SMED30034004

Overview
NameSMED30034004
Smed IDSMED30034004
Length (bp)1300
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 SMED30034004 (SMED30034004) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034004 (SMED30034004) 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 SMED30034004 (SMED30034004) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034004 (SMED30034004) 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



SMED30034004

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30034004h1SMcG0021971 SmedASXL_003584SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
gutSMED30034004h1SMcG0021971 dd_Smed_v4_1659_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034004h1SMcG0021971 dd_Smed_v4_1659_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30034004h1SMcG0021971 dd_Smed_v4_1659_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
SMED30034004 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001488:63125..64424 -6464
Homology
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BLAST of SMED30034004 vs. Planmine SMEST
Match: SMESG000004927.1 (SMESG000004927.1)

HSP 1 Score: 476.863 bits (1226), Expect = 3.139e-170
Identity = 233/233 (100.00%), Postives = 233/233 (100.00%), Query Frame = 3 
Query:  294 MNDNELNQYLATYVKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHIDPKISHVGIVVEGKDLQEYHDCSLHSAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK 992
            MNDNELNQYLATYVKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHIDPKISHVGIVVEGKDLQEYHDCSLHSAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK
Sbjct:    1 MNDNELNQYLATYVKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHIDPKISHVGIVVEGKDLQEYHDCSLHSAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK 233
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BLAST of SMED30034004 vs. Planmine SMEST
Match: SMESG000005002.1 (SMESG000005002.1)

HSP 1 Score: 205.297 bits (521), Expect = 1.608e-63
Identity = 98/225 (43.56%), Postives = 148/225 (65.78%), Query Frame = 3 
Query:  333 VKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHID--PKISHVGIVVEGKDLQEYHDCSLH---SAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK 992
            ++TFDLIGF+G EF+SKLI+H+++ A+ ++   ID  P+ISHVG+ + GKD++ +    L      I+ ++IY+FESTA+G   D+ KDV+ ++ FG QLR L  +I  Y G ++ SSKLF    +        +++ NH+P+EKS + L  N C   ++++  +S FCSELV+  L  S +L   +NPE VVP DFY DP N  +TLDVDGE+P++Y +PV +K
Sbjct:   10 IETFDLIGFKGSEFISKLIIHIQRNALHDRHFSIDNFPEISHVGLAIHGKDMKPFMGNVLSEFCGKINESEIYVFESTASGTPFDRAKDVFKQFHFGVQLRSLNILIDKYPGKIYWSSKLFKTNEDHYLKLANCIKDLNHKPFEKSLKVLLSNFCEFSKVKQTKNSFFCSELVARILQRSNILPRKINPEKVVPFDFYIDPRNPEKTLDVDGEVPILYKNPVRIK 234
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BLAST of SMED30034004 vs. Planmine SMEST
Match: SMESG000004999.1 (SMESG000004999.1)

HSP 1 Score: 197.978 bits (502), Expect = 9.813e-61
Identity = 97/225 (43.11%), Postives = 143/225 (63.56%), Query Frame = 3 
Query:  333 VKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHI--DPKISHVGIVVEGKDLQEYHD---CSLHSAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK 992
            ++TFDLIGF+G E +S  ++ +++ ++KN +I     PKISHVG+ V GKD++ +        H  I   +IY+FEST +G   D+ KDV+  + FG QLR L  VI +Y G ++ S K F           E ++E+N++PYE+S ++LF +I + +   E  DS FCSELV+  L  S +L++T+NPE VVPLDFY DP N   TLD+D EIPL+Y +PV ++
Sbjct:    9 IETFDLIGFKGSELISDFVISIQRISLKNGNISPIHTPKISHVGLAVHGKDMKPFMADVLSEFHGKISEQEIYVFESTKSGTPFDQGKDVFNTFSFGVQLRSLNMVIENYPGKIYWSPKRFETNETHHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQ 233
[Close]
BLAST of SMED30034004 vs. Planmine SMEST
Match: SMESG000004998.1 (SMESG000004998.1)

HSP 1 Score: 194.126 bits (492), Expect = 2.627e-59
Identity = 94/225 (41.78%), Postives = 145/225 (64.44%), Query Frame = 3 
Query:  333 VKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHID--PKISHVGIVVEGKDLQEYHD---CSLHSAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK 992
            +++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:   12 IESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIK 236
[Close]
BLAST of SMED30034004 vs. Planmine SMEST
Match: SMESG000005006.1 (SMESG000005006.1)

