GCR143

Overview
NameGCR143
Smed IDSMED30023160
Length (bp)1249
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 GCR143 (SMED30023160) t-SNE clustered cells

Violin plots show distribution of expression levels for GCR143 (SMED30023160) 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 GCR143 (SMED30023160) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for GCR143 (SMED30023160) 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



SMED30023160

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 regionSMED30023160h1SMcG0012212 SmedASXL_007572SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30023160h1SMcG0012212 dd_Smed_v6_50225_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30023160h1SMcG0012212 dd_Smed_v6_59018_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30023160h1SMcG0012212 GCR143smed_ncbi_20240424PMID:27163480
Saberi et al., 2016		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
ovarySMED30023160h1SMcG0012212 GCR143smed_ncbi_20240424PMID:27163480
Saberi et al., 2016		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
oviductSMED30023160h1SMcG0012212 GCR143smed_ncbi_20240424PMID:27163480
Saberi et al., 2016		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
vitelline glandSMED30023160h1SMcG0012212 GCR143smed_ncbi_20240424PMID:27163480
Saberi et al., 2016		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of GCR143 vs. TrEMBL
Match: A0A193KUU6 (GCR143 OS=Schmidtea mediterranea OX=79327 GN=gcr143 PE=2 SV=1)

HSP 1 Score: 748.043 bits (1930), Expect = 0.000e+0
Identity = 364/364 (100.00%), Postives = 364/364 (100.00%), Query Frame = 2 
Query:  113 MNNSTIHVINYIKTSCFFAGNVTNILLLWMIRNHLKRCPYRYSAYCNTIIPALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAWYLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMKILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLENSPDQSRRQTESSMV 1204
            MNNSTIHVINYIKTSCFFAGNVTNILLLWMIRNHLKRCPYRYSAYCNTIIPALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAWYLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMKILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLENSPDQSRRQTESSMV
Sbjct:    1 MNNSTIHVINYIKTSCFFAGNVTNILLLWMIRNHLKRCPYRYSAYCNTIIPALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAWYLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMKILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLENSPDQSRRQTESSMV 364
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BLAST of GCR143 vs. Planmine SMEST
Match: SMESG000044783.1 (SMESG000044783.1)

HSP 1 Score: 768.074 bits (1982), Expect = 0.000e+0
Identity = 368/368 (100.00%), Postives = 368/368 (100.00%), Query Frame = 2 
Query:  101 IKIPMNNSTIHVINYIKTSCFFAGNVTNILLLWMIRNHLKRCPYRYSAYCNTIIPALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAWYLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMKILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLENSPDQSRRQTESSMV 1204
            IKIPMNNSTIHVINYIKTSCFFAGNVTNILLLWMIRNHLKRCPYRYSAYCNTIIPALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAWYLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMKILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLENSPDQSRRQTESSMV
Sbjct: 1057 IKIPMNNSTIHVINYIKTSCFFAGNVTNILLLWMIRNHLKRCPYRYSAYCNTIIPALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAWYLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMKILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLENSPDQSRRQTESSMV 1424
[Close]
BLAST of GCR143 vs. Planmine SMEST
Match: SMESG000056837.1 (SMESG000056837.1)

HSP 1 Score: 690.263 bits (1780), Expect = 0.000e+0
Identity = 335/335 (100.00%), Postives = 335/335 (100.00%), Query Frame = 2 
Query:  200 MIRNHLKRCPYRYSAYCNTIIPALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAWYLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMKILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLENSPDQSRRQTESSMV 1204
            MIRNHLKRCPYRYSAYCNTIIPALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAWYLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMKILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLENSPDQSRRQTESSMV
Sbjct:    1 MIRNHLKRCPYRYSAYCNTIIPALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAWYLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMKILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLENSPDQSRRQTESSMV 335
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BLAST of GCR143 vs. Planmine SMEST
Match: SMESG000005357.1 (SMESG000005357.1)

