SMED30000040

Overview
NameSMED30000040
Smed IDSMED30000040
Length (bp)1193
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.
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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30000040

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
intestinal phagocyteSMED30000040SMESG000032328.1 Contig2482GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30000040SMESG000001726.1 Contig2482GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30000040SMESG000001726.1 dd_Smed_v4_2615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30000040SMESG000001726.1 dd_Smed_v4_2615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30000040 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002980:7564..23691 -3852
Homology
BLAST of SMED30000040 vs. Planmine SMEST
Match: SMESG000001726.1 (SMESG000001726.1)

HSP 1 Score: 485.723 bits (1249), Expect = 1.184e-172
Identity = 265/308 (86.04%), Postives = 279/308 (90.58%), Query Frame = 1
Query:  253 SFVILVKMRFKERHIGFRVSSIFMLTNLVAADWLRGVSIFSGTVRYFIIFHTNNGPNRGDPCDADMFCRIQSFFSIWFNMIVSICILFIGIFAIYQITGKTGYMRNIKKKTLVITSIVAWSVPFLLTLIPAIWHKLGQDLTKTTNGWCWISSCEQPKIRLIFMLLYSKXXXXXXXXXXXXXXXXXKYINYKHIKMERQALRIGISISTQSDVDSDKLDIESSTNDSKLLFLINITICWCRVWGLIRTFIEVGKMFSQSSWTRNDFINFIENAILFIQAIFENLQGVFVFSVLILCSNFAKSYIRRLFC 1176
            SF+IL++M+  +   G R+SSIFML NLVA+D LR     +G +RY  I   N   +R       ++C+IQSFFSIWFNMIVSICILFIGIFAIYQITGKTGYMRNIKKKTLVITSIVAWSVPFLLTLIPAIWHKLGQDLTKTTNGWCWISSCEQPKIRLIFMLLYSKILEILIFLINLTLFIFLKYINYKHIKMERQALRIGISISTQSDVDSDKLDIESSTNDSKLLFLINITICWCRVWGLIRTFIEVGKMFS+SSWTRNDFINFIENAILFIQAIFENLQGVFVFSVLILCSNFAKSYIRRLFC
Sbjct:   33 SFLILLRMKVTDCTTGIRMSSIFMLLNLVASDGLRSFFNLTGMIRYLTIIDFNQ-THRNCTKSKYIYCQIQSFFSIWFNMIVSICILFIGIFAIYQITGKTGYMRNIKKKTLVITSIVAWSVPFLLTLIPAIWHKLGQDLTKTTNGWCWISSCEQPKIRLIFMLLYSKILEILIFLINLTLFIFLKYINYKHIKMERQALRIGISISTQSDVDSDKLDIESSTNDSKLLFLINITICWCRVWGLIRTFIEVGKMFSESSWTRNDFINFIENAILFIQAIFENLQGVFVFSVLILCSNFAKSYIRRLFC 339          
BLAST of SMED30000040 vs. Planmine SMEST
Match: SMESG000001727.1 (SMESG000001727.1)

HSP 1 Score: 382.489 bits (981), Expect = 9.353e-132
Identity = 223/348 (64.08%), Postives = 272/348 (78.16%), Query Frame = 1
Query:  148 MSKWAETTETYRTVNKDVTXXXXXXXXXXXXXXXXSFVILVKMRFKERHIGFRVSSIFMLTNLVAADWLRGVSIFSGTVRYFIIFHTNNGPNRGDPCDADMFCRIQSFFSIWFNMIVSICILFIGIFAIYQITGKTGYMRNIKKKTLVITSIVAWSVPFLLTLIPAIWHKLGQDLTKTTNGWCWISSCEQP--KIRLIFMLLYSKXXXXXXXXXXXXXXXXXKYINYKHIKMERQALRIGISISTQSDVDSDKLDIESSTNDSKLLFLINITICWCRVWGLIRTFIEVGKMFSQSSWTRNDFINFIENA---ILFIQAIFENLQGVFVFSVLILCSNFAKSYIRRLFC 1176
            MSKWAETTETYRTVNKDVTIISIVLGIISVVFGLISFVILVKMRFKERHIGFRVSSIFMLTNLVAADWLRGVSIFSGTVRYFIIFHT  GPNRGDPCDAD+FCRIQSFFSIWFNMI+ +CILFIGIFA+YQ+ G     R I KK L++TSI+ W++PF +TLIPAI   LG+D T TTNGWCWI+SC +   +IR+++ML+YS+  + +IFLINLTLFI+LKYI Y   K         +SIST S + ++    ++  NDSKLLFLIN++IC CR+WG++RT +++  M+S  S      +  ++ +    + +Q IF+N+Q  FVF VL+LC NF K+Y+ RL C
Sbjct:    1 MSKWAETTETYRTVNKDVTIISIVLGIISVVFGLISFVILVKMRFKERHIGFRVSSIFMLTNLVAADWLRGVSIFSGTVRYFIIFHTKYGPNRGDPCDADLFCRIQSFFSIWFNMIMLLCILFIGIFAVYQVAG-CQEDRYIGKKVLIVTSILCWTIPFFITLIPAITGALGEDQTVTTNGWCWITSCNRTTREIRVVYMLIYSRAFDAMIFLINLTLFIYLKYITYTSNKSTNNLKICNLSISTASYLITESFGKKNIRNDSKLLFLINLSICTCRIWGIVRTGLDISLMYSVDS----SIVKIVQGSSAIFMILQIIFDNIQTTFVFVVLLLCCNFVKTYLYRLIC 343          
BLAST of SMED30000040 vs. Planmine SMEST
Match: SMESG000001727.1 (SMESG000001727.1)

