SMED30011444

Overview
NameSMED30011444
Smed IDSMED30011444
Length (bp)1295
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ 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




 

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 SMED30011444 (SMED30011444) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011444 (SMED30011444) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30011444 (SMED30011444) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011444 (SMED30011444) 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.
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

 

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Anatomical Expression

PAGE et. al., 2020




SMED30011444

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
parenchymal cellSMED30011444SMESG000043191.1 dd_Smed_v4_27684_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
testis primordiumSMED30011444SMESG000043191.1 Contig5071_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011444 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004089:4981..6275 -6466
Homology
BLAST of SMED30011444 vs. Planmine SMEST
Match: SMESG000043191.1 (SMESG000043191.1)

HSP 1 Score: 710.679 bits (1833), Expect = 0.000e+0
Identity = 370/370 (100.00%), Postives = 370/370 (100.00%), Query Frame = 2
Query:   38 MRHKEVKIESQRKTGKTLFKSFKPDKGNANLESSDINQNNVESNSNSKFKTVKKSTNKALLSKSNFGDHYDNNVNTTQHGSLKQYCIKGNEVILRDIHFIKNEKSKMLMITVDNKQHQTDTYNILFTKDVCPYTFKDINAFVLKVTDNNKKLKSMTFQSLKEDDKNVWLNRYGLDMNIASDLLNICINEVERRRFQLGVKKRSEEKSKIKVEVDMLEEIFNSLTKKLPIDLNNQTNWTVGXXXXXXXXXXXXXXXXXXPFTNQKSLRKLENNEAVSEQISKQILANLQPINRAMLTGLLNHMERLSKYYLIIMSSPKKILPQIRRNICKRLAPIIFRIQHDMENEALNTKCSELLYNIMIRVNNTTDTYD 1147
            MRHKEVKIESQRKTGKTLFKSFKPDKGNANLESSDINQNNVESNSNSKFKTVKKSTNKALLSKSNFGDHYDNNVNTTQHGSLKQYCIKGNEVILRDIHFIKNEKSKMLMITVDNKQHQTDTYNILFTKDVCPYTFKDINAFVLKVTDNNKKLKSMTFQSLKEDDKNVWLNRYGLDMNIASDLLNICINEVERRRFQLGVKKRSEEKSKIKVEVDMLEEIFNSLTKKLPIDLNNQTNWTVGNLERLIQLLLNELPQPLIPFTNQKSLRKLENNEAVSEQISKQILANLQPINRAMLTGLLNHMERLSKYYLIIMSSPKKILPQIRRNICKRLAPIIFRIQHDMENEALNTKCSELLYNIMIRVNNTTDTYD
Sbjct:    1 MRHKEVKIESQRKTGKTLFKSFKPDKGNANLESSDINQNNVESNSNSKFKTVKKSTNKALLSKSNFGDHYDNNVNTTQHGSLKQYCIKGNEVILRDIHFIKNEKSKMLMITVDNKQHQTDTYNILFTKDVCPYTFKDINAFVLKVTDNNKKLKSMTFQSLKEDDKNVWLNRYGLDMNIASDLLNICINEVERRRFQLGVKKRSEEKSKIKVEVDMLEEIFNSLTKKLPIDLNNQTNWTVGNLERLIQLLLNELPQPLIPFTNQKSLRKLENNEAVSEQISKQILANLQPINRAMLTGLLNHMERLSKYYLIIMSSPKKILPQIRRNICKRLAPIIFRIQHDMENEALNTKCSELLYNIMIRVNNTTDTYD 370          
BLAST of SMED30011444 vs. Planmine SMEST
Match: SMESG000026155.1 (SMESG000026155.1)

