SMED30035610

Overview
NameSMED30035610
Smed IDSMED30035610
Length (bp)392
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30035610

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30035610SMESG000021277.1 SmedASXL_002095SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30035610SMESG000021277.1 dd_Smed_v4_16056_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035610SMESG000021277.1 dd_Smed_v4_16056_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30035610SMESG000021277.1 dd_Smed_v4_16056_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30035610SMESG000021277.1 dd_Smed_v4_16056_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30035610SMESG000021277.1 dd_Smed_v6_16056_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30035610SMESG000021277.1 OX_Smed_1.0.10682ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30035610 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008280:17900..18270 -1819
Homology
[Close]
BLAST of SMED30035610 vs. TrEMBL
Match: A0A3P7END8 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS13936 PE=4 SV=1)

HSP 1 Score: 68.5514 bits (166), Expect = 8.681e-11
Identity = 35/122 (28.69%), Postives = 63/122 (51.64%), Query Frame = 3 
Query:   72 PGAPKIT---DIKNKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQ-------------LDQNRYALSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQI 389
            PG+P I    ++ + I+ +EG+S++L+CQS+P G PPG + W W     ++              D++R+     +     D   L S + +P +DRS++GL I+C   H L  +Q  ++ +
Sbjct:  232 PGSPVILSEGNLIDSIVRTEGESVNLTCQSKPPGSPPGELIWRWEKSAAQKDPVSSSSSSPMFSFDKSRFPSLDQYARNSFDRTQLESHLYLPSVDRSHNGLSIVCATRHKLGVEQKVKILV 353
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BLAST of SMED30035610 vs. TrEMBL
Match: A0A183TBT8 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 PE=4 SV=1)

HSP 1 Score: 68.5514 bits (166), Expect = 8.766e-11
Identity = 35/122 (28.69%), Postives = 63/122 (51.64%), Query Frame = 3 
Query:   72 PGAPKIT---DIKNKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQ-------------LDQNRYALSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQI 389
            PG+P I    ++ + I+ +EG+S++L+CQS+P G PPG + W W     ++              D++R+     +     D   L S + +P +DRS++GL I+C   H L  +Q  ++ +
Sbjct:  232 PGSPVILSEGNLIDSIVRTEGESVNLTCQSKPPGSPPGELIWRWEKSAAQKDPVSSSSSSPMFSFDKSRFPSLDQYARNSFDRTQLESHLYLPSVDRSHNGLSIVCATRHKLGVEQKVKILV 353
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BLAST of SMED30035610 vs. TrEMBL
Match: A0A0X3PCA2 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=TR137300 PE=4 SV=1)

HSP 1 Score: 65.855 bits (159), Expect = 8.644e-10
Identity = 35/122 (28.69%), Postives = 62/122 (50.82%), Query Frame = 3 
Query:   72 PGAPKIT---DIKNKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQ-------------LDQNRYALSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQI 389
            PG+P I    ++ + I  +EG+S++L+CQS+P G PPG + W W     ++              D++R+     +     D   L S + +P +DRS++GL I+C   H L  +Q  ++ +
Sbjct:  333 PGSPVILSEGNLIDSIGRTEGESVNLTCQSKPPGSPPGELIWRWEKSAAQKDPVSSSSSSPMFSFDKSRFPSLDQYARNSFDRTQLESHLYLPSVDRSHNGLSIVCATRHKLGVEQKVKILV 454
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BLAST of SMED30035610 vs. TrEMBL
Match: A0A0X3Q8H4 (Irregular chiasm C-roughest protein OS=Schistocephalus solidus OX=70667 GN=ICCR PE=4 SV=1)

