCTTTCCATTAGAACTCAGC
GAAAATAAAATTATCAAACAGAATAAAAGTTTAATTTTACTCATTTTGTG
TGAAACAAGCAAAATTATGGAATTAATTTCGATGGTAATTCTAAACAATA
TATATTCAGTTGTCAAATTAAGACAGATGTTCAAATGTGCAACTTGACAA
TATTCTAACTAGGAACATTTGTTGAAGAACCTCTTCAATATAAAACCATT
AATAATAATAATAATAATAA
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protein sequence of SMED30013479-orf-1

>SMED30013479-orf-1 ID=SMED30013479-orf-1|Name=SMED30013479-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
MERLKFMIWKREKPTEMFKELVSENFLHIFVNKFDILIFRQHQHEIELDI
TKIPSMSSTIHWGSRSVNWTGIQEEVFENEKFPRKQNKPIVWETTFNKQT
KAFASSKI*
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protein sequence of SMED30013479-orf-2

>SMED30013479-orf-2 ID=SMED30013479-orf-2|Name=SMED30013479-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=569bp
MKLNWTLRKYLQCQARFTGALGRLIGLESRKRYLKMRNFLENKINRLFGK
RHSINKRKHLRVRKFKNENQLIKKCLRNNLKEIYQIIKRKIINEYHYKLI
KKRINFMRRIIRHAKIRNSRIILKQIRNLKIFLTKIKRTNGLKSLKMEHF
LKDGKIGHRKRLENYIRHILVTRSKSKQSRSFEYNKYKNWIGKSLSRQRF
RVERTRNRFDSDRQYRYSGSKQMKIHKNSYKNRFFSRNINKNNKNQNSLK
FMTKNKDLGDLLESLKRLNKFYSSRREGNNYQSLKRNNKSRVGKKNKSKR
DYKLYKLRYKLTHQKKNKSRKYRAQFLNKNKKRRVNKKYFAKHFRILQKL
KQLNKYYLKQLQKHKNMKRNRLKKYIEKITSNDKEIQNIKRHISKYKTSK
TRKLSMNSKLSGLQFIRSKKFKKQSSRNRNHKIVKKIANKSLLRVKKEKL
KPKQSLTNEKHFKTLVKFLWNHRYQLLRRKARINNRRHKKSKKQTKNSTK
RINRRISKNHNKKHITKSLRRMKNKGKYHSKLSDSQRNSKQNRILMHGKQ
KSHRLIKSRKTQNKIKITK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000418head
PLANA:0000419prepharyngeal region
PLANA:0002089reproductive organ