SMED30006310

Overview
NameSMED30006310
Smed IDSMED30006310
Length (bp)990
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30006310 (SMED30006310) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30006310 (SMED30006310) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30006310

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
reproductive organSMED30006310SMESG000043711.1 SMESG000043707.1 Contig32919newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30006310SMESG000043711.1 SMESG000043707.1 Contig32919uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30006310 vs. Planmine SMEST
Match: SMESG000043707.1 (SMESG000043707.1)

HSP 1 Score: 560.836 bits (1444), Expect = 0.000e+0
Identity = 302/322 (93.79%), Postives = 307/322 (95.34%), Query Frame = 3 
Query:   39 MIKLLYFYELIQRTFTFKLFQANTTLISK-----TGNAAATYDVEFDNVKWXXXXXXXXXXQDEKPLKVSVNGKQLNVRINSYGFITTESNDSMLGYFHMNEKYEITGLFELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTNILKQNIFNKHCYAKVIIGPYLYSRFSETLDFVTXXXXXXXXXXXXXNIFIRLNLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGPVYQAAMDAYCNLSITSFDLITSFDNVHSDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRNFFLNLLPKHLMKSSYSISLLL 989
            MIKLLYF ELI R F+FKLFQANT LI K     TGNA ATYD+EFDNVKWKIKIFYYKY QDEKPLKVSVNGKQLNVRINSYGFI TESN+SMLGYFHMNEKYEITGL ELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTNILKQNIFNKHCYAKVIIGPYLYSRFSETLDFVTEREKLIRLKLLLENIFIRLNLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGPVYQAAMDAYCNLSITSFDL+TSFDNV SDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRNFFLNLLPKHLMKSSYSISL+L
Sbjct:    1 MIKLLYFLELILRIFSFKLFQANTRLIGKIGDIKTGNATATYDIEFDNVKWKIKIFYYKYLQDEKPLKVSVNGKQLNVRINSYGFIITESNNSMLGYFHMNEKYEITGLVELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTNILKQNIFNKHCYAKVIIGPYLYSRFSETLDFVTEREKLIRLKLLLENIFIRLNLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGPVYQAAMDAYCNLSITSFDLMTSFDNVLSDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRNFFLNLLPKHLMKSSYSISLIL 322
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BLAST of SMED30006310 vs. Planmine SMEST
Match: SMESG000043711.1 (SMESG000043711.1)

HSP 1 Score: 544.273 bits (1401), Expect = 0.000e+0
Identity = 300/322 (93.17%), Postives = 304/322 (94.41%), Query Frame = 3 
Query:   39 MIKLLYFYELIQRTFTFKLFQANTTLISK-----TGNAAATYDVEFDNVKWXXXXXXXXXXQDEKPLKVSVNGKQLNVRINSYGFITTESNDSMLGYFHMNEKYEITGLFELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTNILKQNIFNKHCYAKVIIGPYLYSRFSETLDFVTXXXXXXXXXXXXXNIFIRLNLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGPVYQAAMDAYCNLSITSFDLITSFDNVHSDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRNFFLNLLPKHLMKSSYSISLLL 989
            MIKLLY  ELI R F+FKLFQANT LI K     TGNA  TYD+EFDNVKWKIKIFYYKY QDEKPLKVSVNGKQLNVRINSYGFITTESN+SMLGYFHMNEKYEITGL ELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQT ILKQNIFNKHCYAKVIIGPYLYSRFSETLDFVTEREKLIRLKLLLENIFIRLNLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGP YQAAMDAYCNLSITSFDLITSFDNV SDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRNFFLNLLPKHLMKSSYSISL+L
Sbjct:    1 MIKLLYLLELILRIFSFKLFQANTRLIGKIGDIKTGNATVTYDIEFDNVKWKIKIFYYKYLQDEKPLKVSVNGKQLNVRINSYGFITTESNNSMLGYFHMNEKYEITGLVELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTKILKQNIFNKHCYAKVIIGPYLYSRFSETLDFVTEREKLIRLKLLLENIFIRLNLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGPAYQAAMDAYCNLSITSFDLITSFDNVLSDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRNFFLNLLPKHLMKSSYSISLIL 322
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BLAST of SMED30006310 vs. Planmine SMEST
Match: SMESG000043766.1 (SMESG000043766.1)

