SMED30001211

Overview
NameSMED30001211
Smed IDSMED30001211
Length (bp)1173
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 SMED30001211 (SMED30001211) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001211 (SMED30001211) 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 SMED30001211 (SMED30001211) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001211 (SMED30001211) 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



SMED30001211

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
head regionSMED30001211SMESG000004998.1 SmedASXL_001150SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Category 4 cellSMED30001211SMESG000004998.1 dd_Smed_v4_18299_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001211 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000357:58468..60076 -5839
Homology
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BLAST of SMED30001211 vs. Planmine SMEST
Match: SMESG000004998.1 (SMESG000004998.1)

HSP 1 Score: 493.041 bits (1268), Expect = 2.578e-177
Identity = 238/238 (100.00%), Postives = 238/238 (100.00%), Query Frame = 3 
Query:  198 MIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIKLY 911
            MIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIKLY
Sbjct:    1 MIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIKLY 238
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BLAST of SMED30001211 vs. Planmine SMEST
Match: SMESG000004999.1 (SMESG000004999.1)

HSP 1 Score: 367.466 bits (942), Expect = 1.018e-127
Identity = 174/234 (74.36%), Postives = 199/234 (85.04%), Query Frame = 3 
Query:  207 LDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIKL 908
            +++ +KCNIE+FDLIGFKGSE IS+ +I IQR SL N   S  + PKISHVGLAVHGKDMKPFM DVLSEFHGKI+EQEIYVFESTKSGT FDQG+DVF+TF FGVQLRSL MVIENYPGKIYWSPKRFETN  HHLKLAECIKE+ YKPYE+S KTLFAS+ K   A ETK S FCSELVARCLQ+S++L  T+NPE+VVPLDFY+DPN P  TLD+  EIP+LYENP++I+ 
Sbjct:    1 METNEKCNIETFDLIGFKGSELISDFVISIQRISLKNGNISPIHTPKISHVGLAVHGKDMKPFMADVLSEFHGKISEQEIYVFESTKSGTPFDQGKDVFNTFSFGVQLRSLNMVIENYPGKIYWSPKRFETNETHHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQF 234
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BLAST of SMED30001211 vs. Planmine SMEST
Match: SMESG000005002.1 (SMESG000005002.1)

HSP 1 Score: 315.464 bits (807), Expect = 3.408e-107
Identity = 153/234 (65.38%), Postives = 183/234 (78.21%), Query Frame = 3 
Query:  207 LDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIKL 908
            LDS  + NIE+FDLIGFKGSEFIS  II IQR +LH+  FS  N P+ISHVGLA+HGKDMKPFM +VLSEF GKINE EIYVFEST SGT FD+ +DVF  F FGVQLRSL ++I+ YPGKIYWS K F+TN DH+LKLA CIK+  +KP+EKS K L ++  +  K K+TK S FCSELVAR LQ+SN+L   +NPEKVVP DFY DP  P +TLD+  E+PILY+NP++IK 
Sbjct:    2 LDSADEFNIETFDLIGFKGSEFISKLIIHIQRNALHDRHFSIDNFPEISHVGLAIHGKDMKPFMGNVLSEFCGKINESEIYVFESTASGTPFDRAKDVFKQFHFGVQLRSLNILIDKYPGKIYWSSKLFKTNEDHYLKLANCIKDLNHKPFEKSLKVLLSNFCEFSKVKQTKNSFFCSELVARILQRSNILPRKINPEKVVPFDFYIDPRNPEKTLDVDGEVPILYKNPVRIKF 235
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BLAST of SMED30001211 vs. Planmine SMEST
Match: SMESG000005001.1 (SMESG000005001.1)

HSP 1 Score: 266.544 bits (680), Expect = 1.637e-88
Identity = 136/238 (57.14%), Postives = 166/238 (69.75%), Query Frame = 3 
Query:  195 IMIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIKL 908
            +M+ LDS+ + NIE+FDLIGFKGSE IS+ +I IQR SL+N+  S +NLP+ISH+GLAVHGKDMKPFM+++L EF GKINE+EIYV EST+SGT FD+GRDVF   FFGVQLRS+ ++I+NYPG   W                  +K     P                  KET+ S FCSELVARCLQKS++L  TVNPE+VVPLDFY+DPN P  TLD+  EIP+LYENP QIKL
Sbjct:    1 MMVLLDSEDEVNIETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLPEISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGRDVFKRSFFGVQLRSMKIIIKNYPGN--WR---------------SVLKNLIINP------------------KETEDSFFCSELVARCLQKSDILSSTVNPERVVPLDFYQDPNNPEITLDVDGEIPVLYENPNQIKL 203
[Close]
BLAST of SMED30001211 vs. Planmine SMEST
Match: SMESG000004927.1 (SMESG000004927.1)

HSP 1 Score: 193.741 bits (491), Expect = 9.223e-60
Identity = 94/225 (41.78%), Postives = 145/225 (64.44%), Query Frame = 3 
Query:  231 IESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIK 905
            +++FDLIGF+G EF+S  I+ ++++++ N+       PKISHVG+ V GKD++ + +      H  I+  +IY+FEST +G   D+ +DV+  +FFG QLR L  VI +Y G ++ S K F    +      E ++EY ++PYEKS ++LF ++ +  + +E   S+FCSELV+  L  S +L +TVNPE VVPLDFY DP    RTLD+  EIP++Y +P+ +K
Sbjct:   14 VKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHID--PKISHVGIVVEGKDLQEYHD---CSLHSAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK 233
The following BLAST results are available for this feature:
BLAST of SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 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 SMED30001211 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000004998.12.578e-177100.00SMESG000004998.1[more]
SMESG000004999.11.018e-12774.36SMESG000004999.1[more]
SMESG000005002.13.408e-10765.38SMESG000005002.1[more]
SMESG000005001.11.637e-8857.14SMESG000005001.1[more]
SMESG000004927.19.223e-6041.78SMESG000004927.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001211 ID=SMED30001211|Name=SMED30001211|organism=Schmidtea mediterranea sexual|type=transcript|length=1173bp
TTATTGTCAATTTTTGCAATGAAATATACTTAAATAGACCATGACTGCTT
GGTAAAGGTTTTATGACTGATGTGAGTGTTCAACCGGATTGATCGGTTCA
ATGATCATTTAGTTGTTCAACATTTTCTACAACAGTTCTTGACAATGCAC
AAGTAAATCTAACAAACTAAACAACATTTCAGAACATAAATTCAATCATG
ATTTGGCTTGACTCAAAGAAGAAATGCAACATTGAAAGTTTTGATTTAAT
TGGATTCAAGGGATCTGAGTTTATATCAAATTCAATTATTTGTATTCAAA
GAAGAAGTCTACACAATGAAAGATTTTCAACAAAAAACTTACCAAAAATT
TCACACGTCGGACTAGCTGTCCATGGGAAAGATATGAAGCCGTTTATGGA
GGATGTTTTAAGCGAATTTCATGGGAAAATAAATGAACAAGAAATTTATG
TATTTGAATCGACGAAATCTGGAACGTCTTTTGATCAAGGTAGAGATGTT
TTCAGCACTTTCTTTTTCGGTGTCCAACTGAGATCCTTAACTATGGTAAT
TGAGAATTATCCTGGAAAAATTTATTGGTCCCCAAAGCGTTTTGAGACAA
ATGGAGATCATCATTTGAAATTGGCGGAGTGTATTAAAGAATATTATTAT
AAACCGTATGAAAAGTCTTTTAAAACTTTATTTGCTAGTGTGTCTAAACG
GTTTAAAGCCAAAGAAACAAAAGGCTCATTATTTTGCTCAGAATTAGTCG
CAAGATGTTTGCAAAAATCTAATCTATTATTAGACACGGTAAATCCTGAA
AAGGTGGTGCCTTTGGACTTCTATAAAGACCCAAACCAACCCAACAGAAC
ACTCGATATACACCACGAAATTCCGATTTTGTACGAAAATCCAATTCAGA
TAAAATTGTACTAAAATCAATAGTCCACGTGTGTAACCCGGAGATTCGGA
CTCTTGACTCATGTTTCTTGACCTCTTACCGCAAACATTCGCAAAACAGT
TCAAGTCGGGATTTTGAGCTGGCCATTGATAGAAGTTCAGTATTATATTT
CGGAATTTTCCAAATTTCCATATTCTATTTGCTATGTAAAGCTAATCTGT
GTTTCACTGAATTGATATTTAACATCTAATTTATTTTGTATAGTTTAATA
GCTAAAAAAATTGTGAAGTTACC
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protein sequence of SMED30001211-orf-1

>SMED30001211-orf-1 ID=SMED30001211-orf-1|Name=SMED30001211-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=239bp
MIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPK
ISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRD
VFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYY
YKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNP
EKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIKLY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR038765Papain-like_cys_pep_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:3.90.1720.10coord: 11..218
e-value: 5.8E-9
score: 37.7
IPR038765Papain-like cysteine peptidase superfamilySUPERFAMILYSSF54001Cysteine proteinasescoord: 16..212