HSP 1 Score: 317.005 bits (811), Expect = 2.247e-106
Identity = 202/348 (58.05%), Postives = 250/348 (71.84%), Query Frame = 1
Query:  148 MSKWAETTETYRTVNKDVTXXXXXXXXXXXXXXXXSFVILVKMRFKERHIGFRVSSIFMLTNLVAADWLRGVSIFSGTVRYFIIFHTNNGPNRGDPCDADMFCRIQSFFSIWFNMIVSICILFIGIFAIYQITGKTGYMRNIKKKTLVITSIVAWSVPFLLTLIPAIWHKLGQDLTKTTNGWCWISSCEQP--KIRLIFMLLYSKXXXXXXXXXXXXXXXXXKYINYKHIKMERQALRIGISISTQSDVDSDKLDIESSTNDSKLLFLINITICWCRVWGLIRTFIEVGKMFSQSSWTRNDFINFIENA---ILFIQAIFENLQGVFVFSVLILCSNFAKSYIRRLFC 1176
            MSKWAETTETYRTVNKDVTIISIVLGIISVVFGLISFVILVKMRFKERHIGFRVSSIFMLTNLVAADWLRGVSIFSGTV                        RIQSFFSIWFNMI+ +CILFIGIFA+YQ+ G     R I KK L++TSI+ W++PF +TLIPAI   LG+D T TTNGWCWI+SC +   +IR+++ML+YS+  + +IFLINLTLFI+LKYI Y   K         +SIST S + ++    ++  NDSKLLFLIN++IC CR+WG++RT +++  M+S  S      +  ++ +    + +Q IF+N+Q  FVF VL+LC NF K+Y+ RL C
Sbjct:    1 MSKWAETTETYRTVNKDVTIISIVLGIISVVFGLISFVILVKMRFKERHIGFRVSSIFMLTNLVAADWLRGVSIFSGTV------------------------RIQSFFSIWFNMIMLLCILFIGIFAVYQVAG-CQEDRYIGKKVLIVTSILCWTIPFFITLIPAITGALGEDQTVTTNGWCWITSCNRTTREIRVVYMLIYSRAFDAMIFLINLTLFIYLKYITYTSNKSTNNLKICNLSISTASYLITESFGKKNIRNDSKLLFLINLSICTCRIWGIVRTGLDISLMYSVDS----SIVKIVQGSSAIFMILQIIFDNIQTTFVFVVLLLCCNFVKTYLYRLIC 319          
The following BLAST results are available for this feature:
BLAST of SMED30000040 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30000040 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000001726.11.184e-17286.04SMESG000001726.1[more]
SMESG000001727.19.353e-13264.08SMESG000001727.1[more]
SMESG000001727.12.247e-10658.05SMESG000001727.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000040 ID=SMED30000040|Name=SMED30000040|organism=Schmidtea mediterranea sexual|type=transcript|length=1193bp
TTTCATGATATTCATTAAAATGTTTAAAATATGTCTCTACTACCTACAAA
TAAAAGTAATATAAAATGAAGACGTGATAACAATATTATGCAATAAATAT
TTGACCTTCGGAATCAATTGAAACTTTCACAATTAGGTAAAAAAAATATG
TCTAAATGGGCCGAAACGACTGAAACTTATCGAACTGTCAATAAAGATGT
AACAATAATATCCATTGTTTTGGGAATTATCTCAGTTGTTTTTGGATTGA
TTTCATTCGTCATTCTCGTGAAGATGCGGTTCAAAGAACGGCATATTGGA
TTTAGAGTTTCATCGATTTTCATGTTGACAAATTTGGTAGCCGCTGATTG
GCTGAGAGGAGTTTCGATTTTTTCGGGAACTGTGCGGTACTTCATTATCT
TTCACACGAACAACGGACCGAATCGAGGGGATCCATGCGATGCTGATATG
TTTTGCAGAATTCAGAGCTTTTTCAGTATTTGGTTTAACATGATTGTTTC
AATATGTATTTTGTTTATTGGAATTTTTGCCATTTATCAAATAACCGGAA
AAACGGGTTACATGAGAAATATCAAGAAGAAAACATTGGTCATTACTAGC
ATAGTAGCATGGTCAGTTCCTTTTTTGCTAACTTTGATTCCAGCAATATG
GCACAAACTCGGACAGGATTTAACTAAAACGACAAACGGCTGGTGCTGGA
TTTCATCTTGCGAGCAGCCAAAAATACGTTTAATTTTTATGCTTCTCTAC
AGCAAAATTTTAGAAATTCTAATTTTTCTAATTAATTTGACCTTGTTTAT
TTTTCTCAAATACATAAATTACAAACATATAAAAATGGAAAGACAGGCGT
TGAGAATCGGTATTTCTATCAGCACTCAATCTGATGTCGACTCTGATAAA
CTGGACATAGAAAGCTCCACAAATGATTCTAAACTCCTATTTTTAATCAA
CATCACCATTTGTTGGTGTAGGGTCTGGGGTCTTATTAGAACTTTCATTG
AAGTTGGTAAGATGTTCTCACAGAGCAGCTGGACTAGAAATGATTTCATA
AATTTCATAGAAAATGCCATATTGTTCATACAAGCCATTTTCGAAAATTT
GCAAGGTGTATTTGTATTCTCGGTGCTAATTCTGTGTAGCAATTTTGCAA
AGTCATACATACGTAGACTGTTCTGTTAATAAATAAAACAGTG
back to top

