SMED30034708

Overview
NameSMED30034708
Smed IDSMED30034708
Length (bp)834
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 SMED30034708 (SMED30034708) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034708 (SMED30034708) 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 SMED30034708 (SMED30034708) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034708 (SMED30034708) 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



SMED30034708

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
prepharyngeal regionSMED30034708SMESG000035316.1 SmedASXL_007896SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
gutSMED30034708SMESG000035316.1 dd_Smed_v4_1491_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30034708SMESG000035316.1 dd_Smed_v6_1491_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
goblet cellSMED30034708SMESG000035316.1 dd_Smed_v6_1491_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30034708 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011943:4758..8348 -3972
Homology
[Close]
BLAST of SMED30034708 vs. Planmine SMEST
Match: SMESG000035316.1 (SMESG000035316.1)

HSP 1 Score: 486.108 bits (1250), Expect = 2.522e-176
Identity = 245/245 (100.00%), Postives = 245/245 (100.00%), Query Frame = 2 
Query:   35 MTFYLTFVLSFSLAFCNPYKGGQFSNQPETIKRQEIGKSSQLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSLSLIQRSIKGNGIRSGEKEITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSSPDQKGYIQDLIDILSEASKRGSEYLIIFDKVIANFKQLIELVDEKMKKEKL 769
            MTFYLTFVLSFSLAFCNPYKGGQFSNQPETIKRQEIGKSSQLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSLSLIQRSIKGNGIRSGEKEITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSSPDQKGYIQDLIDILSEASKRGSEYLIIFDKVIANFKQLIELVDEKMKKEKL
Sbjct:    1 MTFYLTFVLSFSLAFCNPYKGGQFSNQPETIKRQEIGKSSQLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSLSLIQRSIKGNGIRSGEKEITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSSPDQKGYIQDLIDILSEASKRGSEYLIIFDKVIANFKQLIELVDEKMKKEKL 245
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BLAST of SMED30034708 vs. Planmine SMEST
Match: SMESG000035313.1 (SMESG000035313.1)

HSP 1 Score: 75.0998 bits (183), Expect = 4.367e-15
Identity = 72/270 (26.67%), Postives = 122/270 (45.19%), Query Frame = 2 
Query:   35 MTFYLTFVLSFSLAFCNPYKGGQFSNQPETIKRQEIGKSSQLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSLSLIQRSIKGNGIRSG------------EKEITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKR---NIKLYK------VNVYKRN--------SSPDQKGYIQDLIDILSEASKRGSEYLIIFDKVIANFKQLIELVDEKMK 757
            M  Y    L+ SL  C+ ++      +    K     KSS LL + I  L   YEKG  E++ +  D  I+ +++ MD  T+ +AES++ +F++ I   D       +  KR   ++S  L      I  N  + G             + I  +   LSR+  + ++ + RE++++IDEATK    NEKR   +I+L K      +  Y +         + P+ K     ++D L   S+R +E       +I NF++LI+ +DE  K
Sbjct:    1 MISYFILALTISLVSCDTFEARSLEFEERYFKE----KSSSLLVELIRTLRTAYEKGAEEFDRVINDSDIKGILDHMDALTRRLAESIINKFKELIKKIDEATKPISEPSKRNLKESSTKLMKRLVQILLNAYKQGLEYFDRVVNDSDVQGILEHLGPLSRKIADGIINQFRELIEKIDEATKETQTNEKRSESSIELLKKLNEILLKAYNKGGEYVAQVINDPNVKA----ILDHLGPLSRRVAE------SIINNFRELIKKIDEATK 256

HSP 2 Score: 63.929 bits (154), Expect = 2.515e-11
Identity = 59/196 (30.10%), Postives = 97/196 (49.49%), Query Frame = 2 
Query:  149 SSQLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSLSLIQRSI--------KGN-----GIRSGE-KEITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSSPDQKGYIQDLIDILSEASKRGSEYLI 694
            S +LL K    L K Y KG     ++  DP ++ +++ +   ++ VAES++  F + I   D    E  + EKR  +K S S+ L+++ +        KG+      I   + KEI N+ + LSRR   F++ K +E+V ++DE T  K  +E+  I+             D K   + LI IL  AS++G+EY I
Sbjct:  191 SIELLKKLNEILLKAYNKGGEYVAQVINDPNVKAILDHLGPLSRRVAESIINNFRELIKKIDEATKEKTEVEKR-DFKES-SVRLLKKLVNILVKAFEKGSEAFYKAINDPDVKEILNSLDSLSRRTANFIIEKFKELVIKLDELTTEKPKSERGLIE-------------DSKNNFKKLIQILINASRKGAEYFI 371