HSP 1 Score: 451.44 bits (1160), Expect = 6.184e-155
Identity = 246/317 (77.60%), Postives = 274/317 (86.44%), Query Frame = 3 
Query:   39 MIKLLYFYELIQRTFTFKLFQANTTLISKTGNAAATYDVEFDNVKWXXXXXXXXXXQDEKPLKVSVNGKQLNVRINSYGFITTESNDSMLGYFHMNEKYEITGLFELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTNILKQNIFNKHCYAKVIIGPYLYSRFSETLDFVTXXXXXXXXXXXXXNIFIRLNLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGPVYQAAMDAYCNLSITSFDLITSFDNVHSDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRNFFLNLLPKHLMKSSYSISLLL 989
            MIKLLYF++LIQRTFTFKLFQANTTLISKTGNAAATYDVEFDNVKWKIKIFYYKYFQDEKPLKV+ NGK+L V INSYGFITTESN+SMLGYFHMNEKYEI G  EL NKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQT ILK+NIFNK CY KVIIGPYLY+  SE L+F TEREKL+RLKL+++NIF+R+NLIFNELPW++RT+F VDHL+I+TPKMC   YKGP YQA + +YCNL+IT F+L+ SF  V SDN YCM  S +HH +IT   GY  +GTLCQ  YN+RNFFLNLL K LMKSS   SLLL
Sbjct:    1 MIKLLYFFQLIQRTFTFKLFQANTTLISKTGNAAATYDVEFDNVKWKIKIFYYKYFQDEKPLKVTFNGKRLIVLINSYGFITTESNESMLGYFHMNEKYEIIGSVELHNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTKILKENIFNKRCYVKVIIGPYLYTSLSENLEFGTEREKLLRLKLVIQNIFLRINLIFNELPWELRTEFFVDHLIIMTPKMCTSSYKGPAYQAIVKSYCNLNITPFELLGSFAKVRSDNNYCMQVSFIHHPRITPKIGYGRVGTLCQRLYNVRNFFLNLLSKSLMKSSNYTSLLL 317
[Close]
BLAST of SMED30006310 vs. Planmine SMEST
Match: SMESG000043787.1 (SMESG000043787.1)

HSP 1 Score: 435.647 bits (1119), Expect = 4.356e-149
Identity = 231/289 (79.93%), Postives = 257/289 (88.93%), Query Frame = 3 
Query:  123 KTGNAAATYDVEFDNVKWXXXXXXXXXXQDEKPLKVSVNGKQLNVRINSYGFITTESNDSMLGYFHMNEKYEITGLFELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTNILKQNIFNKHCYAKVIIGPYLYSRFSETLDFVTXXXXXXXXXXXXXNIFIRLNLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGPVYQAAMDAYCNLSITSFDLITSFDNVHSDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRNFFLNLLPKHLMKSSYSISLLL 989
            KTGNA ATYDVEFDNVKWKIKIFYYKYFQDEKPLKV+ NGK+LNV  NS+GFITT SN+SMLGYFHMNEK+EI GL EL NKRYQLINIAHGTVIILSEITEIVEVN KEFIVQT ILKQNIFNK CYAK+IIGPYLY   S+ L F TEREK++++KLL++NIF+RLNLIFNELPWD+RT+F VDHLLILTPKMC+IPYKGP YQAAMDAYCNLSIT+FDL+ SF+NV SDN YC++SSLVHHNQITK+ GY   GTLCQI  N+R+FFLNLL K LMKSSY  SL+L
Sbjct:    5 KTGNATATYDVEFDNVKWKIKIFYYKYFQDEKPLKVTFNGKRLNVLFNSFGFITTPSNESMLGYFHMNEKHEIAGLVELHNKRYQLINIAHGTVIILSEITEIVEVNMKEFIVQTKILKQNIFNKRCYAKIIIGPYLYESLSKNLQFRTEREKILKVKLLIQNIFLRLNLIFNELPWDLRTEFFVDHLLILTPKMCVIPYKGPAYQAAMDAYCNLSITAFDLLKSFENVLSDNTYCVVSSLVHHNQITKYAGYAQSGTLCQILNNLRHFFLNLLSKSLMKSSYYTSLIL 293
[Close]
BLAST of SMED30006310 vs. Planmine SMEST
Match: SMESG000043716.1 (SMESG000043716.1)