HSP 1 Score: 65.855 bits (159), Expect = 9.087e-10
Identity = 35/122 (28.69%), Postives = 62/122 (50.82%), Query Frame = 3 
Query:   72 PGAPKIT---DIKNKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQ-------------LDQNRYALSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQI 389
            PG+P I    ++ + I  +EG+S++L+CQS+P G PPG + W W     ++              D++R+     +     D   L S + +P +DRS++GL I+C   H L  +Q  ++ +
Sbjct:  333 PGSPVILSEGNLIDSIGRTEGESVNLTCQSKPPGSPPGELIWRWEKSAAQKDPVSSSSSSPMFSFDKSRFPSLDQYARNSFDRTQLESHLYLPSVDRSHNGLSIVCATRHKLGVEQKVKILV 454
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BLAST of SMED30035610 vs. TrEMBL
Match: A0A158QED8 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS7227 PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 7.341e-9
Identity = 38/115 (33.04%), Postives = 58/115 (50.43%), Query Frame = 3 
Query:   72 PGAPKIT----DIKNKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQ-------LDQNRYALSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQV 383
            PGAP +     +I + II +EG +L+L CQS+P G PPG + W W   N+ Q        D N+      +     D   L S +++P + R+ +GL ILC   H L  +Q  ++
Sbjct:  317 PGAPVVLSSEGNIVDSIIANEGDTLNLVCQSKPPGSPPGELIWRW---NQPQDSPHLSLTDLNKLPSLDQYSRHTSDRHQLESHLSLPSVKRNQNGLAILCVTRHKLGMEQKTKI 428
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BLAST of SMED30035610 vs. Planmine SMEST
Match: SMESG000021277.1 (SMESG000021277.1)

HSP 1 Score: 228.794 bits (582), Expect = 2.278e-70
Identity = 108/109 (99.08%), Postives = 108/109 (99.08%), Query Frame = 3 
Query:   66 ALPGAPKITDIKNKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQLDQNRYALSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQIW 392
             LPGAPKITDIKNKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQLDQNRYALSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQIW
Sbjct:  294 TLPGAPKITDIKNKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQLDQNRYALSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQIW 402
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BLAST of SMED30035610 vs. Planmine SMEST
Match: SMESG000028689.1 (SMESG000028689.1)

HSP 1 Score: 54.6842 bits (130), Expect = 2.031e-9
Identity = 30/138 (21.74%), Postives = 64/138 (46.38%), Query Frame = 3 
Query:    9 VHGDLRTYNIDNNCYNYYLALPGAPKITDIK----NKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQLDQNRYA------LSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQIW 392
            VH D    ++    +      PG P+I D+        ++ +  ++ ++C+S P+G+P GS+ W W     ++L  NR+       +S  +    +    ++S +TIP +    HG  + C   + ++  Q+  V+++
Sbjct:  263 VHQDPERRSLSTEVFIVIHTPPGQPQIVDMNPHKTTPYVVDD--NIIMTCESSPSGKPAGSLLWRWKYPKVRELYNNRFENYTTKDISPQYYQQTISKNKMVSTLTIPALTSKEHGAQLFCVATNPVISYQSTAVKLY 398
[Close]
BLAST of SMED30035610 vs. Planmine SMEST
Match: SMESG000028689.1 (SMESG000028689.1)

HSP 1 Score: 54.6842 bits (130), Expect = 2.068e-9
Identity = 30/138 (21.74%), Postives = 64/138 (46.38%), Query Frame = 3 
Query:    9 VHGDLRTYNIDNNCYNYYLALPGAPKITDIK----NKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQLDQNRYA------LSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQIW 392
            VH D    ++    +      PG P+I D+        ++ +  ++ ++C+S P+G+P GS+ W W     ++L  NR+       +S  +    +    ++S +TIP +    HG  + C   + ++  Q+  V+++
Sbjct:  239 VHQDPERRSLSTEVFIVIHTPPGQPQIVDMNPHKTTPYVVDD--NIIMTCESSPSGKPAGSLLWRWKYPKVRELYNNRFENYTTKDISPQYYQQTISKNKMVSTLTIPALTSKEHGAQLFCVATNPVISYQSTAVKLY 374
[Close]
BLAST of SMED30035610 vs. Planmine SMEST
Match: SMESG000028689.1 (SMESG000028689.1)

HSP 1 Score: 54.299 bits (129), Expect = 2.369e-9
Identity = 30/138 (21.74%), Postives = 64/138 (46.38%), Query Frame = 3 
Query:    9 VHGDLRTYNIDNNCYNYYLALPGAPKITDIK----NKIIISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKKQLDQNRYA------LSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQIW 392
            VH D    ++    +      PG P+I D+        ++ +  ++ ++C+S P+G+P GS+ W W     ++L  NR+       +S  +    +    ++S +TIP +    HG  + C   + ++  Q+  V+++
Sbjct:  258 VHQDPERRSLSTEVFIVIHTPPGQPQIVDMNPHKTTPYVVDD--NIIMTCESSPSGKPAGSLLWRWKYPKVRELYNNRFENYTTKDISPQYYQQTISKNKMVSTLTIPALTSKEHGAQLFCVATNPVISYQSTAVKLY 393
[Close]
BLAST of SMED30035610 vs. Planmine SMEST
Match: SMESG000056135.1 (SMESG000056135.1)