HSP 3 Score: 56.225 bits (134), Expect = 7.627e-9
Identity = 52/196 (26.53%), Postives = 95/196 (48.47%), Query Frame = 2 
Query:  149 SSQLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSLSLIQRSIKGNGI------RSGE-----------KEITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSSPDQKGYIQDLIDILSEASKRGSE 685
            S++L+ + +  L   Y++G+  ++ +  D  ++ ++E +   ++ +A+ ++ QF + I   D    E    EKR    +  S+ L++   K N I      + GE           K I ++   LSRR  E ++   RE++ +IDEATK K   EKR+ K   V + K+            L++IL +A ++GSE
Sbjct:  114 STKLMKRLVQILLNAYKQGLEYFDRVVNDSDVQGILEHLGPLSRKIADGIINQFRELIEKIDEATKETQTNEKR----SESSIELLK---KLNEILLKAYNKGGEYVAQVINDPNVKAILDHLGPLSRRVAESIINNFRELIKKIDEATKEKTEVEKRDFKESSVRLLKK------------LVNILVKAFEKGSE 290
[Close]
BLAST of SMED30034708 vs. Planmine SMEST
Match: SMESG000035313.1 (SMESG000035313.1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.515e-14
Identity = 63/229 (27.51%), Postives = 105/229 (45.85%), Query Frame = 2 
Query:   35 MTFYLTFVLSFSLAFCNPYKGGQFSNQPETIKRQEIGKSSQLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSLSLIQRSIKGNGIRSG------------EKEITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSSPDQKGYIQDLIDILSEASKRGSE 685
            M  Y    L+ SL  C+ ++      +    K     KSS LL + I  L   YEKG  E++ +  D  I+ +++ MD  T+ +AES++ +F++ I   D       +  KR   ++S  L      I  N  + G             + I  +   LSR+  + ++ + RE++ +IDEATK K   EKR+ K   V + K+            L++IL +A ++GSE
Sbjct:    1 MISYFILALTISLVSCDTFEARSLEFEERYFKE----KSSSLLVELIRTLRTAYEKGAEEFDRVINDSDIKGILDHMDALTRRLAESIINKFKELIKKIDEATKPISEPSKRNLKESSTKLMKRLVQILLNAYKQGLEYFDRVVNDSDVQGILEHLGPLSRKIADGIINQFRELIKKIDEATKEKTEVEKRDFKESSVRLLKK------------LVNILVKAFEKGSE 213

HSP 2 Score: 62.003 bits (149), Expect = 1.006e-10
Identity = 53/196 (27.04%), Postives = 100/196 (51.02%), Query Frame = 2 
Query:  149 SSQLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSLSLIQRSI--------KGN-----GIRSGE-KEITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSSPDQKGYIQDLIDILSEASKRGSEYLI 694
            S++L+ + +  L   Y++G+  ++ +  D  ++ ++E +   ++ +A+ ++ QF + I   D    E  + EKR  +K S S+ L+++ +        KG+      I   + KEI N+ + LSRR   F++ K +E+V ++DE T  K  +E+  I+             D K   + LI IL  AS++G+EY I
Sbjct:  114 STKLMKRLVQILLNAYKQGLEYFDRVVNDSDVQGILEHLGPLSRKIADGIINQFRELIKKIDEATKEKTEVEKR-DFKES-SVRLLKKLVNILVKAFEKGSEAFYKAINDPDVKEILNSLDSLSRRTANFIIEKFKELVIKLDELTTEKPKSERGLIE-------------DSKNNFKKLIQILINASRKGAEYFI 294
[Close]
BLAST of SMED30034708 vs. Planmine SMEST
Match: SMESG000035312.1 (SMESG000035312.1)

HSP 1 Score: 71.633 bits (174), Expect = 5.910e-14
Identity = 68/265 (25.66%), Postives = 123/265 (46.42%), Query Frame = 2 
Query:   35 MTFYLTFVLSFSLAFCNPYKGGQFSNQPETIKRQEIGKSSQLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSLSLIQRSIKGNGIRSG------------EKEITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSS----PDQKGY-----------IQDLIDILSEASKRGSEYLIIFDKVIANFKQLIELVDE 748
            M  Y    L+ SL    P +  +F  Q    K     KSS LL + I  L   YEKG  E++ +  D  I+ +++ MD  T+ +AES++ +F++ I   D       +  KR   ++S  L      I  N  + G             + I ++   LSR+  + ++ + RE+++++DEATK K   +KR+ K   +++ K+ +       QKG            ++++++ LS  S+R + ++      I  FK+L+  +DE
Sbjct:    1 MIAYFLLFLTISLVSSTPLEQNEFKLQERYFKE----KSSSLLVELIRTLRTAYEKGAEEFDRVINDSDIKGILDHMDALTRRLAESIINKFKELIKKIDEATKPISEPSKRNLKESSTKLMKRLVQILLNAYKQGLEYFDRVVNDSDVQGILDHLGPLSRKIADGIINQFRELLEKLDEATKEKTEIQKRDFKESSISLLKKLTHILTQAFQKGSAAFNEALEDPDVKEILNSLSGISRRTANFM------IEKFKELVIKIDE 255

