SMED30031360

Overview
NameSMED30031360
Smed IDSMED30031360
Length (bp)903
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 SMED30031360 (SMED30031360) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031360 (SMED30031360) 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 SMED30031360 (SMED30031360) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031360 (SMED30031360) 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



SMED30031360

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 regionSMED30031360h1SMcG0003499 SmedASXL_006618SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30031360h1SMcG0003499 SmedASXL_006618SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30031360h1SMcG0003499 dd_Smed_v6_8434_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30031360h1SMcG0003499 OX_Smed_1.0.23082ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30031360 vs. Ensembl Zebrafish
Match: tmed5 (transmembrane p24 trafficking protein 5 [Source:ZFIN;Acc:ZDB-GENE-040426-1302])

HSP 1 Score: 48.521 bits (114), Expect = 2.464e-6
Identity = 44/191 (23.04%), Postives = 89/191 (46.60%), Query Frame = 1 
Query:  193 DFNFVLNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKYGFTFDTLEVVINETSEWQFCFANIFNEDKQLYVYGSFYHPYSIGPTKEERNKTIKAKIE----ISEQSRKMMSSLENIXXXXXXXXXXXXXXXXHEFVDSIAQESNQVFILKWAIFQLFVIIGVGVCQVYVVRHWF 753
            DF F L   GR +ECF + +  ++ + + ++VL G++  +D+      G   A      D +  V  E  ++ FCF N F+   +  +   F+        ++E ++  KA ++    +  +   +M ++ N++ +  K   + +  ++ E  D   QESN   +  W+   + V++ V   QVY++R  F
Sbjct:   32 DFTFTL-AAGR-RECFFQTMKKDASLEIEYQVLDGASLDVDFQLNSPSGHIIASDYRKSDGVHTVETEEGDYMFCFDNTFSAVSEKVI---FFELILDNMGEDEESEDWKAYVQGADLLDMKLEDIMDTINNVKSRLGKSLQIQTLLRAFEARDRNLQESNYERVNLWSCTNVLVMVIVSGVQVYLLRSLF 217
[Close]
BLAST of SMED30031360 vs. Ensembl Zebrafish
Match: tmed5 (transmembrane p24 trafficking protein 5 [Source:ZFIN;Acc:ZDB-GENE-040426-1302])

HSP 1 Score: 48.521 bits (114), Expect = 2.707e-6
Identity = 44/191 (23.04%), Postives = 89/191 (46.60%), Query Frame = 1 
Query:  193 DFNFVLNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKYGFTFDTLEVVINETSEWQFCFANIFNEDKQLYVYGSFYHPYSIGPTKEERNKTIKAKIE----ISEQSRKMMSSLENIXXXXXXXXXXXXXXXXHEFVDSIAQESNQVFILKWAIFQLFVIIGVGVCQVYVVRHWF 753
            DF F L   GR +ECF + +  ++ + + ++VL G++  +D+      G   A      D +  V  E  ++ FCF N F+   +  +   F+        ++E ++  KA ++    +  +   +M ++ N++ +  K   + +  ++ E  D   QESN   +  W+   + V++ V   QVY++R  F
Sbjct:   32 DFTFTL-AAGR-RECFFQTMKKDASLEIEYQVLDGASLDVDFQLNSPSGHIIASDYRKSDGVHTVETEEGDYMFCFDNTFSAVSEKVI---FFELILDNMGEDEESEDWKAYVQGADLLDMKLEDIMDTINNVKSRLGKSLQIQTLLRAFEARDRNLQESNYERVNLWSCTNVLVMVIVSGVQVYLLRSLF 217
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BLAST of SMED30031360 vs. Ensembl Xenopus
Match: tmed5 (transmembrane p24 trafficking protein 5 [Source:NCBI gene;Acc:549314])

