SMED30033641

Overview
NameSMED30033641
Smed IDSMED30033641
Length (bp)1665
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 SMED30033641 (SMED30033641) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033641 (SMED30033641) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30033641

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
neoblastSMED30033641 dd_Smed_v4_31126_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033641 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001302:28850..30513 +8302
Homology
[Close]
BLAST of SMED30033641 vs. Planmine SMEST
Match: SMESG000052418.1 (SMESG000052418.1)

HSP 1 Score: 144.05 bits (362), Expect = 5.159e-36
Identity = 67/149 (44.97%), Postives = 108/149 (72.48%), Query Frame = 2 
Query: 1082 PTEIKPMIPTKIFKEPDD*LMETASQPLMAELQGAIRIKNEPEVKERLLKIDKENIIRKPVSADVNGFEPM*YKRPNVHWKPRA*KYNNLPVTSMAINTNPRYEIFDVDGIPYVASTLILSSDVDDKPLAVSFDGDLVKRRKAKAKKEY 1528
            P++    IPTKIF EPDD + E + +P  A+LQ  +++K EPEV E+L +I++EN+I K +S D +G++PM Y+RPN H +PR  +Y+   +T MA+N+NP+Y+  DVDGIPY+ S++IL S +D + LA+S++ + + +R AK+ +E+
Sbjct:  665 PSQSSSAIPTKIFNEPDDDIEEVSYKPPNADLQKQLKVKTEPEVVEKL-RINRENLILKQISVDTDGYDPMWYRRPNCHLRPRVTQYDEKEITRMAVNSNPKYQEIDVDGIPYLVSSVILVSSLDKEALALSYEPETMAKRLAKSLREH 812

HSP 2 Score: 91.6633 bits (226), Expect = 4.380e-19
Identity = 38/68 (55.88%), Postives = 54/68 (79.41%), Query Frame = 2 
Query:  254 LIQITIVGMNGENLLRAIMASRYSVKHYQTHQHKLKEPDVRGNLDEDVCHHIIRKICDQKIVVGMILK 457
            L++I+I   +G+ LL  I+  R  ++HYQTHQ+ LKE DVRGNLD++ C H+IRKICD+KIVVG+++K
Sbjct:  473 LLEISISDFSGQQLLNTIVTPREPIRHYQTHQYHLKESDVRGNLDDEECCHMIRKICDKKIVVGLMIK 540
[Close]
BLAST of SMED30033641 vs. Planmine SMEST
Match: SMESG000069268.1 (SMESG000069268.1)

HSP 1 Score: 53.9138 bits (128), Expect = 2.839e-7
Identity = 32/114 (28.07%), Postives = 56/114 (49.12%), Query Frame = 2 
Query:  257 IQITIVGMNGENLLRAIMASRYSVKHYQTHQHKLKEPDVRGNLDEDVCHHIIRKICDQKIVVGMILKGNMEIAHLPVQKLLGIRDLSNNKLLESRNVLKVHGYYHLGFLTMTFL 598
            + + ++  +G  L   I+  R  V +Y+   + L E DVRG LDE+ C + +R I    I+VG  +  N+    + ++++ GIRDLS     +          Y L +L+ + L
Sbjct:  575 LAVVVLDYDGNVLFEEIVTPRGFVANYRQEINGLLETDVRGCLDEEECTNQLRNILRDSIIVGFKVAPNLFSLRIELERIFGIRDLSTGLCFDKTPNSSEKCLYTLKYLSSSIL 688
[Close]
BLAST of SMED30033641 vs. Planmine SMEST
Match: SMESG000069268.1 (SMESG000069268.1)