HSP 1 Score: 175.252 bits (443), Expect = 3.852e-52
Identity = 89/223 (39.91%), Postives = 137/223 (61.43%), Query Frame = 3 
Query:  333 VKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHIDPKISHVGIVVEGKDLQEYHD---CSLHSAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK 992
            ++TFDLIGF+G   +S+   +++K+ +  +  +++  I+HVG+ + G D+          L + ID  K+YIFES    R +D V DV+G +  G +LR L +++S+Y G VF+S+  F   +  +  FV+F+ + N RPYE+S + L  N+ RC +  + TDSVFCSELV+  L    VL   VNPE VVPLDFY  P +    LDVD EIP+++ + V++K
Sbjct:    4 IQTFDLIGFQGTGIISRTFAYLQKRMLSKRSKNLEVVITHVGLAIRGSDINNLPKNVISILENRIDSTKVYIFESHIIPRRMDSVPDVFGSFPRGVKLRPLDEIVSNYNGRVFYSAHKFQTDQSMISEFVDFIIQNNQRPYERSIQILLSNVSRCFKTDQQTDSVFCSELVAKLLKKVKVLPEFVNPEKVVPLDFYCKPYDPTVGLDVDKEIPVLFHERVSLK 226
The following BLAST results are available for this feature:
BLAST of SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 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 SMED30034004 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000004927.13.139e-170100.00SMESG000004927.1[more]
SMESG000005002.11.608e-6343.56SMESG000005002.1[more]
SMESG000004999.19.813e-6143.11SMESG000004999.1[more]
SMESG000004998.12.627e-5941.78SMESG000004998.1[more]
SMESG000005006.13.852e-5239.91SMESG000005006.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034004 ID=SMED30034004|Name=SMED30034004|organism=Schmidtea mediterranea sexual|type=transcript|length=1300bp
CATGACCTTATTTTATTTGCAATGATGAATTATAATTAAGTCTTTTTATT
ATTATAATTTAATTTCGACGAGTTTTAAGCTGAAAATGTTCATAGAGGCT
TGATATTCAATGATAAAATGTTTCAATATCAAATAATATTGTGTTATTTA
TTACTAATTTCATTTGTGACAATAAATCAGGATGTGTACATGCAGATTTT
TTAGCTGATTGCACTCTAGTCATACTAATCACAATATTTAATAATACTCG
AATTGAAGATCTGTTCACTATTTACGTTAATTATAACAATCCAATGAATG
ACAACGAATTGAACCAGTATTTAGCAACATATGTGAAAACATTTGATTTA
ATTGGATTTAGGGGTCGAGAATTTGTGTCTAAGCTCATAGTTCATATGGA
AAAGAAAGCTATCAAAAATAAAGACATTCATATTGATCCAAAAATTTCTC
ATGTAGGAATTGTTGTTGAAGGCAAAGATTTGCAAGAATATCACGATTGT
TCTCTTCACAGCGCTATTGATGTGAATAAGATTTATATATTTGAATCAAC
AGCCACAGGACGAATAATTGACAAAGTTAAAGATGTTTATGGGAAATATT
TTTTTGGAGCTCAACTGAGAGACTTGAAAAAAGTCATTTCCAGCTATAAA
GGATGTGTTTTTCATTCTTCAAAACTTTTTCCAGTTACTCGTGAACAAGT
GAAACTGTTCGTTGAATTTGTTCAGGAATATAATCATCGACCATATGAAA
AATCTTGTAGATCTCTATTTGGAAATATTTGTCGGTGCATTGAAATTCGT
GAGAATACAGATAGTGTTTTCTGTTCAGAATTAGTCAGTTTGGCTTTAAT
TAACAGCGGTGTTCTGGCAAATACGGTTAATCCAGAATTAGTTGTTCCAC
TAGATTTCTATCCAGACCCTATTAACATAGGTAGGACTCTTGATGTTGAC
GGCGAAATTCCTTTAATATATAGCGATCCAGTGGCTATGAAATAAAATTG
TTTAATAATTATTTTTATTAAATTATCTATATTAATTCAGTCTTTAGTAT
TTTTAATTTAGTTGTTATTTAGTGATTCGGAGAAAATATTACATATTTAT
AGAAATGGACAGTAGCAGATTAATAAAGTGTCTCGAAATAATAAAGGCTT
TGAGGTCTTGAAATGTCTTCATTAGGGTTTCAGGAAAATTAAGTGTCTTT
TTATCTGTCAAATAAATATATTTTGTGTTTTAAATATTATTCTGTATATA
GAGCTGGAAACTTAAAACCGAATTAATGAATTTTCAAGAAGTAAAACAAG
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protein sequence of SMED30034004-orf-1

>SMED30034004-orf-1 ID=SMED30034004-orf-1|Name=SMED30034004-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=234bp
MNDNELNQYLATYVKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHIDPK
ISHVGIVVEGKDLQEYHDCSLHSAIDVNKIYIFESTATGRIIDKVKDVYG
KYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRP
YEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELV
VPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0002075pigment cell
PLANA:0003116parenchymal cell
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: 2..213
e-value: 1.6E-8
score: 36.2
IPR038765Papain-like cysteine peptidase superfamilySUPERFAMILYSSF54001Cysteine proteinasescoord: 15..209