HSP 1 Score: 239.195 bits (609), Expect = 3.321e-75
Identity = 141/291 (48.45%), Postives = 211/291 (72.51%), Query Frame = 2
Query:  275 GSLKQYCIKGNEVILRDIHFIKNEKSKMLMITVDNKQHQTDTYNILFTKDVCPYTFKDINAFVLKVTDNNKKLKSMTFQSLKEDDKNVWLNRYGLDMNIASDLLNICINEVERRRFQLGVKKRSEEKSKIKVEVDMLEEIFNSLTKKLPIDLNNQTNWTVGXXXXXXXXXXXXXXXXXXPFTNQKSLRKLENNEAVSEQISKQILANLQPINRAMLTGLLNHMERLSKYYLIIMSSPKKILPQIRRNICKRLAPIIFRIQHDMENEALNTKCSELLYNIMIRVNNTTDTYD 1147
            G + QYC+KG++VILR I+FI+N+K+K L I  DN +  T+ Y ILF+K+VCPY FKD +AFV+KV D    LKSMTF++   +DKN+WL  YG++  +A  LL  CI E+E+RRF LG+KKR+E+++K+KV  ++L ++ N++     I L++   W+V +LERLIQ+LLNEL +PLIP+ NQ+++RK  +    +   ++++L  L   NR +L+ LL+H+ERLSKYYLIIM SP+K L  IR NIC+RL PIIFR+Q ++++E + ++  +LLY+ M+ VN  T++ D
Sbjct:   69 GKMMQYCVKGSDVILRQIYFIRNDKTKTLSIAADNGKQVTNNYIILFSKNVCPYNFKDTDAFVIKVLDGQHNLKSMTFKTETFEDKNLWLETYGIEFEVAQKLLEGCIEEIEKRRFHLGIKKRNEDRNKVKVNSEVLMDLINAIRYSNKIILDDNNKWSVTSLERLIQILLNELTEPLIPYNNQRTIRKGNHATFNAPNETRKLLNTLPNKNRKLLSSLLSHLERLSKYYLIIMGSPRKDLQHIRLNICQRLTPIIFRLQEELDSEIIVSRACDLLYHTMLCVNGATESSD 359          
BLAST of SMED30011444 vs. Planmine SMEST
Match: SMESG000019669.1 (SMESG000019669.1)

HSP 1 Score: 106.301 bits (264), Expect = 5.820e-25
Identity = 98/279 (35.13%), Postives = 150/279 (53.76%), Query Frame = 2
Query:  218 LSKSNFGDHYDNNVNTTQHGSLKQYCIKGNE-VILRDIHFIKNEKSKMLMITVDNKQHQTDTYNILFTKDVCPYTFKDINAFVLKVTDNNKKLKS-MTFQSLKEDDKNVWLNRYGLDMNIASDLLNICINEVERRRFQLGVKKRSEEKSKIKVEVDMLEEIFNSLTKKLPIDLNNQTNWTVGXXXXXXXXXXXXXXXXXXPFTNQKSLRKLENNEAVSEQISKQILANLQPINRAMLTGLLNHMERLSKYYLIIMSSPKKILPQIRRNICKRLAPIIFR 1048
            L K NFGD   N++   + G + +Y  + +   I + +H+  +    +L +    K     +Y IL +K++C    KD  AF LKV   +K++ S +  ++    DK  WL  +GL M+++ DLL ICI EVE RRF  G KKR+E K    V++  L      L     + L+N   W V  +E+LIQ+LLNE+PQPL+PF  Q+ L K    +++    +K +L  L   +  ML  L+ H+E L+ YY   +++      +IRRNIC RL P+I R
Sbjct:   86 LVKINFGD--GNSI--KEQGRIFKYVFQDDGGAIQKLLHYSLDLNEGLLTLYDSRKLTNKRSYFILSSKEICYDHIKDHEAFHLKVKKVDKEIVSDLILKAKSSSDKYCWLEEFGLKMHLSCDLLKICIEEVENRRFCKGQKKRNEIKELKDVDIGTLLRALEGLDSN-KLKLSNNKRWNVSRIEKLIQVLLNEIPQPLVPFQLQEILEK-STAKSLQRDYAK-VLKRLPVDSNRMLQMLIEHLENLTNYYANQLNASANETERIRRNICGRLTPLIIR 357          
The following BLAST results are available for this feature:
BLAST of SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 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 SMED30011444 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000043191.10.000e+0100.00SMESG000043191.1[more]
SMESG000026155.13.321e-7548.45SMESG000026155.1[more]
SMESG000019669.15.820e-2535.13SMESG000019669.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011444 ID=SMED30011444|Name=SMED30011444|organism=Schmidtea mediterranea sexual|type=transcript|length=1295bp
CAATATACATATATTATCAATTAATTAATTTGGCCTAATGCGACATAAAG
AAGTTAAAATCGAATCACAACGAAAAACTGGCAAGACTTTGTTTAAATCA
TTCAAACCGGATAAAGGAAATGCAAATTTAGAAAGTTCAGATATAAACCA
AAACAATGTTGAATCCAATTCCAATTCTAAATTTAAAACTGTGAAAAAGT
CAACAAATAAAGCTTTACTTAGCAAATCGAATTTTGGAGACCATTATGAT
AATAATGTAAATACGACTCAACATGGAAGCTTGAAGCAGTATTGTATAAA
GGGTAACGAAGTTATATTAAGAGACATCCATTTCATTAAAAATGAAAAAT
CGAAAATGCTTATGATCACAGTTGATAATAAACAACATCAAACAGATACA
TATAATATATTGTTTACCAAAGACGTCTGTCCATACACTTTCAAAGACAT
CAATGCATTTGTGCTAAAGGTGACAGATAATAACAAAAAATTGAAAAGTA
TGACGTTTCAGTCATTGAAAGAAGACGATAAAAACGTTTGGCTCAACCGT
TACGGATTGGACATGAATATTGCCTCAGACTTGTTAAACATTTGCATTAA
CGAAGTAGAACGAAGACGGTTTCAATTGGGTGTGAAAAAACGATCAGAAG
AAAAGAGCAAAATCAAAGTCGAAGTTGACATGTTGGAGGAAATTTTCAAT
TCATTGACAAAAAAACTACCAATAGACTTAAACAACCAAACCAATTGGAC
TGTAGGCAATTTGGAAAGATTAATTCAATTGTTATTGAACGAACTTCCGC
AGCCGTTAATTCCATTTACCAATCAAAAAAGTTTGCGTAAACTTGAGAAC
AATGAAGCAGTTTCAGAACAGATTTCTAAACAAATTTTGGCAAATTTACA
ACCAATAAATAGAGCAATGTTAACCGGGCTTCTCAATCACATGGAACGTT
TGTCCAAGTATTACTTGATCATAATGAGTTCACCAAAAAAGATTTTGCCA
CAAATTCGACGAAATATTTGCAAACGGTTGGCGCCCATCATTTTTCGAAT
CCAACATGACATGGAAAATGAAGCTTTAAACACAAAATGCAGTGAACTTT
TGTATAATATTATGATTCGCGTTAATAATACTACTGACACTTATGACTAA
AAAATTCTCCCTTTGAAATTGGTTCTATCTCTCATCAAATTGCAAAAAAC
TATTAAAATATATTTAAAATTAACTAATATTGATGTTAGCTTAAACATCG
TAAACAATAGAATTTATATTCGTTTTCTCTTTACTGGCAAAATAA
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protein sequence of SMED30011444-orf-1