HSP 2 Score: 53.9138 bits (128), Expect = 3.986e-8
Identity = 63/249 (25.30%), Postives = 116/249 (46.59%), Query Frame = 2 
Query:  125 IKRQEIGKSS-QLLSKFIVELAKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRDSPKSEFDDFEKRYTYKTSKSL-SLIQRSIKGNGIRSGEK------------EITNNFEQLSRRRTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSSPDQKGYIQDLIDILSEASKRGSEYLIIFDKV------------------------IANFKQLIELVDEKMK 757
            I++++  +SS  LL K    L + ++KG   +NE  +DP +++++  +   ++  A  ++ +F++ +I  D   +E    E+     T+K++ +LIQ  IK +  + G +             I  +   L +R  + +++K  EI D+ID+ATK ++         Y V+ +K     D K  ++ L  IL +A ++G EY   FDKV                        I NF++LIE +D   K
Sbjct:  184 IQKRDFKESSISLLKKLTHILTQAFQKGSAAFNEALEDPDVKEILNSLSGISRRTANFMIEKFKELVIKIDEATNEKQKTERGLIDNTTKNVKNLIQILIKAS--KQGSEYFRTILNDPDVIAIREHLNILEQRIIDSIIKKFIEIFDKIDQATKPESDYP------YAVSDWKE----DAKDQLKRLTQILLKAYRKGGEY---FDKVVNDPDVQNILQHLGPLTRKVANSIIENFRELIEKIDNATK 417
The following BLAST results are available for this feature:
BLAST of SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 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 SMED30034708 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000035316.12.522e-176100.00SMESG000035316.1[more]
SMESG000035313.14.367e-1526.67SMESG000035313.1[more]
SMESG000035313.11.515e-1427.51SMESG000035313.1[more]
SMESG000035312.15.910e-1425.66SMESG000035312.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034708 ID=SMED30034708|Name=SMED30034708|organism=Schmidtea mediterranea sexual|type=transcript|length=834bp
AAGAACTTTATGGATGTTTAATCTTGTTAGCTAAATGACTTTTTATTTAA
CTTTTGTTCTTTCATTCTCACTGGCCTTTTGCAATCCTTACAAAGGTGGA
CAATTTTCAAATCAACCCGAAACAATAAAAAGGCAAGAAATAGGAAAGTC
TTCGCAACTGCTATCAAAATTTATCGTCGAACTTGCCAAATTGTATGAGA
AAGGAATTTATGAATATAACGAAATTTTTCAAGATCCAAAAATTAGAAAA
CTTATTGAAAAAATGGATGAATTTACTAAATTAGTGGCTGAATCACTTGT
TATACAATTTGAAGATGAAATCATAAGTAGGGATTCACCAAAGTCTGAAT
TCGACGATTTTGAGAAGAGATATACATACAAAACTTCCAAAAGTTTAAGT
CTTATTCAACGTTCGATCAAGGGAAACGGAATCCGTTCTGGTGAAAAAGA
AATTACTAATAATTTCGAACAACTTTCAAGGAGACGCACTGAATTTCTAG
TTAGGAAATTAAGAGAGATTGTTGATCAAATTGACGAGGCTACGAAACTG
AAAGCGGCGAATGAAAAGAGAAATATAAAACTATATAAAGTAAATGTTTA
TAAAAGAAACAGTTCACCGGATCAAAAGGGATATATACAAGACTTGATTG
ACATTCTATCAGAAGCTTCCAAAAGAGGCTCTGAGTATTTAATAATATTC
GATAAAGTTATTGCAAACTTTAAACAGTTAATAGAACTAGTTGATGAGAA
GATGAAAAAGGAAAAATTATAATAAATAAATTTTCACTGTCAATGTTGTT
GTTAAATACATCCGAATTTTATTTTCAAAAAAAA
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protein sequence of SMED30034708-orf-1

>SMED30034708-orf-1 ID=SMED30034708-orf-1|Name=SMED30034708-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=246bp
MTFYLTFVLSFSLAFCNPYKGGQFSNQPETIKRQEIGKSSQLLSKFIVEL
AKLYEKGIYEYNEIFQDPKIRKLIEKMDEFTKLVAESLVIQFEDEIISRD
SPKSEFDDFEKRYTYKTSKSLSLIQRSIKGNGIRSGEKEITNNFEQLSRR
RTEFLVRKLREIVDQIDEATKLKAANEKRNIKLYKVNVYKRNSSPDQKGY
IQDLIDILSEASKRGSEYLIIFDKVIANFKQLIELVDEKMKKEKL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000067goblet cell
PLANA:0000419prepharyngeal region
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.666