GCR098

Overview
NameGCR098
Smed IDSMED30007555
Length (bp)1023
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 GCR098 (SMED30007555) t-SNE clustered cells

Violin plots show distribution of expression levels for GCR098 (SMED30007555) 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 GCR098 (SMED30007555) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for GCR098 (SMED30007555) 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



SMED30007555

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



PAGE Curations: 15

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30007555SMESG000016695.1 Contig4585newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30007555SMESG000016695.1 Contig4585uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30007555SMESG000016695.1 Contig4585newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30007555SMESG000016695.1 Contig4585uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30007555SMESG000016695.1 Contig4585newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30007555SMESG000016695.1 Contig4585uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30007555SMESG000033655.1 Contig4585newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30007555SMESG000033655.1 Contig4585uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30007555SMESG000033655.1 Contig4585newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30007555SMESG000033655.1 Contig4585uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30007555SMESG000033655.1 Contig4585newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30007555SMESG000033655.1 Contig4585uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30007555SMESG000016695.1 SmedASXL_001820SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
muscle cellSMED30007555SMESG000016695.1 dd_Smed_v4_17729_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30007555SMESG000016695.1 dd_Smed_v6_17729_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of GCR098 vs. TrEMBL
Match: A0A193KUB5 (GCR098 OS=Schmidtea mediterranea OX=79327 GN=gcr098 PE=2 SV=1)

HSP 1 Score: 288.115 bits (736), Expect = 2.986e-92
Identity = 157/340 (46.18%), Postives = 239/340 (70.29%), Query Frame = 3 
Query:   12 MNYSLNYTKTYSVNSPEENT---VIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQXXXXXXXXXXXXXXXXXXXPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM 1022
            M  +LN T   ++   EE     ++ +F+++++I+LF  GSV +S  LWRL+ L+   NV+  A+ +L+  L +DLSNLIVSG  +WL+N L V   LSD+S  KN+LCKSFNM TH C FLNQW +S +++ERC+F+++ K+NK+ FS+LR++IGLFLGFCLSFALFCNY+S+YG+ L++N  Y+C V    M+IY   V YLE++LEF++PQ +T++SIV +++ LC++ + K GLF    S + V L+   KPS+++ +L  + +S K+QI+ I++ Y++ IIDI LDFPK+L ++   V+N+  FES  +E +   LHL KF  K + V ++IS+M
Sbjct:    1 MRLALNSTLKDNLLIKEELRQMYIMAMFNIFALIILFAFGSVANSFALWRLRNLEAVKNVRCGALFILRTMLFVDLSNLIVSGLFYWLINSLGVFNYLSDQSIFKNILCKSFNMLTHFCFFLNQWTVSIMALERCVFVISRKLNKSLFSMLRLRIGLFLGFCLSFALFCNYLSMYGLRLEENNTYSCDVLAEIMAIYLNLVPYLEMILEFLIPQTVTILSIVTMAILLCHTQRLKLGLFVRGQSDEEVGLDRTTKPSISHFVLLPSRLSEKNQIFLIHVCYILSIIDIGLDFPKSLTRMYFTVTNSIFFESFIFENILIALHLFKFCCKGVGVHVYISIM 340
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BLAST of GCR098 vs. Planmine SMEST
Match: SMESG000016695.1 (SMESG000016695.1)

HSP 1 Score: 620.542 bits (1599), Expect = 0.000e+0
Identity = 337/337 (100.00%), Postives = 337/337 (100.00%), Query Frame = 3 
Query:   12 MNYSLNYTKTYSVNSPEENTVIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQXXXXXXXXXXXXXXXXXXXPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM 1022
            MNYSLNYTKTYSVNSPEENTVIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQIYFIYISYLICIIDICLDFPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM
Sbjct:    1 MNYSLNYTKTYSVNSPEENTVIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQIYFIYISYLICIIDICLDFPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM 337
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BLAST of GCR098 vs. Planmine SMEST
Match: SMESG000016694.1 (SMESG000016694.1)