HSP 1 Score: 48.1358 bits (113), Expect = 5.663e-6
Identity = 41/191 (21.47%), Postives = 84/191 (43.98%), Query Frame = 1 
Query:  187 SRDFNFVLNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKYGFTFDTLEVVINETSEWQFCFANIFNE--DKQLYVYGSFYHPYSIGPTKEERNKTIKAKIEISEQSRKMMSSLENIXXXXXXXXXXXXXXXXHEFVDSIAQESNQVFILKWAIFQLFVIIGVGVCQVYVVRHWF 753
            S D ++   +    KECF + +  ++ + + ++VL G+   +D+      G          D +  V     ++QFCF N F+   +K ++      H    G   E+    I     +  +   ++ ++ +++ +  K   + +  ++ E  D   QESN   +  W++F L V++ V   QVY++R  F
Sbjct:   25 SVDSDYTFTLPAGQKECFFQPMKRDATLEIEYQVLDGAGLDVDFSLTSPNGELLLSEERQSDGVHSVETIDGDYQFCFDNSFSRMSEKVIFFELILDHLNDEGNELEDWKSYITGTDLLDMKLEDILETINSVKGRLTKSAQIQTLLKAFEARDRNLQESNFERVTFWSVFNLTVMVVVSALQVYMLRSLF 215
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BLAST of SMED30031360 vs. Ensembl Cavefish
Match: tmed5 (transmembrane emp24 domain-containing protein 5 [Source:NCBI gene;Acc:103032944])

HSP 1 Score: 47.3654 bits (111), Expect = 5.200e-6
Identity = 38/190 (20.00%), Postives = 84/190 (44.21%), Query Frame = 1 
Query:  187 SRDFNFVLNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKYGFTFDTLEVVINETSEWQFCFANIFNE-DKQLYVYGSFYHPYSIGPTKEERNKTIKAKIEISEQSRKMMSSLENIXXXXXXXXXXXXXXXXHEFVDSIAQESNQVFILKWAIFQLFVIIGVGVCQVYVVRHWF 753
            S D +F   +    KECF + +  ++ + + ++VL G+   +D+Y     G          D +  V  E  ++ FCF N F+   +++  +         G   E+  + ++    +  +   +M ++ +++ +  K   + +  ++ E  D   QESN   +  W+   + +++ V   QVY++R  F
Sbjct:   28 SLDSDFTFTLPPGHKECFFQTMRKDASLEIEYQVLDGAGLDVDFYLSSPSGHVLVSDFRKSDGVHTVETEEGDYMFCFDNTFSTVSEKIIFFELILDNMDDGQDPEDWKEFVQGADLLDMKLEDIMDTINSVKARLGKSLQIQTVLRAFEARDRNLQESNYERVNVWSCTNVVLMVVVSCIQVYLLRSLF 217
[Close]
BLAST of SMED30031360 vs. Ensembl Cavefish
Match: tmed5 (transmembrane emp24 domain-containing protein 5 [Source:NCBI gene;Acc:103032944])

HSP 1 Score: 46.9802 bits (110), Expect = 7.654e-6
Identity = 38/190 (20.00%), Postives = 84/190 (44.21%), Query Frame = 1 
Query:  187 SRDFNFVLNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKYGFTFDTLEVVINETSEWQFCFANIFNE-DKQLYVYGSFYHPYSIGPTKEERNKTIKAKIEISEQSRKMMSSLENIXXXXXXXXXXXXXXXXHEFVDSIAQESNQVFILKWAIFQLFVIIGVGVCQVYVVRHWF 753
            S D +F   +    KECF + +  ++ + + ++VL G+   +D+Y     G          D +  V  E  ++ FCF N F+   +++  +         G   E+  + ++    +  +   +M ++ +++ +  K   + +  ++ E  D   QESN   +  W+   + +++ V   QVY++R  F
Sbjct:   30 SLDSDFTFTLPPGHKECFFQTMRKDASLEIEYQVLDGAGLDVDFYLSSPSGHVLVSDFRKSDGVHTVETEEGDYMFCFDNTFSTVSEKIIFFELILDNMDDGQDPEDWKEFVQGADLLDMKLEDIMDTINSVKARLGKSLQIQTVLRAFEARDRNLQESNYERVNVWSCTNVVLMVVVSCIQVYLLRSLF 219
[Close]
BLAST of SMED30031360 vs. Ensembl Cavefish
Match: tmed5 (transmembrane emp24 domain-containing protein 5 [Source:NCBI gene;Acc:103032944])

