GCR108

Overview
NameGCR108
Smed IDSMED30034586
Length (bp)1953
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 GCR108 (SMED30034586) t-SNE clustered cells

Violin plots show distribution of expression levels for GCR108 (SMED30034586) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 GCR108 (SMED30034586) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for GCR108 (SMED30034586) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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



SMED30034586

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
intestinal phagocyteSMED30034586SMESG000064545.1 SMESG000047762.1 SMESG000046800.1 SMESG000012864.1 SMESG000003895.1 SMESG000070132.1 SMESG000068326.1 SMESG000067883.1 SMESG000062229.1 SMESG000061668.1 SMESG000058705.1 SMESG000030728.1 SMESG000022905.1 SMESG000020613.1 Contig65newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30034586SMESG000064545.1 SMESG000047762.1 SMESG000046800.1 SMESG000012864.1 SMESG000003895.1 SMESG000070132.1 SMESG000067883.1 SMESG000061668.1 SMESG000058705.1 SMESG000020613.1 Contig337newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30034586SMESG000064545.1 SMESG000047762.1 SMESG000046800.1 SMESG000012864.1 SMESG000003895.1 SMESG000070132.1 SMESG000067883.1 SMESG000061668.1 SMESG000058705.1 SMESG000020613.1 Contig337uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30034586SMESG000035344.1 Contig337newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30034586SMESG000035344.1 Contig337uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30034586SMESG000001797.1 Contig65newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
testisSMED30034586SMESG000072702.1 GCR108smed_ncbi_20200123PMID:27163480
Saberi et al., 2016		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of GCR108 vs. TrEMBL
Match: A0A193KUM7 (GCR108 OS=Schmidtea mediterranea OX=79327 GN=gcr108 PE=2 SV=1)

HSP 1 Score: 723.776 bits (1867), Expect = 0.000e+0
Identity = 374/374 (100.00%), Postives = 374/374 (100.00%), Query Frame = 2 
Query:   92 MKFNITYKLLIDLILIWTIFLMNIIFIGTLLVRSKVKKNDINRSFFFLSLMHLPNGLVILPLKFVQQIMKLNRGEITVEHCHNLMTMTWFGIQSTTVAVTVFCLYHLYLSNPSVKNLYSNKFYRFFSFGILIIWMIGSALVTFNFTYYYSEIRFNTCVISKSVTASGMLLLIVFVAPYTLCLVCYIKIFPATSWLSDLTSFSRISSLQKESQSTINTDHDSQEKCRWNRMFDFSKRSSKLSNEDKLSKKKSNGTNLEXXXXXXXXXXXXXXXXQAMTDPILEKKITKLLHIDIEKTNKNTYSKSSVVVGFVFISYFAFWAPFIAIILVEMMSRRIMVKYISWTIRLGYCNSFALPIMFAFYLRFHKPETKNTKG 1213
            MKFNITYKLLIDLILIWTIFLMNIIFIGTLLVRSKVKKNDINRSFFFLSLMHLPNGLVILPLKFVQQIMKLNRGEITVEHCHNLMTMTWFGIQSTTVAVTVFCLYHLYLSNPSVKNLYSNKFYRFFSFGILIIWMIGSALVTFNFTYYYSEIRFNTCVISKSVTASGMLLLIVFVAPYTLCLVCYIKIFPATSWLSDLTSFSRISSLQKESQSTINTDHDSQEKCRWNRMFDFSKRSSKLSNEDKLSKKKSNGTNLEFSSSDSTNTNSNNDFSQAMTDPILEKKITKLLHIDIEKTNKNTYSKSSVVVGFVFISYFAFWAPFIAIILVEMMSRRIMVKYISWTIRLGYCNSFALPIMFAFYLRFHKPETKNTKG
Sbjct:    1 MKFNITYKLLIDLILIWTIFLMNIIFIGTLLVRSKVKKNDINRSFFFLSLMHLPNGLVILPLKFVQQIMKLNRGEITVEHCHNLMTMTWFGIQSTTVAVTVFCLYHLYLSNPSVKNLYSNKFYRFFSFGILIIWMIGSALVTFNFTYYYSEIRFNTCVISKSVTASGMLLLIVFVAPYTLCLVCYIKIFPATSWLSDLTSFSRISSLQKESQSTINTDHDSQEKCRWNRMFDFSKRSSKLSNEDKLSKKKSNGTNLEFSSSDSTNTNSNNDFSQAMTDPILEKKITKLLHIDIEKTNKNTYSKSSVVVGFVFISYFAFWAPFIAIILVEMMSRRIMVKYISWTIRLGYCNSFALPIMFAFYLRFHKPETKNTKG 374
[Close]
BLAST of GCR108 vs. Planmine SMEST
Match: SMESG000072702.1 (SMESG000072702.1)

HSP 1 Score: 629.787 bits (1623), Expect = 0.000e+0
Identity = 324/324 (100.00%), Postives = 324/324 (100.00%), Query Frame = 2 
Query:  242 MHLPNGLVILPLKFVQQIMKLNRGEITVEHCHNLMTMTWFGIQSTTVAVTVFCLYHLYLSNPSVKNLYSNKFYRFFSFGILIIWMIGSALVTFNFTYYYSEIRFNTCVISKSVTASGMLLLIVFVAPYTLCLVCYIKIFPATSWLSDLTSFSRISSLQKESQSTINTDHDSQEKCRWNRMFDFSKRSSKLSNEDKLSKKKSNGTNLEXXXXXXXXXXXXXXXXQAMTDPILEKKITKLLHIDIEKTNKNTYSKSSVVVGFVFISYFAFWAPFIAIILVEMMSRRIMVKYISWTIRLGYCNSFALPIMFAFYLRFHKPETKNTKG 1213
            MHLPNGLVILPLKFVQQIMKLNRGEITVEHCHNLMTMTWFGIQSTTVAVTVFCLYHLYLSNPSVKNLYSNKFYRFFSFGILIIWMIGSALVTFNFTYYYSEIRFNTCVISKSVTASGMLLLIVFVAPYTLCLVCYIKIFPATSWLSDLTSFSRISSLQKESQSTINTDHDSQEKCRWNRMFDFSKRSSKLSNEDKLSKKKSNGTNLEFSSSDSTNTNSNNDFSQAMTDPILEKKITKLLHIDIEKTNKNTYSKSSVVVGFVFISYFAFWAPFIAIILVEMMSRRIMVKYISWTIRLGYCNSFALPIMFAFYLRFHKPETKNTKG
Sbjct:    1 MHLPNGLVILPLKFVQQIMKLNRGEITVEHCHNLMTMTWFGIQSTTVAVTVFCLYHLYLSNPSVKNLYSNKFYRFFSFGILIIWMIGSALVTFNFTYYYSEIRFNTCVISKSVTASGMLLLIVFVAPYTLCLVCYIKIFPATSWLSDLTSFSRISSLQKESQSTINTDHDSQEKCRWNRMFDFSKRSSKLSNEDKLSKKKSNGTNLEFSSSDSTNTNSNNDFSQAMTDPILEKKITKLLHIDIEKTNKNTYSKSSVVVGFVFISYFAFWAPFIAIILVEMMSRRIMVKYISWTIRLGYCNSFALPIMFAFYLRFHKPETKNTKG 324
The following BLAST results are available for this feature:
BLAST of GCR108 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 GCR108 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 GCR108 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 GCR108 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 GCR108 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 GCR108 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 GCR108 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 GCR108 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUM70.000e+0100.00GCR108 OS=Schmidtea mediterranea OX=79327 GN=gcr10... [more]
back to top
BLAST of GCR108 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 GCR108 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 GCR108 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 GCR108 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 GCR108 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 GCR108 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000072702.10.000e+0100.00SMESG000072702.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034586 ID=SMED30034586|Name=GCR108|organism=Schmidtea mediterranea sexual|type=transcript|length=1953bp
GAATAATTTGTTATTGAAATATGTTAATCAATATCGGAAGCCATATTGAA
ATGAATTAAATTTCCATAGTAGATAAACTTTGTGAGGCCTGATGAAATTC
AACATCACCTACAAGTTGCTTATAGACCTAATCCTGATCTGGACAATATT
CCTCATGAATATCATATTCATCGGCACCCTTTTGGTGCGAAGTAAAGTCA
AGAAAAACGACATTAATAGATCCTTTTTTTTCCTATCATTGATGCACCTT
CCGAATGGACTGGTCATCTTGCCGTTGAAGTTCGTCCAGCAGATAATGAA
ACTAAATAGAGGTGAGATTACTGTGGAGCACTGCCATAACCTAATGACTA
TGACTTGGTTTGGGATTCAATCGACGACTGTTGCAGTGACAGTCTTTTGT
TTATATCATCTGTATTTGAGCAATCCTTCGGTAAAGAATCTCTATTCAAA
CAAATTCTATCGTTTTTTTTCATTTGGAATTCTCATAATATGGATGATCG
GTTCAGCACTGGTCACTTTCAATTTCACCTATTACTATTCGGAGATTAGA
TTCAATACCTGTGTGATCAGCAAATCTGTCACGGCGTCGGGGATGCTTCT
TTTGATAGTGTTCGTCGCGCCATATACTCTCTGTCTCGTATGCTATATTA
AAATCTTCCCAGCTACAAGCTGGCTTTCGGACTTGACTTCTTTTTCTAGG
ATATCTAGCCTACAAAAGGAAAGCCAATCAACCATAAATACCGACCATGA
CAGTCAGGAAAAGTGTCGATGGAACCGAATGTTTGACTTTTCAAAGCGGT
CGAGTAAGTTGTCGAATGAAGACAAACTTAGCAAAAAAAAATCTAATGGA
ACCAACCTTGAGTTTAGTAGTTCCGACAGCACCAACACGAACTCCAACAA
TGATTTCAGTCAGGCAATGACTGATCCAATTTTGGAAAAGAAAATTACAA
AACTGTTGCACATTGACATTGAAAAAACAAACAAAAATACATATTCGAAA
TCATCAGTTGTAGTTGGGTTCGTTTTCATTTCATACTTTGCTTTCTGGGC
ACCTTTTATTGCAATAATTCTTGTGGAGATGATGTCGAGAAGGATTATGG
TGAAGTATATCAGTTGGACGATCCGGTTGGGATATTGCAACTCGTTTGCG
TTACCAATTATGTTTGCGTTTTATCTCAGATTCCACAAGCCGGAAACAAA
AAACACTAAAGGCTGACCGTTTGACCTTGGATTTCATTTCCGATGTTTTT
TACTGTTGGAATTTTAATTGAATATACATTATAGCATTGACAGTATTACG
AATTTGTTTTATTGAATTTGGAAATTATATCTATTTCTTAAAGTATCCTA
GTGTTGAGACGGACGGAGTCACTAAATCATGGGCTAGGCTTAGAGGATGA
CAGCAAAACACCTGGGGGAACTTTGGCAAACAGATGTCTGGGCCTTATGG
TGATATATTTCGAATAAATTTACTTTTCAACTGAAATGATTTTATTCTGC
GGCTATTGAAACCTGTAAATCAGAGCTTCTTAAACTTTTGTAATTCACGA
CCCCATTTATGATTGCGAGTTTCTTGACGACCCCATACAAATATAAAAGA
AAAATAAATTTATATTTTTTTAAAATTCCTATAACATCTTCTAATTCATA
GTAAATGTTATTCAAGTTATTACAATACTCTTAATAGAAATGCAGGTACA
AACAATCTTTCCGAACTAGAAGATTTTATGATATATTTATCTACGATAAT
TGTTATTTTATCTTTATAACAATAATTTTACAAGTTAAAAAACATTTTCT
GTTAAATTGTATTTTTATCTCTCGCGACCCCAGAATTTTGCTACGCGACC
CATGGTTTAAGAAGCCCTGGTTTATATTTAATTAATAGTGTTGTTCATTT
ACCAGTGCAATTTTAAATAAAGTTAAATTTTTATTTTATGAATATTAAAA
TGC
back to top

protein sequence of SMED30034586-orf-1

>SMED30034586-orf-1 ID=SMED30034586-orf-1|Name=SMED30034586-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=375bp
MKFNITYKLLIDLILIWTIFLMNIIFIGTLLVRSKVKKNDINRSFFFLSL
MHLPNGLVILPLKFVQQIMKLNRGEITVEHCHNLMTMTWFGIQSTTVAVT
VFCLYHLYLSNPSVKNLYSNKFYRFFSFGILIIWMIGSALVTFNFTYYYS
EIRFNTCVISKSVTASGMLLLIVFVAPYTLCLVCYIKIFPATSWLSDLTS
FSRISSLQKESQSTINTDHDSQEKCRWNRMFDFSKRSSKLSNEDKLSKKK
SNGTNLEFSSSDSTNTNSNNDFSQAMTDPILEKKITKLLHIDIEKTNKNT
YSKSSVVVGFVFISYFAFWAPFIAIILVEMMSRRIMVKYISWTIRLGYCN
SFALPIMFAFYLRFHKPETKNTKG*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000208testis
Vocabulary: INTERPRO
TermDefinition
IPR000276GPCR_Rhodpsn
IPR017452GPCR_Rhodpsn_7TM
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
GO:0016020membrane
Vocabulary: biological process
TermDefinition
GO:0007186G-protein coupled receptor signaling pathway
Vocabulary: molecular function
TermDefinition
GO:0004930G-protein coupled receptor activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000276G protein-coupled receptor, rhodopsin-likePRINTSPR00237GPCRRHODOPSNcoord: 340..366
score: 21.71
coord: 166..189
score: 23.14
coord: 304..328
score: 19.03
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 15..361
e-value: 1.3E-12
score: 49.6
NoneNo IPR availableGENE3DG3DSA:1.20.120.10coord: 198..295
e-value: 1.3E-12
score: 49.6
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 252..266
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 242..266
NoneNo IPR availablePANTHERPTHR24248ADRENERGIC RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTORcoord: 9..360
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 11..361
NoneNo IPR availableTMHMMTMhelixcoord: 45..67
NoneNo IPR availableTMHMMTMhelixcoord: 122..144
NoneNo IPR availableTMHMMTMhelixcoord: 342..364
NoneNo IPR availableTMHMMTMhelixcoord: 87..109
NoneNo IPR availableTMHMMTMhelixcoord: 164..186
NoneNo IPR availableTMHMMTMhelixcoord: 305..327
NoneNo IPR availableTMHMMTMhelixcoord: 10..32
IPR017452GPCR, rhodopsin-like, 7TMPROSITEPS50262G_PROTEIN_RECEP_F1_2coord: 22..358
score: 11.144