HSP 1 Score: 287.73 bits (735), Expect = 7.208e-96
Identity = 151/317 (47.63%), Postives = 230/317 (72.56%), Query Frame = 3 
Query:   72 VIHLFSVYSIIVLFLIGSVTDSICLWRLKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVELNIVGKPSVANMILTIAPVSHKHQXXXXXXXXXXXXXXXXXXXPKNLLKLLKIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM 1022
            ++ +F+++++I+LF  GSV +S  LWRL+ L+   NV+  A+ +L+  L +DLSNLIVSG  +WL+N L V   LSD+S  KN+LCKSFNM TH C FLNQW +S +++ERC+F+++ K+NK+ FS+LR++IGLFLGFCLSFALFCNY+S+YG+ L++N  Y+C V    M+IY   V YLE++LEF++PQ +T++SIV +++ LC++ + K GLF    S + V L+   KPS+++ +L  + +S K+QI+ I++ Y++ IIDI LDFPK+L ++   V+N+  FES  +E +   LHL KF  K + V ++IS+M
Sbjct:    3 IMAMFNIFALIILFAFGSVANSFALWRLRNLEAVKNVRCGALFILRTMLFVDLSNLIVSGLFYWLINSLGVFNYLSDQSIFKNILCKSFNMLTHFCFFLNQWTVSIMALERCVFVISRKLNKSLFSMLRLRIGLFLGFCLSFALFCNYLSMYGLRLEENNTYSCDVLAEIMAIYLNLVPYLEMILEFLIPQTVTILSIVTMAILLCHTQRLKLGLFVRGQSDEEVGLDRTTKPSISHFVLLPSRLSEKNQIFLIHVCYILSIIDIGLDFPKSLTRMYFTVTNSIFFESFIFENILIALHLFKFCCKGVGVHVYISIM 319
[Close]
BLAST of GCR098 vs. Planmine SMEST
Match: SMESG000051040.1 (SMESG000051040.1)

HSP 1 Score: 88.9669 bits (219), Expect = 9.558e-20
Identity = 50/165 (30.30%), Postives = 90/165 (54.55%), Query Frame = 3 
Query:  183 KFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSDKSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSILRIKIGLFLGFCLSFALFCNYISIYG-IYLDDNGEYTCTVSFAFMSIYYGSVIYLEILLEFMLPQMITLISIVVI 674
            K   + +L+   I+++ NL  SGFL WL N   V   +       N++CK +N   H  + + +W+   +S++R ++ ++ + ++ YF++ R+KIG+ + F +  +   NY+ I+G I  D +G   C V   F  IYY  +  LEI  E  LP+ ITL  ++++
Sbjct:   54 KIGGLFVLECVSIVEILNLFNSGFLNWLFNYTEVMLKIQSSKFGINLICKLYNFLPHTGLLIGEWLGVWLSVDRLLYTISKRKSRQYFTVFRLKIGMIMFFAVLLSALFNYLWIFGWILPDPSGHRQCYVLPEFFYIYYNFINKLEIFFEIFLPESITLTLLIIV 218
The following BLAST results are available for this feature:
BLAST of GCR098 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 GCR098 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 GCR098 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 GCR098 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 GCR098 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 GCR098 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 GCR098 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 GCR098 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUB52.986e-9246.18GCR098 OS=Schmidtea mediterranea OX=79327 GN=gcr09... [more]
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BLAST of GCR098 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 GCR098 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 GCR098 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 GCR098 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 GCR098 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 GCR098 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000016695.10.000e+0100.00SMESG000016695.1[more]
SMESG000016694.17.208e-9647.63SMESG000016694.1[more]
SMESG000051040.19.558e-2030.30SMESG000051040.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007555 ID=SMED30007555|Name=GCR098|organism=Schmidtea mediterranea sexual|type=transcript|length=1023bp
CCCAACAACAAATGAATTATTCTTTAAATTATACAAAAACATATTCAGTA
AATTCCCCTGAAGAAAACACTGTAATACATTTGTTTAGTGTTTACTCAAT
TATTGTGCTATTTCTGATCGGATCAGTGACAGATTCAATTTGTTTATGGA
GACTGAAACGGTTGAAATGTTTTGCAAATGTAAAATTTAGTGCAATAATT
TTGTTAAAGTTTGCGTTAATAATCGACTTGTCAAATTTAATTGTGTCGGG
ATTTCTTTTCTGGCTACTCAATTGTTTGATTGTTCACAGGAATCTCTCGG
ACAAGTCGACCTTGAAAAATGTTCTTTGCAAATCGTTCAACATGTCAACG
CACCTTTGTATTTTCCTCAACCAGTGGATCATTTCTACGATTTCAATAGA
ACGGTGCATTTTTATTCTCAACGCAAAAGTGAATAAAACTTATTTCAGTA
TCTTACGAATTAAAATCGGTTTGTTTTTGGGATTCTGTCTCTCGTTTGCG
CTGTTTTGCAATTATATTTCTATTTATGGAATTTATCTAGATGACAACGG
AGAGTACACTTGTACGGTGTCCTTTGCGTTTATGTCGATTTATTATGGGT
CCGTTATTTATTTGGAAATCCTTCTGGAATTCATGCTACCTCAGATGATT
ACTCTGATATCTATTGTTGTGATTTCTGTTAAACTCTGTTACAGCTATCA
ACGGAAATCCGGTTTGTTTTCCCATTACGGCTCGTCCCAAAATGTCGAAT
TGAACATTGTTGGGAAGCCATCGGTAGCTAACATGATTTTGACAATAGCT
CCCGTTTCTCACAAACACCAGATCTATTTCATCTATATTTCGTATTTAAT
TTGTATAATTGACATTTGTTTAGATTTTCCAAAGAATCTGTTGAAACTCT
TGAAAATCGTTTCTAATACGAATCATTTTGAATCTATTTTTTATGAAATT
GTGCCATTTTTGCTTCATTTACTGAAATTTTCTGTAAAATCGATAATTGT
GCAAATTTTTATTTCATTGATGC
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protein sequence of SMED30007555-orf-1

