SMED30011796

Overview
NameSMED30011796
Smed IDSMED30011796
Length (bp)881
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

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



Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30011796 (SMED30011796) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011796 (SMED30011796) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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



SMED30011796

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30011796h1SMcG0005548 SmedASXL_065904SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011796 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.015187:4469..5349 -4306
Homology
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BLAST of SMED30011796 vs. Planmine SMEST
Match: SMESG000024960.1 (SMESG000024960.1)

HSP 1 Score: 374.015 bits (959), Expect = 1.889e-132
Identity = 195/200 (97.50%), Postives = 197/200 (98.50%), Query Frame = 1 
Query:  112 MNLPTIKLPRVHLPVVRLPGIHLPAVRLPEVNLYGHNQNMSYNPNPCPSYYASTSEVGNSHHITMAPPRRPKNKFVTRYPKSNYILSIIVILLGFVIMVIDPLFAANRRYLGSFAIQAFFMIIGGVVCIHGVWNNNRCCLTAALVMHCHAIGGSPYGFCVLSAVNDSSVYFVVNXXXXXXXXXFTISHLFVVSIDICKKR 711
            MNLPTI LPRVHLPVVR PGIHLPAVRLPEVNLYGHNQNMSYNPNPCPSYYASTSEVGNSHHIT+APPR PKNKFVTRYPKSNYILSIIVILLGFVIMVIDPLFAANRRYLGSFA+QAFFMIIGGVVCIHGVWNNNRCCLTAALVMHCHAIGGSPYGFCVLSAVNDSSVYFVVNLIIGIIGLLFTISHLFVVSIDICKKR
Sbjct:    1 MNLPTITLPRVHLPVVRPPGIHLPAVRLPEVNLYGHNQNMSYNPNPCPSYYASTSEVGNSHHITVAPPRIPKNKFVTRYPKSNYILSIIVILLGFVIMVIDPLFAANRRYLGSFAVQAFFMIIGGVVCIHGVWNNNRCCLTAALVMHCHAIGGSPYGFCVLSAVNDSSVYFVVNLIIGIIGLLFTISHLFVVSIDICKKR 200
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BLAST of SMED30011796 vs. Planmine SMEST
Match: SMESG000046778.1 (SMESG000046778.1)

HSP 1 Score: 65.855 bits (159), Expect = 8.296e-13
Identity = 45/143 (31.47%), Postives = 67/143 (46.85%), Query Frame = 1 
Query:  286 NSHHITMAPPRRPKNKFVTRYPKSNYILSIIVILLGFVIMVIDPLFAANRRYLGSFAIQAFFMIIGGVVCIHGVWNNNRCCLTAALVMHCHAIGGSPYGFCVLSAVNDSSVY-FVVNXXXXXXXXXFTISHLFVVSIDICKKR 711
            N   + ++ P    +KF    P  +Y   II++ LG +I+  DPL      +  + +    FMII G+  IHG WN++R CL  A+VM+  A+ G   GF   S      +Y F+V L          IS L ++   IC  R
Sbjct:   30 NLATVNLSIPNTLNSKFTLTRPNLHYRFGIIILFLGTLIICFDPLLPFTHTFTNTNSGGTIFMIISGISSIHGSWNHSRGCLITAIVMNSLAVVGLFTGFLFASMAGGFGLYNFIVGL----------ISFLILLVDQICLSR 162
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BLAST of SMED30011796 vs. Planmine SMEST
Match: SMESG000046853.1 (SMESG000046853.1)

HSP 1 Score: 53.1434 bits (126), Expect = 2.629e-8
Identity = 27/93 (29.03%), Postives = 45/93 (48.39%), Query Frame = 1 
Query:  292 HHITMAPPRRPKNKFVTRYPKSNYILSIIVILLGFVIMVIDPLFAANRRYLGSFAIQAFFMIIGGVVCIHGVWNNNRCCLTAALVMHCHAIGG 570
            H +T        ++   RY + +    +  + +G +IM++DPL         +  +    + IGG+  +HG WNNNRCCL   LV +  A+ G
Sbjct:   36 HSLTPEIVISEDSRKTFRYQRHHIRYGVNAMFVGMLIMILDPLMPVLLLSSTTIFVGGLMIFIGGITSVHGGWNNNRCCLINTLVFNILALFG 128
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BLAST of SMED30011796 vs. Planmine SMEST
Match: SMESG000046817.1 (SMESG000046817.1)

