SMED30018674

Overview
NameSMED30018674
Smed IDSMED30018674
Length (bp)1904
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 SMED30018674 (SMED30018674) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018674 (SMED30018674) 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




SMED30018674

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30018674 dd_Smed_v4_13483_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30018674h1SMcG0015580 Contig53170uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30018674h1SMcG0015580 Contig53170newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018674 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001398:35995..38232 +9312
v31.000850:83760..85894 +7622
v31.016212:11687..13631 -4209
Homology
BLAST of SMED30018674 vs. Planmine SMEST
Match: SMESG000019752.1 (SMESG000019752.1)

HSP 1 Score: 164.466 bits (415), Expect = 1.978e-43
Identity = 94/144 (65.28%), Postives = 104/144 (72.22%), Query Frame = 1
Query: 1342 KNRTINLKNSTDPVTEECLKMEYTKQVLGKWSKPTKTEEILATNNSKTREAFKKQKLSLVFN*LVLALSKETSTIHKWFRREDNMTEKQYISAVKI*GSLKETKXXXXXXXXXXDGLYDAQCG*PDSLGQIHQGCWRTHEMRVE 1773
            +NR  NLK S DPVT EC +MEYTKQVLGKWSKP K  E LATN S+ +EA++KQ L    +   L    ET TIHKW RR DNMT KQYISAVKI  +L  TKSR SRGR E+D L +AQCG PDSLG I QGCWRTH MRVE
Sbjct:  298 RNRITNLKKSKDPVTRECFQMEYTKQVLGKWSKPAKIGEALATNKSQLKEAYRKQLLQ-TLDGKGLQDHHETPTIHKWIRRGDNMTGKQYISAVKIRRNLVATKSRNSRGRPEQDKLCEAQCGRPDSLGHILQGCWRTHGMRVE 440          
BLAST of SMED30018674 vs. Planmine SMEST
Match: SMESG000030694.1 (SMESG000030694.1)

HSP 1 Score: 164.851 bits (416), Expect = 2.247e-42
Identity = 91/144 (63.19%), Postives = 108/144 (75.00%), Query Frame = 1
Query: 1342 KNRTINLKNSTDPVTEECLKMEYTKQVLGKWSKPTKTEEILATNNSKTREAFKKQKLSLVFN*LVLALSKETSTIHKWFRREDNMTEKQYISAVKI*GSLKETKXXXXXXXXXXDGLYDAQCG*PDSLGQIHQGCWRTHEMRVE 1773
            + R  NL+ S DPVT+ECL+MEYTKQVLGKWS+PTK  E LATN S+ +EAF+KQ L +  +   L    ET TIHKW RR +NMT KQ+I+AVKI G+L  TKSR SRGR E++ L +AQCG PDSLG I QGCWRTH MRVE
Sbjct:  709 RERITNLRKSNDPVTKECLRMEYTKQVLGKWSRPTKIGETLATNKSQLKEAFRKQML-ITLDGKGLKDHHETPTIHKWIRRGENMTGKQFITAVKIRGNLVATKSRNSRGRPEQEKLCEAQCGRPDSLGHILQGCWRTHGMRVE 851          
BLAST of SMED30018674 vs. Planmine SMEST
Match: SMESG000031049.1 (SMESG000031049.1)

HSP 1 Score: 104.76 bits (260), Expect = 5.788e-23
Identity = 59/66 (89.39%), Postives = 61/66 (92.42%), Query Frame = 2
Query:    2 RPADKIVPCIPAXXXXXXXXXSDDETEYNQIGGSVNIEINDEPEIEVDLRGSRKNIRFECSGIPLV 199
            RPADKIVPCIPAKIKKIEIIISDDETEYNQIGGSVNIEINDEPEIE+DLRGSRKNIRF+     LV
Sbjct:  670 RPADKIVPCIPAKIKKIEIIISDDETEYNQIGGSVNIEINDEPEIEIDLRGSRKNIRFDLENQNLV 735          
BLAST of SMED30018674 vs. Planmine SMEST
Match: SMESG000031049.1 (SMESG000031049.1)

HSP 1 Score: 104.76 bits (260), Expect = 6.183e-23
Identity = 59/66 (89.39%), Postives = 61/66 (92.42%), Query Frame = 2
Query:    2 RPADKIVPCIPAXXXXXXXXXSDDETEYNQIGGSVNIEINDEPEIEVDLRGSRKNIRFECSGIPLV 199
            RPADKIVPCIPAKIKKIEIIISDDETEYNQIGGSVNIEINDEPEIE+DLRGSRKNIRF+     LV
Sbjct:  927 RPADKIVPCIPAKIKKIEIIISDDETEYNQIGGSVNIEINDEPEIEIDLRGSRKNIRFDLENQNLV 992          
BLAST of SMED30018674 vs. Planmine SMEST
Match: SMESG000066165.1 (SMESG000066165.1)