HSP 1 Score: 46.9802 bits (110), Expect = 8.167e-6
Identity = 38/190 (20.00%), Postives = 84/190 (44.21%), Query Frame = 1 
Query:  187 SRDFNFVLNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKYGFTFDTLEVVINETSEWQFCFANIFNE-DKQLYVYGSFYHPYSIGPTKEERNKTIKAKIEISEQSRKMMSSLENIXXXXXXXXXXXXXXXXHEFVDSIAQESNQVFILKWAIFQLFVIIGVGVCQVYVVRHWF 753
            S D +F   +    KECF + +  ++ + + ++VL G+   +D+Y     G          D +  V  E  ++ FCF N F+   +++  +         G   E+  + ++    +  +   +M ++ +++ +  K   + +  ++ E  D   QESN   +  W+   + +++ V   QVY++R  F
Sbjct:   30 SLDSDFTFTLPPGHKECFFQTMRKDASLEIEYQVLDGAGLDVDFYLSSPSGHVLVSDFRKSDGVHTVETEEGDYMFCFDNTFSTVSEKIIFFELILDNMDDGQDPEDWKEFVQGADLLDMKLEDIMDTINSVKARLGKSLQIQTVLRAFEARDRNLQESNYERVNVWSCTNVVLMVVVSCIQVYLLRSLF 219
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BLAST of SMED30031360 vs. Planmine SMEST
Match: SMESG000080787.1 (SMESG000080787.1)