HSP 1 Score: 424.091 bits (1089), Expect = 1.519e-144
Identity = 224/289 (77.51%), Postives = 254/289 (87.89%), Query Frame = 3 
Query:  123 KTGNAAATYDVEFDNVKWXXXXXXXXXXQDEKPLKVSVNGKQLNVRINSYGFITTESNDSMLGYFHMNEKYEITGLFELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTNILKQNIFNKHCYAKVIIGPYLYSRFSETLDFVTXXXXXXXXXXXXXNIFIRLNLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGPVYQAAMDAYCNLSITSFDLITSFDNVHSDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRNFFLNLLPKHLMKSSYSISLLL 989
            KTGNA ATYDVEFDN+KW IKIFYYKYFQDEK LKVSVNGK+LNV INSYGFITTESN SMLGYFHMNEKYEITGL EL NKRYQLINI HGTVIILSEITEIVE+NTKEFIVQT ILK+NIFNK CY KVIIGPYLY+  SE LDFVTEREK I++KLL++N+F RLNLIFNELPW +RT+FLVD L+I+TP+MC+ PYKGP YQAAMD YCNLS+T+ +L+ SF  V SDNR+CM+SSLVHH QI+ H GY H+GTLCQ + N+RN FLNL+ KHLM +S+SISL+L
Sbjct:    5 KTGNAIATYDVEFDNIKWTIKIFYYKYFQDEKHLKVSVNGKRLNVLINSYGFITTESNKSMLGYFHMNEKYEITGLVELHNKRYQLINIVHGTVIILSEITEIVEINTKEFIVQTKILKENIFNKRCYVKVIIGPYLYANLSENLDFVTEREKFIKIKLLIQNVFFRLNLIFNELPWHLRTEFLVDRLIIMTPRMCMSPYKGPAYQAAMDGYCNLSVTAVNLLKSFIKVRSDNRFCMVSSLVHHRQIS-HVGYAHIGTLCQKHSNLRNLFLNLVAKHLMANSHSISLIL 292
The following BLAST results are available for this feature:
BLAST of SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 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 SMED30006310 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000043707.10.000e+093.79SMESG000043707.1[more]
SMESG000043711.10.000e+093.17SMESG000043711.1[more]
SMESG000043766.16.184e-15577.60SMESG000043766.1[more]
SMESG000043787.14.356e-14979.93SMESG000043787.1[more]
SMESG000043716.11.519e-14477.51SMESG000043716.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006310 ID=SMED30006310|Name=SMED30006310|organism=Schmidtea mediterranea sexual|type=transcript|length=990bp
TGATTAATTATTGATAATTGATAGAAATGGCTTTTATAATGATAAAACTT
TTATATTTTTATGAGCTTATCCAAAGGACTTTTACGTTCAAATTATTTCA
AGCTAATACAACGCTGATAAGCAAAACTGGAAACGCAGCCGCAACGTATG
ACGTTGAATTTGACAACGTAAAATGGAAAATTAAGATCTTTTATTACAAA
TATTTCCAAGATGAGAAACCTTTGAAGGTTTCCGTCAATGGGAAACAGTT
GAATGTGCGGATCAACTCGTATGGATTTATCACCACGGAGTCCAATGATT
CAATGTTGGGATATTTTCATATGAATGAGAAATATGAAATCACCGGATTG
TTTGAGTTACGTAATAAACGATATCAATTGATTAACATTGCCCATGGAAC
AGTGATTATTTTGTCTGAAATTACAGAAATAGTTGAAGTCAACACGAAAG
AATTTATAGTTCAAACAAATATTTTAAAACAAAATATTTTCAATAAACAT
TGTTATGCCAAAGTCATAATTGGGCCCTATCTCTACTCAAGGTTCAGTGA
AACCCTAGATTTTGTTACAGAACGGGAGAAGTTAATAAGGCTCAAATTGT
TGTTAGAGAATATATTTATTCGTCTAAATCTAATATTTAATGAATTACCG
TGGGACATTAGAACCAAATTCTTGGTTGATCATTTATTAATTTTGACACC
TAAGATGTGTATTATTCCTTATAAAGGTCCAGTTTATCAAGCGGCTATGG
ATGCTTATTGCAATTTGAGTATAACATCATTTGATTTAATTACATCCTTC
GATAATGTTCATTCGGATAACCGTTACTGTATGATATCCTCCTTGGTGCA
TCACAACCAAATTACCAAACATCCTGGATATACACATATGGGTACTTTAT
GTCAAATAAACTACAACATGAGAAATTTTTTTCTCAACTTATTACCGAAA
CACTTGATGAAAAGTTCTTATTCTATCAGTTTATTACTGG
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protein sequence of SMED30006310-orf-1

>SMED30006310-orf-1 ID=SMED30006310-orf-1|Name=SMED30006310-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=321bp
MAFIMIKLLYFYELIQRTFTFKLFQANTTLISKTGNAAATYDVEFDNVKW
KIKIFYYKYFQDEKPLKVSVNGKQLNVRINSYGFITTESNDSMLGYFHMN
EKYEITGLFELRNKRYQLINIAHGTVIILSEITEIVEVNTKEFIVQTNIL
KQNIFNKHCYAKVIIGPYLYSRFSETLDFVTEREKLIRLKLLLENIFIRL
NLIFNELPWDIRTKFLVDHLLILTPKMCIIPYKGPVYQAAMDAYCNLSIT
SFDLITSFDNVHSDNRYCMISSLVHHNQITKHPGYTHMGTLCQINYNMRN
FFLNLLPKHLMKSSYSISLLL
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