HSP 1 Score: 103.99 bits (258), Expect = 1.324e-22
Identity = 59/66 (89.39%), Postives = 61/66 (92.42%), Query Frame = 2
Query:    2 RPADKIVPCIPAXXXXXXXXXSDDETEYNQIGGSVNIEINDEPEIEVDLRGSRKNIRFECSGIPLV 199
            RPADKIVPCIPAKIKKIEIIISDDETEYNQIGGSVNIEINDEPEIE+DLRGSRKNIRF+     LV
Sbjct:   82 RPADKIVPCIPAKIKKIEIIISDDETEYNQIGGSVNIEINDEPEIEIDLRGSRKNIRFDLENQNLV 147          
The following BLAST results are available for this feature:
BLAST of SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 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 SMED30018674 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000019752.11.978e-4365.28SMESG000019752.1[more]
SMESG000030694.12.247e-4263.19SMESG000030694.1[more]
SMESG000031049.15.788e-2389.39SMESG000031049.1[more]
SMESG000031049.16.183e-2389.39SMESG000031049.1[more]
SMESG000066165.11.324e-2289.39SMESG000066165.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018674 ID=SMED30018674|Name=SMED30018674|organism=Schmidtea mediterranea sexual|type=transcript|length=1904bp
AAGACCTGCTGATAAAATCGTGCCGTGTATCCCTGCTAAAATTAAAAAAA
TAGAAATCATCATTAGTGATGACGAAACTGAATATAATCAAATAGGGGGT
TCTGTAAATATTGAAATAAACGATGAACCTGAAATAGAGGTTGACTTAAG
GGGTTCCCGTAAAAATATTCGATTTGAATGTTCTGGAATTCCACTAGTCC
TACCACTAGTGTGTGTGTTCAGGTGAGGAAGTATGTTTTTTCCTTTGTTA
GTTTTTCTTTATTCTTTAGTCACGGGGATCCATTCACTCTTGGACTCTGA
CATTAGTGGAATTAGAATACCGTAAACAGGTTAATCTAGTATTAGATAAT
TGGCGAATTCGCCATTTGTGCTCGGTTAGTATCGATGGTGGTAGTAGAAA
TTTTACTCAGGTAATTTTATACATTTTATTTAGGTTAGGCCACTTGTTCA
CAATTTCATCGGGGAATTAATTTTACTAGTGGTACCATAACTCATGAGTG
GGTTTGTAATGACGTTGGGGTTTACTGACGATTTTCCTAAGATGAAACTT
GACAGTGAAATATGGATTCAATACTGTGGTTCATTAATTTTATTTCTGGC
TAGTTCCTTGTTCAGTGTATTTTATCGTTTGGGTTTGGAATTGATTTATT
CGATTTTTTGGGTTCGGATCTGCGGATTTCTCGGGGTTTGTTCTTCCTAT
TTTATAGCTGCTCCTTATTTTATCGATGATCGACGGCAGTTTACTTGGTG
GATCCCATTTATTATTGTTGTCAATTGGTCATTTTTCTTTGATTATTTCG
ATGCAGTGTTTGTGTTTGAATTGAGTAGTTCTTTAAGTTTGGACTAGGAA
ACCCAATTGTCTCATTCCCAAATGTGATTTACTATATTTGATTTTTAATT
TGTTTATGCTGCTGACTCAAATTCTCTGTTTTCATTAATGTGATTAAATG
TATTGATTTAAATCGTTCTATTACTCAGTTATGATTAACCTAACGTATCA
TTTTTGCTAATGTAACGAAATATATTTGGCTTAGGCCGTTTGTTTAATTA
TTTATCTTTAAATTTGATTTGTCATTGATACCTACTCAAACTACAATAGT
TGGATCTTGGTTGTTCGTCTATTTATCACTATCAATTAGTCCGAATAATT
TATGGCTCTACTACGCATATACTTTCGGCTAACATTTTAACGCGTAATTA
CGATATAGTATTCTCGTACTGTCGTGTTGATGTGGATTTGGTTTGTTTTC
GACCTTTTGTTTAACTCTGTTTCAATCTTAATTGACTCAATTATATTGCG
GCTACTTTAATGAAATTATTAATGTAGCATTTATAGGGGTGAAAAATCGA
ACAATAAACCTAAAGAACTCAACTGATCCAGTAACCGAAGAATGCCTAAA
AATGGAGTACACAAAACAAGTACTAGGCAAATGGAGTAAGCCAACCAAAA
CAGAGGAAATACTGGCTACTAACAACAGCAAAACAAGGGAAGCCTTTAAA
AAGCAGAAACTCTCACTAGTGTTCAATTAACTTGTCTTGGCGCTTTCTAA
AGAAACCTCTACCATCCATAAATGGTTCAGAAGAGAAGATAATATGACTG
AAAAGCAGTATATATCAGCAGTGAAGATATGAGGAAGTCTGAAAGAAACA
AAATCGAGAAGAAGTAGAGGACGCCGTGAGAGAGATGGTCTATATGATGC
CCAATGTGGATGACCAGATAGTTTGGGTCAAATACACCAAGGGTGCTGGA
GAACCCACGAAATGAGAGTAGAAAGCCTATTTTCGAACACTATTTTCAAA
AGTTTTAACTTCTGCCCGCAGACTCAATGAAAGATTTAATATTATTATTA
AATTAATAATTTTAAAAGGAAGCTTTCAGCTAGAGATTAAGGGGAATAAT
TTCA
back to top

protein sequence of SMED30018674-orf-1

>SMED30018674-orf-1 ID=SMED30018674-orf-1|Name=SMED30018674-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=118bp
MSGFVMTLGFTDDFPKMKLDSEIWIQYCGSLILFLASSLFSVFYRLGLEL
IYSIFWVRICGFLGVCSSYFIAAPYFIDDRRQFTWWIPFIIVVNWSFFFD
YFDAVFVFELSSSLSLD*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