HSP 1 Score: 472.626 bits (1215), Expect = 1.406e-170
Identity = 247/247 (100.00%), Postives = 247/247 (100.00%), Query Frame = 1 
Query:   58 MNCWLSIFLSYIYIGITGINNSGVVPKEGGGFEVLDWDEYERGSRDFNFVLNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKYGFTFDTLEVVINETSEWQFCFANIFNEDKQLYVYGSFYHPYSIGPTKEERNKTIKAKIEISEQSRKMMSSLENIXXXXXXXXXXXXXXXXHEFVDSIAQESNQVFILKWAIFQLFVIIGVGVCQVYVVRHWFFIQEPNYLSRNKTPF 798
            MNCWLSIFLSYIYIGITGINNSGVVPKEGGGFEVLDWDEYERGSRDFNFVLNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKYGFTFDTLEVVINETSEWQFCFANIFNEDKQLYVYGSFYHPYSIGPTKEERNKTIKAKIEISEQSRKMMSSLENIQQQSLKLQLLTSQTQSHEFVDSIAQESNQVFILKWAIFQLFVIIGVGVCQVYVVRHWFFIQEPNYLSRNKTPF
Sbjct:    1 MNCWLSIFLSYIYIGITGINNSGVVPKEGGGFEVLDWDEYERGSRDFNFVLNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKYGFTFDTLEVVINETSEWQFCFANIFNEDKQLYVYGSFYHPYSIGPTKEERNKTIKAKIEISEQSRKMMSSLENIQQQSLKLQLLTSQTQSHEFVDSIAQESNQVFILKWAIFQLFVIIGVGVCQVYVVRHWFFIQEPNYLSRNKTPF 247
The following BLAST results are available for this feature:
BLAST of SMED30031360 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 SMED30031360 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 SMED30031360 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 SMED30031360 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
tmed52.464e-623.04transmembrane p24 trafficking protein 5 [Source:ZF... [more]
tmed52.707e-623.04transmembrane p24 trafficking protein 5 [Source:ZF... [more]
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BLAST of SMED30031360 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
tmed55.663e-621.47transmembrane p24 trafficking protein 5 [Source:NC... [more]
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BLAST of SMED30031360 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 SMED30031360 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 SMED30031360 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 SMED30031360 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 3
Match NameE-valueIdentityDescription
tmed55.200e-620.00transmembrane emp24 domain-containing protein 5 [S... [more]
tmed57.654e-620.00transmembrane emp24 domain-containing protein 5 [S... [more]
tmed58.167e-620.00transmembrane emp24 domain-containing protein 5 [S... [more]
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BLAST of SMED30031360 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 SMED30031360 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 SMED30031360 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 SMED30031360 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 SMED30031360 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000080787.11.406e-170100.00SMESG000080787.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031360 ID=SMED30031360|Name=SMED30031360|organism=Schmidtea mediterranea sexual|type=transcript|length=903bp
ATTTAAACCTGTAAAGTTCACTACTGGGAACATAACTCTGTCAGGAAAAA
ATTAAATATGAATTGCTGGTTGAGTATTTTTCTCAGTTACATTTATATAG
GAATTACTGGTATTAACAACTCTGGTGTCGTTCCGAAGGAGGGAGGTGGA
TTCGAAGTACTTGACTGGGATGAATATGAAAGAGGAAGTCGAGATTTCAA
TTTCGTTCTTAATGTTCACGGTAGAACGAAGGAATGTTTTTGCGAACACT
TACTTGACGAGTCTAAAATTTTTTTATCATTTGAGGTGTTGACAGGCTCG
ACAAGAATACTTGATTATTATTTTTTACATGAAAAAGGAACTTTTACTGC
CAAATATGGTTTTACATTCGATACTTTAGAAGTGGTAATTAATGAAACAA
GTGAATGGCAGTTTTGTTTTGCTAATATTTTTAATGAAGATAAACAACTT
TATGTTTATGGTTCATTTTATCATCCATACTCAATTGGACCTACGAAAGA
AGAACGAAATAAAACTATAAAGGCTAAAATTGAAATATCAGAACAATCAA
GAAAAATGATGTCAAGCTTAGAGAATATCCAACAGCAGTCACTCAAGCTA
CAACTGTTGACTTCTCAGACTCAAAGCCATGAATTTGTCGATTCGATAGC
GCAAGAATCTAATCAGGTTTTCATACTAAAATGGGCAATATTTCAGCTAT
TTGTAATAATTGGTGTTGGAGTCTGTCAAGTTTACGTCGTTAGACATTGG
TTTTTCATCCAAGAACCGAACTATTTATCACGAAATAAAACTCCATTTTA
AAAATTTGCATTGAAATTTTATTTTACTGAAATAAAAATTGGTTTTCAAA
ATTTTATTACAATAACTGCTCTTATTAATCAATTCCTTCAATTAATCTCA
GCG
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protein sequence of SMED30031360-orf-1

>SMED30031360-orf-1 ID=SMED30031360-orf-1|Name=SMED30031360-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=248bp
MNCWLSIFLSYIYIGITGINNSGVVPKEGGGFEVLDWDEYERGSRDFNFV
LNVHGRTKECFCEHLLDESKIFLSFEVLTGSTRILDYYFLHEKGTFTAKY
GFTFDTLEVVINETSEWQFCFANIFNEDKQLYVYGSFYHPYSIGPTKEER
NKTIKAKIEISEQSRKMMSSLENIQQQSLKLQLLTSQTQSHEFVDSIAQE
SNQVFILKWAIFQLFVIIGVGVCQVYVVRHWFFIQEPNYLSRNKTPF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR015720TMP21-related
IPR009038GOLD_dom
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
GO:0016020membrane
Vocabulary: biological process
TermDefinition
GO:0006810transport
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR009038GOLD domainSMARTSM01190EMP24_GP25L_2coord: 46..233
e-value: 4.2E-9
score: 46.2
IPR009038GOLD domainPFAMPF01105EMP24_GP25Lcoord: 52..232
e-value: 1.1E-12
score: 48.2
NoneNo IPR availablePANTHERPTHR22811:SF59OPOSSUM, ISOFORM Acoord: 46..232
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.603
NoneNo IPR availableTMHMMTMhelixcoord: 211..233
IPR015720TMP21-relatedPANTHERPTHR22811TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEINcoord: 46..232