SMED30023204

Overview
NameSMED30023204
Smed IDSMED30023204
Length (bp)511
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



SMED30023204

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30023204SMESG000035930.1 SMESG000035929.1 Contig43503newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023204SMESG000035930.1 SMESG000035929.1 Contig43503uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
reproductive organSMED30023204SMESG000035930.1 SMESG000035929.1 Contig43503newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30023204SMESG000035930.1 SMESG000035929.1 Contig43503uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023204 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000391:74336..74839 +2520
Homology
[Close]
BLAST of SMED30023204 vs. TrEMBL
Match: A0A4S2M441 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_004135 PE=4 SV=1)

HSP 1 Score: 95.9005 bits (237), Expect = 1.849e-22
Identity = 49/112 (43.75%), Postives = 64/112 (57.14%), Query Frame = 2 
Query:  122 ESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKIYK 457
            E+  R +F  YAKTRRGL T+NYE IE +L R  L+ PP   ES  +RE+ + YG   ++E D   F      V+S   AK +NI   EA+ II E  I K P S +E+I K
Sbjct:    2 ENPFRDAFYAYAKTRRGLVTLNYEMIEAMLTRAGLFTPPAFNESVFQREFKRAYGNTESKERDFQDFTDVCKKVISPCLAKARNISPDEAFKIIQEELIAKQPKSASERIIK 113
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BLAST of SMED30023204 vs. Planmine SMEST
Match: SMESG000035930.1 (SMESG000035930.1)

HSP 1 Score: 253.832 bits (647), Expect = 3.581e-88
Identity = 124/124 (100.00%), Postives = 124/124 (100.00%), Query Frame = 2 
Query:   86 MAKYPMEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKIYK 457
            MAKYPMEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKIYK
Sbjct:    1 MAKYPMEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKIYK 124
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BLAST of SMED30023204 vs. Planmine SMEST
Match: SMESG000035930.1 (SMESG000035930.1)

HSP 1 Score: 243.432 bits (620), Expect = 4.770e-84
Identity = 119/119 (100.00%), Postives = 119/119 (100.00%), Query Frame = 2 
Query:  101 MEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKIYK 457
            MEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKIYK
Sbjct:    1 MEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKIYK 119
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BLAST of SMED30023204 vs. Planmine SMEST
Match: SMESG000059037.1 (SMESG000059037.1)

HSP 1 Score: 184.496 bits (467), Expect = 1.065e-60
Identity = 85/121 (70.25%), Postives = 103/121 (85.12%), Query Frame = 2 
Query:   89 AKYPMEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKI 451
             KYPMEKRYDAESELRT++ KY KTRRGL T++Y AIE+ILKRC LY PP LTESTL+RE++KF+GG++ QELD P FDKF+I++VSKL+AK KNIEHQ AYDI++E  I+KAP S  EKI
Sbjct:    3 GKYPMEKRYDAESELRTAYKKYTKTRRGLATLDYTAIEKILKRCGLYAPPILTESTLEREFVKFFGGNMKQELDFPSFDKFLIEIVSKLFAKVKNIEHQHAYDIMVEAIIKKAPKSPIEKI 123
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BLAST of SMED30023204 vs. Planmine SMEST
Match: SMESG000003066.1 (SMESG000003066.1)

HSP 1 Score: 184.111 bits (466), Expect = 1.325e-60
Identity = 82/121 (67.77%), Postives = 104/121 (85.95%), Query Frame = 2 
Query:   89 AKYPMEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKI 451
             K+PMEKRYD ESELRT+F KY  TRR +GT+NYE+IE+I KRC LYVPP LTESTL+RE+ K +GG+L+QELDL  FDKF+IDV+SK+YAK KNI+HQ+AYDIII+ FI+ +P S+NE++
Sbjct:    4 GKHPMEKRYDMESELRTAFEKYTATRRAVGTLNYESIEKIFKRCGLYVPPVLTESTLRREFTKVHGGNLSQELDLYSFDKFLIDVISKMYAKAKNIDHQQAYDIIIDGFIEHSPQSINEQL 124
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BLAST of SMED30023204 vs. Planmine SMEST
Match: SMESG000003036.1 (SMESG000003036.1)

HSP 1 Score: 184.111 bits (466), Expect = 1.325e-60
Identity = 82/121 (67.77%), Postives = 104/121 (85.95%), Query Frame = 2 
Query:   89 AKYPMEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVPPGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQEAYDIIIETFIQKAPTSVNEKI 451
             K+PMEKRYD ESELRT+F KY  TRR +GT+NYE+IE+I KRC LYVPP LTESTL+RE+ K +GG+L+QELDL  FDKF+IDV+SK+YAK KNI+HQ+AYDIII+ FI+ +P S+NE++
Sbjct:    4 GKHPMEKRYDMESELRTAFEKYTATRRAVGTLNYESIEKIFKRCGLYVPPVLTESTLRREFTKVHGGNLSQELDLYSFDKFLIDVISKMYAKAKNIDHQQAYDIIIDGFIEHSPQSINEQL 124
The following BLAST results are available for this feature:
BLAST of SMED30023204 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 SMED30023204 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 SMED30023204 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 SMED30023204 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 SMED30023204 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 SMED30023204 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 SMED30023204 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 SMED30023204 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A4S2M4411.849e-2243.75Uncharacterized protein OS=Opisthorchis felineus O... [more]
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BLAST of SMED30023204 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 SMED30023204 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 SMED30023204 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 SMED30023204 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 SMED30023204 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 SMED30023204 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000035930.13.581e-88100.00SMESG000035930.1[more]
SMESG000035930.14.770e-84100.00SMESG000035930.1[more]
SMESG000059037.11.065e-6070.25SMESG000059037.1[more]
SMESG000003066.11.325e-6067.77SMESG000003066.1[more]
SMESG000003036.11.325e-6067.77SMESG000003036.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023204 ID=SMED30023204|Name=SMED30023204|organism=Schmidtea mediterranea sexual|type=transcript|length=511bp
AGATTTAATAATTGTTGTTAAGATATTCAAAAATAATTTAATGAAATCTA
ATAAATAAAATTATATCAAAAGTAAATTTTAAGAGATGGCGAAGTACCCA
ATGGAAAAGAGATATGATGCGGAATCAGAACTGAGAACGTCTTTTGCTAA
ATATGCTAAAACTCGCCGAGGATTAGGAACTGTAAATTACGAAGCAATTG
AACAGATTTTGAAGCGATGCAATCTTTATGTGCCCCCAGGATTGACTGAA
AGCACATTGAAAAGAGAATACATCAAATTTTACGGCGGTGACCTCAATCA
GGAATTAGATTTGCCGAAATTTGATAAGTTTATCATAGATGTGGTTTCAA
AATTGTACGCAAAAGGGAAAAATATTGAACATCAAGAAGCCTATGACATT
ATTATTGAGACGTTCATCCAAAAGGCTCCAACGTCTGTAAATGAAAAAAT
TTATAAATGACTTTATTGATACATTTGTCACTCATTAAAAATATTCTCAG
TCAAAAAAAAA
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protein sequence of SMED30023204-orf-1

>SMED30023204-orf-1 ID=SMED30023204-orf-1|Name=SMED30023204-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
MAKYPMEKRYDAESELRTSFAKYAKTRRGLGTVNYEAIEQILKRCNLYVP
PGLTESTLKREYIKFYGGDLNQELDLPKFDKFIIDVVSKLYAKGKNIEHQ
EAYDIIIETFIQKAPTSVNEKIYK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