HSP 1 Score: 53.5286 bits (127), Expect = 3.778e-8
Identity = 28/93 (30.11%), Postives = 45/93 (48.39%), Query Frame = 1 
Query:  286 NSHHITMAPPRRPKNKFVTRYPKSNYILSIIVILLGFVIMVIDPLFAANRRYLGSFAIQAFFMIIGGVVCIHGVWNNNRCCLTAALVMHCHAI 564
            N   +   P   P    + R+ K++  L I++ ++G + M++DPL  A   Y  S      FM+I G+  IHG    +RC L A+L     A+
Sbjct:   62 NQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDILAL 154
[Close]
BLAST of SMED30011796 vs. Planmine SMEST
Match: SMESG000046814.1 (SMESG000046814.1)

HSP 1 Score: 53.5286 bits (127), Expect = 3.778e-8
Identity = 28/93 (30.11%), Postives = 45/93 (48.39%), Query Frame = 1 
Query:  286 NSHHITMAPPRRPKNKFVTRYPKSNYILSIIVILLGFVIMVIDPLFAANRRYLGSFAIQAFFMIIGGVVCIHGVWNNNRCCLTAALVMHCHAI 564
            N   +   P   P    + R+ K++  L I++ ++G + M++DPL  A   Y  S      FM+I G+  IHG    +RC L A+L     A+
Sbjct:   62 NQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDILAL 154
The following BLAST results are available for this feature:
BLAST of SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 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 SMED30011796 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000024960.11.889e-13297.50SMESG000024960.1[more]
SMESG000046778.18.296e-1331.47SMESG000046778.1[more]
SMESG000046853.12.629e-829.03SMESG000046853.1[more]
SMESG000046817.13.778e-830.11SMESG000046817.1[more]
SMESG000046814.13.778e-830.11SMESG000046814.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011796 ID=SMED30011796|Name=SMED30011796|organism=Schmidtea mediterranea sexual|type=transcript|length=881bp
GAAAAATGCTGTTGATGAGATATTTATAAATCTGTATCGTTTAGCAGTTT
GCATTGTGATTTGAATCTGATTCAAAACCAACTAACCCTACCTTTAATTC
ATTAAATTACGATGAATCTCCCAACAATTAAACTTCCGAGAGTGCATTTA
CCAGTAGTCAGACTACCGGGAATTCACCTGCCGGCGGTTAGGTTGCCGGA
AGTGAATCTGTATGGACATAATCAGAATATGTCTTATAATCCAAATCCTT
GTCCAAGTTATTATGCAAGCACATCTGAAGTTGGAAATAGTCATCATATT
ACCATGGCCCCTCCAAGAAGACCGAAAAATAAATTTGTCACCAGATATCC
AAAGTCAAATTATATTTTATCAATAATAGTAATATTACTTGGATTTGTAA
TTATGGTAATTGACCCTCTTTTTGCTGCTAACCGAAGATATTTAGGTTCA
TTTGCGATTCAAGCGTTTTTCATGATTATTGGAGGGGTTGTCTGTATTCA
TGGAGTTTGGAATAACAATCGATGCTGTTTAACTGCTGCTTTGGTGATGC
ATTGTCATGCGATTGGGGGGTCACCTTATGGATTTTGTGTATTATCTGCA
GTTAATGATAGTTCCGTGTATTTTGTCGTTAACCTCATTATAGGTATCAT
TGGGCTATTATTCACAATTTCTCATTTGTTTGTTGTCAGCATTGATATCT
GTAAAAAGCGATAATTTGTACATCATTTTAAATAAACTTATCCAGTTCCA
ATCATTCTTTCCTCTAAATACGGAGAGAAATGTATCTTCATCCATTTTTA
CCAACTTATTCATACATTTGTGAATCTTAGTCCTTCCAAGAAGCATTTCT
TCCCAAAATCCTTTCAGAAATATAATTTTGG
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protein sequence of SMED30011796-orf-1

>SMED30011796-orf-1 ID=SMED30011796-orf-1|Name=SMED30011796-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=201bp
MNLPTIKLPRVHLPVVRLPGIHLPAVRLPEVNLYGHNQNMSYNPNPCPSY
YASTSEVGNSHHITMAPPRRPKNKFVTRYPKSNYILSIIVILLGFVIMVI
DPLFAANRRYLGSFAIQAFFMIIGGVVCIHGVWNNNRCCLTAALVMHCHA
IGGSPYGFCVLSAVNDSSVYFVVNLIIGIIGLLFTISHLFVVSIDICKKR
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 84..106
NoneNo IPR availableTMHMMTMhelixcoord: 170..192
NoneNo IPR availableTMHMMTMhelixcoord: 138..160
NoneNo IPR availableTMHMMTMhelixcoord: 111..133