>SMED30011444-orf-1 ID=SMED30011444-orf-1|Name=SMED30011444-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=371bp
MRHKEVKIESQRKTGKTLFKSFKPDKGNANLESSDINQNNVESNSNSKFK
TVKKSTNKALLSKSNFGDHYDNNVNTTQHGSLKQYCIKGNEVILRDIHFI
KNEKSKMLMITVDNKQHQTDTYNILFTKDVCPYTFKDINAFVLKVTDNNK
KLKSMTFQSLKEDDKNVWLNRYGLDMNIASDLLNICINEVERRRFQLGVK
KRSEEKSKIKVEVDMLEEIFNSLTKKLPIDLNNQTNWTVGNLERLIQLLL
NELPQPLIPFTNQKSLRKLENNEAVSEQISKQILANLQPINRAMLTGLLN
HMERLSKYYLIIMSSPKKILPQIRRNICKRLAPIIFRIQHDMENEALNTK
CSELLYNIMIRVNNTTDTYD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
PLANA:0003304testis primordium
Vocabulary: INTERPRO
TermDefinition
IPR000198RhoGAP_dom
IPR008936Rho_GTPase_activation_prot
Vocabulary: biological process
TermDefinition
GO:0007165signal transduction
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000198Rho GTPase-activating protein domainPFAMPF00620RhoGAPcoord: 207..308
e-value: 2.7E-7
score: 30.6
IPR000198Rho GTPase-activating protein domainPROSITEPS50238RHOGAPcoord: 158..369
score: 14.513
IPR008936Rho GTPase activation proteinGENE3DG3DSA:1.10.555.10coord: 179..365
e-value: 5.9E-9
score: 37.6
IPR008936Rho GTPase activation proteinSUPERFAMILYSSF48350GTPase activation domain, GAPcoord: 211..361
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..49
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 27..49
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..20