HSP 1 Score: 46.595 bits (109), Expect = 1.349e-6
Identity = 31/116 (26.72%), Postives = 55/116 (47.41%), Query Frame = 3 
Query:   66 ALPGAPKITDIKNKII--ISEGKSLSLSCQSQPAGEPPGSIKWDWADGNKK------QLDQNRYALSKDWINTFVDSGILLSRITIPKIDRSYHGLFILCKLNHDLLDDQTDQVQI 389
            A P  P+I    N+ +  IS  +S+ L C   P G P  S+ W+W   N+K      ++D   + ++K+ I+T       +S + +  I + +H  F+ C  +H      ++ VQI
Sbjct:  259 APPNVPEIKSFTNEKVLEISVNESIKLFCHCTPPGFPAASLYWEWRWSNEKLNYTKIKIDGLYFTMTKNKIST-------ISSLHLFYISKKFHRGFLHCVADHPTGSVSSNGVQI 367
The following BLAST results are available for this feature:
BLAST of SMED30035610 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 SMED30035610 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 SMED30035610 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 SMED30035610 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 SMED30035610 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 SMED30035610 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 SMED30035610 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 SMED30035610 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3P7END88.681e-1128.69Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A183TBT88.766e-1128.69Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A0X3PCA28.644e-1028.69Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A0X3Q8H49.087e-1028.69Irregular chiasm C-roughest protein OS=Schistoceph... [more]
A0A158QED87.341e-933.04Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
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BLAST of SMED30035610 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 SMED30035610 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 SMED30035610 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 SMED30035610 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 SMED30035610 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 SMED30035610 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000021277.12.278e-7099.08SMESG000021277.1[more]
SMESG000028689.12.031e-921.74SMESG000028689.1[more]
SMESG000028689.12.068e-921.74SMESG000028689.1[more]
SMESG000028689.12.369e-921.74SMESG000028689.1[more]
SMESG000056135.11.349e-626.72SMESG000056135.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035610 ID=SMED30035610|Name=SMED30035610|organism=Schmidtea mediterranea sexual|type=transcript|length=392bp
ACAAAATTGTTCACGGTGATCTAAGGACTTATAATATTGACAATAATTGT
TATAATTATTATTTAGCTCTACCAGGCGCTCCAAAAATAACTGATATAAA
AAATAAAATTATAATATCAGAAGGCAAGTCTTTATCATTATCATGTCAGT
CTCAGCCAGCGGGTGAGCCTCCTGGTTCAATTAAATGGGACTGGGCTGAT
GGTAATAAAAAGCAATTAGATCAAAATAGATACGCACTATCCAAGGATTG
GATCAACACTTTTGTTGATTCAGGAATATTATTGAGTAGAATTACAATTC
CGAAAATTGATAGGAGCTATCACGGACTATTTATCCTTTGTAAATTGAAT
CATGATCTGTTGGACGATCAAACTGACCAAGTGCAAATTTGG
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protein sequence of SMED30035610-orf-1

>SMED30035610-orf-1 ID=SMED30035610-orf-1|Name=SMED30035610-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
KIVHGDLRTYNIDNNCYNYYLALPGAPKITDIKNKIIISEGKSLSLSCQS
QPAGEPPGSIKWDWADGNKKQLDQNRYALSKDWINTFVDSGILLSRITIP
KIDRSYHGLFILCKLNHDLLDDQTDQVQIW
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
PLANA:0002056medial muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR036179Ig-like_dom_sf
IPR013783Ig-like_fold
IPR007110Ig-like_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013783Immunoglobulin-like foldGENE3DG3DSA:2.60.40.10coord: 25..129
e-value: 2.3E-6
score: 29.5
IPR007110Immunoglobulin-like domainPROSITEPS50835IG_LIKEcoord: 27..62
score: 8.085
IPR036179Immunoglobulin-like domain superfamilySUPERFAMILYSSF48726Immunoglobulincoord: 26..114