HSP 1 Score: 53.9138 bits (128), Expect = 2.878e-7
Identity = 32/114 (28.07%), Postives = 56/114 (49.12%), Query Frame = 2 
Query:  257 IQITIVGMNGENLLRAIMASRYSVKHYQTHQHKLKEPDVRGNLDEDVCHHIIRKICDQKIVVGMILKGNMEIAHLPVQKLLGIRDLSNNKLLESRNVLKVHGYYHLGFLTMTFL 598
            + + ++  +G  L   I+  R  V +Y+   + L E DVRG LDE+ C + +R I    I+VG  +  N+    + ++++ GIRDLS     +          Y L +L+ + L
Sbjct:  626 LAVVVLDYDGNVLFEEIVTPRGFVANYRQEINGLLETDVRGCLDEEECTNQLRNILRDSIIVGFKVAPNLFSLRIELERIFGIRDLSTGLCFDKTPNSSEKCLYTLKYLSSSIL 739
The following BLAST results are available for this feature:
BLAST of SMED30033641 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033641 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000052418.15.159e-3644.97SMESG000052418.1[more]
SMESG000069268.12.839e-728.07SMESG000069268.1[more]
SMESG000069268.12.878e-728.07SMESG000069268.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033641 ID=SMED30033641|Name=SMED30033641|organism=Schmidtea mediterranea sexual|type=transcript|length=1665bp
CTCTTGTGTAAAGATTCATCCCCCATTTTTCGGATCTTAACAGTATATAT
AGAGATACTGAATTTCATCAAATCATACTTTATTGTTAGAGAAAATATCC
CAACATTAGTAATCTTAACATTAGTATTTACAACATTATTAAAACGGATA
TTAGTGAATATAGATCATTCGTTTGTAAGCAAATGACTATACAGGAGGAA
GGTCGGGGATTCGCAGTGGGATTCGCTAAGTCCTGGGTGGACTTAAAAAA
ACGTTAATTCAAATAACAATAGTAGGTATGAATGGAGAAAATTTACTTAG
GGCAATTATGGCATCCCGCTATTCAGTAAAACACTACCAAACCCATCAGC
ATAAATTAAAGGAACCGGACGTAAGAGGGAATCTAGATGAAGATGTTTGC
CATCATATAATCAGGAAAATATGTGACCAGAAGATAGTCGTGGGAATGAT
ATTGAAGGGCAATATGGAGATAGCCCATCTACCAGTGCAGAAACTCCTTG
GGATAAGGGACTTATCCAATAATAAATTGCTTGAGTCAAGAAATGTCCTG
AAAGTACATGGATATTATCATTTAGGATTTCTAACAATGACGTTCCTGAA
ATCACCCCCGTACAATCCAGAGTACCTGGTGGTAGAGAACGAACAAGGAC
AATCAGAACAATTTACCTGAATGTTCAGAAAGAATGGCTAAATCATATTA
CCGCCACGGAGGAAAATATAAATTTACTTCATCAGTAAAGGCAGTAGATG
CTGATCGACTGGTAATTTTGACAAGGACACTACAGGCGGTGCCAACCGTG
CAAACCTCGAAAACGGCATTGGAAGATTTGCAACCCCCTCCAAATATTAC
ACGTATGGAAGAAGATACATAAGAAACATGCAACTAAGAAGAAACAGCCC
AACAAAGAAAATTAGAGAATTAGAATCTTCAACAAGTGCTGCCTATCAGC
CAAGAAAAGTCATATTACCCAAACCTAAAGAAACAAGACTAAAAGGTAAA
GTTAAAAAAGTAAACAGAGTACTATCTAAGGTACTGCCCAAGAAATGGAA
TAAGTCAAAACTTAAACTAAAAACTGCACACCCAACAGAAATAAAACCTA
TGATCCCAACGAAAATATTCAAGGAACCTGATGATTAGTTAATGGAAACA
GCATCCCAGCCCCTGATGGCAGAATTACAAGGGGCCATTAGAATCAAAAA
CGAACCTGAGGTGAAAGAGAGATTATTGAAAATAGATAAAGAAAATATAA
TCAGAAAACCTGTATCGGCAGATGTAAACGGTTTTGAACCAATGTGATAT
AAAAGACCAAATGTGCATTGGAAACCGAGGGCTTAAAAGTATAATAACCT
GCCAGTAACATCAATGGCGATTAATACAAATCCCAGATATGAAATTTTCG
ATGTAGATGGGATACCGTATGTGGCGTCAACATTGATTTTATCAAGCGAT
GTGGACGATAAGCCACTAGCAGTTAGCTTTGACGGTGACCTTGTAAAGAG
ACGCAAGGCAAAGGCCAAGAAGGAGTACATTATAGCTGTATTCTGGAATT
TTCACTATTGTATAAATATTGGGATTTTTACTATCAAAAAAATATTGGAA
TTAGAAATTAGAACAAAAGAAAGATTAAAGTTCAGAGAAAGAAGAGTGAA
CAGACAAGATTATTT
back to top

protein sequence of SMED30033641-orf-1

>SMED30033641-orf-1 ID=SMED30033641-orf-1|Name=SMED30033641-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
MAINTNPRYEIFDVDGIPYVASTLILSSDVDDKPLAVSFDGDLVKRRKAK
AKKEYIIAVFWNFHYCINIGIFTIKKILELEIRTKERLKFRERRVNRQDY
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR012337RNaseH-like_sf
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding