SMED30020503

Overview
NameSMED30020503
Smed IDSMED30020503
Length (bp)676
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30020503 (SMED30020503) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020503 (SMED30020503) 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.
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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




SMED30020503

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
parapharyngeal regionSMED30020503SMESG000005001.1 SmedASXL_019520SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30020503SMESG000005001.1 dd_Smed_v4_45152_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
SMED30020503 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000357:52782..53457 -3380
Homology
BLAST of SMED30020503 vs. Planmine SMEST
Match: SMESG000005001.1 (SMESG000005001.1)

HSP 1 Score: 316.235 bits (809), Expect = 1.173e-110
Identity = 168/210 (80.00%), Postives = 169/210 (80.48%), Query Frame = 2
Query:   47 MMVLLDSEDEVNIETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLPEISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGRDVFKRSFFGVQLRSMKIIIKNYPGKIYWSSKLFETDENNYRKLAECIKEFNYKPYERSAKTLISSVFKCVKAKETEDSFFCSELVARCLQKSDILSSTVNPERVVPLDFY 676
            MMVLLDSEDEVNIETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLPEISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGRDVFKRSFFGVQLRSMKIIIKNYPG   W S L                           K LI      +  KETEDSFFCSELVARCLQKSDILSSTVNPERVVPLDFY
Sbjct:    1 MMVLLDSEDEVNIETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLPEISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGRDVFKRSFFGVQLRSMKIIIKNYPGN--WRSVL---------------------------KNLI------INPKETEDSFFCSELVARCLQKSDILSSTVNPERVVPLDFY 175          
BLAST of SMED30020503 vs. Planmine SMEST
Match: SMESG000004999.1 (SMESG000004999.1)

HSP 1 Score: 309.686 bits (792), Expect = 1.727e-107
Identity = 147/206 (71.36%), Postives = 176/206 (85.44%), Query Frame = 2
Query:   59 LDSEDEVNIETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLPEISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGRDVFKRSFFGVQLRSMKIIIKNYPGKIYWSSKLFETDENNYRKLAECIKEFNYKPYERSAKTLISSVFKCVKAKETEDSFFCSELVARCLQKSDILSSTVNPERVVPLDFY 676
            +++ ++ NIETFDLIGFKGSELIS  VI IQR SL N +IS  + P+ISH+GLAVHGKDMKPFM ++L EF GKI+E+EIYV EST+SGT FD+G+DVF    FGVQLRS+ ++I+NYPGKIYWS K FET+E ++ KLAECIKEFNYKPYERS KTL +S+FK + A ET+DSFFCSELVARCLQ+SDILSST+NPERVVPLDFY
Sbjct:    1 METNEKCNIETFDLIGFKGSELISDFVISIQRISLKNGNISPIHTPKISHVGLAVHGKDMKPFMADVLSEFHGKISEQEIYVFESTKSGTPFDQGKDVFNTFSFGVQLRSLNMVIENYPGKIYWSPKRFETNETHHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFY 206          
BLAST of SMED30020503 vs. Planmine SMEST
Match: SMESG000004998.1 (SMESG000004998.1)

HSP 1 Score: 302.753 bits (774), Expect = 8.246e-105
Identity = 145/209 (69.38%), Postives = 177/209 (84.69%), Query Frame = 2
Query:   50 MVLLDSEDEVNIETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLPEISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGRDVFKRSFFGVQLRSMKIIIKNYPGKIYWSSKLFETDENNYRKLAECIKEFNYKPYERSAKTLISSVFKCVKAKETEDSFFCSELVARCLQKSDILSSTVNPERVVPLDFY 676
            M+ LDS+ + NIE+FDLIGFKGSE IS+ +I IQR SL+N+  S +NLP+ISH+GLAVHGKDMKPFM+++L EF GKINE+EIYV EST+SGT FD+GRDVF   FFGVQLRS+ ++I+NYPGKIYWS K FET+ +++ KLAECIKE+ YKPYE+S KTL +SV K  KAKET+ S FCSELVARCLQKS++L  TVNPE+VVPLDFY
Sbjct:    1 MIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFY 209          
BLAST of SMED30020503 vs. Planmine SMEST
Match: SMESG000005002.1 (SMESG000005002.1)

HSP 1 Score: 295.434 bits (755), Expect = 6.843e-102
Identity = 139/207 (67.15%), Postives = 171/207 (82.61%), Query Frame = 2
Query:   56 LLDSEDEVNIETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLPEISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGRDVFKRSFFGVQLRSMKIIIKNYPGKIYWSSKLFETDENNYRKLAECIKEFNYKPYERSAKTLISSVFKCVKAKETEDSFFCSELVARCLQKSDILSSTVNPERVVPLDFY 676
            +LDS DE NIETFDLIGFKGSE IS L+I IQRN+L+++H S +N PEISH+GLA+HGKDMKPFM N+L EF GKINE EIYV EST SGT FDR +DVFK+  FGVQLRS+ I+I  YPGKIYWSSKLF+T+E++Y KLA CIK+ N+KP+E+S K L+S+  +  K K+T++SFFCSELVAR LQ+S+IL   +NPE+VVP DFY
Sbjct:    1 MLDSADEFNIETFDLIGFKGSEFISKLIIHIQRNALHDRHFSIDNFPEISHVGLAIHGKDMKPFMGNVLSEFCGKINESEIYVFESTASGTPFDRAKDVFKQFHFGVQLRSLNILIDKYPGKIYWSSKLFKTNEDHYLKLANCIKDLNHKPFEKSLKVLLSNFCEFSKVKQTKNSFFCSELVARILQRSNILPRKINPEKVVPFDFY 207          
BLAST of SMED30020503 vs. Planmine SMEST
Match: SMESG000004927.1 (SMESG000004927.1)

HSP 1 Score: 176.407 bits (446), Expect = 3.034e-55
Identity = 82/198 (41.41%), Postives = 133/198 (67.17%), Query Frame = 2
Query:   83 IETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLPEISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGRDVFKRSFFGVQLRSMKIIIKNYPGKIYWSSKLFETDENNYRKLAECIKEFNYKPYERSAKTLISSVFKCVKAKETEDSFFCSELVARCLQKSDILSSTVNPERVVPLDFY 676
            ++TFDLIGF+G E +S L++ +++ ++ NK I  +  P+ISH+G+ V GKD++ +    L      I+  +IY+ EST +G + D+ +DV+ + FFG QLR +K +I +Y G ++ SSKLF       +   E ++E+N++PYE+S ++L  ++ +C++ +E  DS FCSELV+  L  S +L++TVNPE VVPLDFY
Sbjct:   14 VKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHID--PKISHVGIVVEGKDLQEYHDCSL---HSAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFY 206          
The following BLAST results are available for this feature:
BLAST of SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 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 SMED30020503 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000005001.11.173e-11080.00SMESG000005001.1[more]
SMESG000004999.11.727e-10771.36SMESG000004999.1[more]
SMESG000004998.18.246e-10569.38SMESG000004998.1[more]
SMESG000005002.16.843e-10267.15SMESG000005002.1[more]
SMESG000004927.13.034e-5541.41SMESG000004927.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020503 ID=SMED30020503|Name=SMED30020503|organism=Schmidtea mediterranea sexual|type=transcript|length=676bp
ATTTTGAATAAATGCACGCACTCTGACAGTCGAGTAAATATATACAATGA
TGGTTTTACTTGATTCAGAAGATGAAGTCAACATTGAAACATTTGATCTA
ATTGGATTCAAGGGGTCCGAATTAATATCGAGTTTGGTTATATTTATTCA
AAGGAATTCACTGAATAATAAACATATTTCAAAAGAAAATTTGCCTGAAA
TTTCACACATTGGATTAGCGGTTCATGGGAAAGATATGAAACCATTTATG
AAGAATATTTTAAAGGAATTTCGTGGGAAAATAAATGAACGAGAAATTTA
TGTGCTAGAATCAACGCAATCTGGAACGCTTTTTGATCGAGGCAGAGACG
TTTTTAAAAGATCTTTCTTCGGTGTTCAGTTGAGATCTATGAAAATAATA
ATAAAGAATTATCCTGGTAAAATTTATTGGTCATCAAAGCTCTTTGAAAC
AGATGAAAATAATTATAGGAAATTGGCGGAGTGTATTAAAGAATTTAATT
ATAAACCGTATGAAAGGTCGGCTAAGACGTTAATTTCCAGTGTGTTTAAA
TGTGTCAAAGCCAAGGAAACCGAAGATTCTTTTTTTTGTTCAGAATTAGT
AGCGAGATGTCTACAAAAATCTGATATATTATCAAGCACAGTAAATCCAG
AGAGAGTTGTCCCTCTGGACTTTTAT
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protein sequence of SMED30020503-orf-1

>SMED30020503-orf-1 ID=SMED30020503-orf-1|Name=SMED30020503-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=210bp
MMVLLDSEDEVNIETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLP
EISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGR
DVFKRSFFGVQLRSMKIIIKNYPGKIYWSSKLFETDENNYRKLAECIKEF
NYKPYERSAKTLISSVFKCVKAKETEDSFFCSELVARCLQKSDILSSTVN
PERVVPLDFY
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000420parapharyngeal region
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: 9..210
e-value: 1.6E-8
score: 36.3
IPR038765Papain-like cysteine peptidase superfamilySUPERFAMILYSSF54001Cysteine proteinasescoord: 31..198