protein sequence of SMED30000040-orf-1

>SMED30000040-orf-1 ID=SMED30000040-orf-1|Name=SMED30000040-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=344bp
MSKWAETTETYRTVNKDVTIISIVLGIISVVFGLISFVILVKMRFKERHI
GFRVSSIFMLTNLVAADWLRGVSIFSGTVRYFIIFHTNNGPNRGDPCDAD
MFCRIQSFFSIWFNMIVSICILFIGIFAIYQITGKTGYMRNIKKKTLVIT
SIVAWSVPFLLTLIPAIWHKLGQDLTKTTNGWCWISSCEQPKIRLIFMLL
YSKILEILIFLINLTLFIFLKYINYKHIKMERQALRIGISISTQSDVDSD
KLDIESSTNDSKLLFLINITICWCRVWGLIRTFIEVGKMFSQSSWTRNDF
INFIENAILFIQAIFENLQGVFVFSVLILCSNFAKSYIRRLFC*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR017452GPCR_Rhodpsn_7TM
IPR017981GPCR_2-like
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
GO:0016020membrane
Vocabulary: molecular function
TermDefinition
GO:0004888transmembrane signaling receptor activity
Vocabulary: biological process
TermDefinition
GO:0007166cell surface receptor signaling pathway
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 1..225
e-value: 1.1E-10
score: 43.2
NoneNo IPR availablePANTHERPTHR23112:SF12G-PROTEIN COUPLED RECEPTOR 157coord: 34..181
NoneNo IPR availablePANTHERPTHR23112G PROTEIN-COUPLED RECEPTOR 157-RELATEDcoord: 34..181
NoneNo IPR availableTMHMMTMhelixcoord: 202..224
NoneNo IPR availableTMHMMTMhelixcoord: 5..27
NoneNo IPR availableTMHMMTMhelixcoord: 40..62
NoneNo IPR availableTMHMMTMhelixcoord: 157..179
NoneNo IPR availableTMHMMTMhelixcoord: 98..117
NoneNo IPR availableTMHMMTMhelixcoord: 18..40