>SMED30007555-orf-1 ID=SMED30007555-orf-1|Name=SMED30007555-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=340bp
QQQMNYSLNYTKTYSVNSPEENTVIHLFSVYSIIVLFLIGSVTDSICLWR
LKRLKCFANVKFSAIILLKFALIIDLSNLIVSGFLFWLLNCLIVHRNLSD
KSTLKNVLCKSFNMSTHLCIFLNQWIISTISIERCIFILNAKVNKTYFSI
LRIKIGLFLGFCLSFALFCNYISIYGIYLDDNGEYTCTVSFAFMSIYYGS
VIYLEILLEFMLPQMITLISIVVISVKLCYSYQRKSGLFSHYGSSQNVEL
NIVGKPSVANMILTIAPVSHKHQIYFIYISYLICIIDICLDFPKNLLKLL
KIVSNTNHFESIFYEIVPFLLHLLKFSVKSIIVQIFISLM
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR000276GPCR_Rhodpsn
Vocabulary: biological process
TermDefinition
GO:0007186G-protein coupled receptor signaling pathway
Vocabulary: molecular function
TermDefinition
GO:0004930G-protein coupled receptor activity
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
GO:0016020membrane
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: 12..336
e-value: 1.2E-11
score: 46.0
NoneNo IPR availableCDDcd006377tm_classA_rhodopsin-likecoord: 78..252
e-value: 3.08335E-4
score: 39.5682
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 18..287
NoneNo IPR availableTMHMMTMhelixcoord: 274..291
NoneNo IPR availableTMHMMTMhelixcoord: 27..49
NoneNo IPR availableTMHMMTMhelixcoord: 202..224
NoneNo IPR availableTMHMMTMhelixcoord: 311..333
NoneNo IPR availableTMHMMTMhelixcoord: 64..86
NoneNo IPR availableTMHMMTMhelixcoord: 155..177
IPR000276G protein-coupled receptor, rhodopsin-likePROSITEPS00237G_PROTEIN_RECEP_F1_1coord: 122..138