HSP 1 Score: 65.855 bits (159), Expect = 1.176e-11
Identity = 52/211 (24.64%), Postives = 85/211 (40.28%), Query Frame = 2 
Query:  344 LFTRFLCSIGQFFQFCTGFLVAWYLTIVS-----------SGIKNFNTPVLVYQCKVVSLVSGLAILSFLS---YFHYVWIMGVHKNECMVLTDFRNLFQIWKKVDFIFADFMPY---------NLTLIFGIKCAVKTFHNW--IITGSDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIKWTLPITCGLLQLP 901
            L  R +C IG +  +C  FL+AW L + S           +  + ++  +           SG+ I+S LS   YFH++W+MGV  ++C  +T++     +WK +D   +  +PY         N+ L   IK     F N   I   +DN +        ++K+                       N  F    +K+ LPI+  LL LP
Sbjct:  107 LLLRMICPIGYYIIYCRNFLLAWILALFSLTQNQVLRQKWNNGRKYDQMLKTIDSLQFLTFSGICIISLLSVVLYFHFIWMMGVSNDKCQFVTEYIAFLSMWKIIDMFISGIIPYSVAVAISFLNVVLCAKIKLNYSRFRNLCQIPQQTDNNNRSLERVKKHMKLI----------------------NNIFKGESVKFVLPISVALLNLP 295
The following BLAST results are available for this feature:
BLAST of GCR143 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 GCR143 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 GCR143 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 GCR143 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 GCR143 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 GCR143 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 GCR143 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 GCR143 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUU60.000e+0100.00GCR143 OS=Schmidtea mediterranea OX=79327 GN=gcr14... [more]
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BLAST of GCR143 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 GCR143 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 GCR143 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 GCR143 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 GCR143 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 GCR143 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000044783.10.000e+0100.00SMESG000044783.1[more]
SMESG000056837.10.000e+0100.00SMESG000056837.1[more]
SMESG000005357.11.176e-1124.64SMESG000005357.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023160 ID=SMED30023160|Name=GCR143|organism=Schmidtea mediterranea sexual|type=transcript|length=1249bp
AACCAATCCGTGTCCGATAAAATTATATTATATATAAATTTTATTTCTAT
TGAAAAAATTCCGGGCGTTTTTATAAAATTTTTATAATCCACTTGATAAT
ATAAAAATTCCTATGAATAACTCAACTATCCATGTGATAAATTACATCAA
AACGAGTTGCTTTTTTGCGGGTAATGTGACAAATATCCTATTATTGTGGA
TGATACGCAACCACCTGAAACGATGTCCATATCGTTACAGTGCTTACTGC
AACACTATCATTCCCGCCTTGATATTTAGTGATTTGTTTCTTTGCACCTT
TGGGTTCTTTGATTCACTTGCAGCTTTTTCCAGATTAGGCTCTTTATTTA
CCAGATTTCTATGTTCGATTGGACAGTTCTTTCAGTTTTGCACTGGATTT
CTTGTCGCTTGGTATTTGACTATTGTGTCGAGTGGAATCAAAAACTTCAA
TACTCCGGTATTGGTTTATCAATGCAAAGTAGTCAGCTTAGTGTCCGGAT
TAGCAATTCTCAGTTTTCTCTCGTATTTTCATTATGTTTGGATCATGGGA
GTTCACAAAAACGAATGCATGGTTTTGACAGATTTTAGAAATCTTTTCCA
GATTTGGAAGAAGGTGGATTTTATTTTTGCTGACTTTATGCCATATAATT
TGACATTGATTTTTGGAATAAAATGTGCTGTGAAAACTTTTCACAATTGG
ATTATAACGGGTAGTGACAATCGGTCTGGTCAAGCTCGGCTGCAATCGAC
TAATATAAAAATTAGCACTTTTGTCCATAAACTCCGCGATAAATATTTTG
AGCAAAACTCCTGTTTTTATGAAGCAACAAAAAACTGTTGGTTTTCTTCA
ACTCATATCAAATGGACACTGCCGATCACTTGTGGACTTTTACAATTACC
AATGTCTTTCTTTGTATTTTATCACCATTTCGTTAATTCTGGCAACGTTG
AACACCATTTGGGTTTACAATATTATCTCACAATTTCAGCAATCGCTGGG
CATTCGATGAAAATTTTAATATTTATAAGTTTTAGTACTTCTTTCCGTCG
GGATCTTATTTTCTTTATCAAAGACATTTTTACAAGTTATCGAGCCGACT
ATTTTACTTCAAACGAACAAAATATCATTTTGTATACCAGTTCAATAATT
CCCTTGGAGAATTCTCCTGACCAAAGTAGGCGACAAACCGAATCTTCAAT
GGTATGATACGCTTGAAAAGGGTTTGTTAAGTAATTAATTTAAAGGCTG
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protein sequence of SMED30023160-orf-1

>SMED30023160-orf-1 ID=SMED30023160-orf-1|Name=SMED30023160-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=365bp
MNNSTIHVINYIKTSCFFAGNVTNILLLWMIRNHLKRCPYRYSAYCNTII
PALIFSDLFLCTFGFFDSLAAFSRLGSLFTRFLCSIGQFFQFCTGFLVAW
YLTIVSSGIKNFNTPVLVYQCKVVSLVSGLAILSFLSYFHYVWIMGVHKN
ECMVLTDFRNLFQIWKKVDFIFADFMPYNLTLIFGIKCAVKTFHNWIITG
SDNRSGQARLQSTNIKISTFVHKLRDKYFEQNSCFYEATKNCWFSSTHIK
WTLPITCGLLQLPMSFFVFYHHFVNSGNVEHHLGLQYYLTISAIAGHSMK
ILIFISFSTSFRRDLIFFIKDIFTSYRADYFTSNEQNIILYTSSIIPLEN
SPDQSRRQTESSMV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000044cephalic ganglia
PLANA:0000204ovary
PLANA:0000205oviduct
PLANA:0000231vitelline gland
PLANA:0000418head
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
NoneNo IPR availableCDDcd149697tmA_Opsins_type2_animalscoord: 7..106
e-value: 0.00197565
score: 37.5709
NoneNo IPR availableTMHMMTMhelixcoord: 86..105
NoneNo IPR availableTMHMMTMhelixcoord: 49..71
NoneNo IPR availableTMHMMTMhelixcoord: 248..270
NoneNo IPR availableTMHMMTMhelixcoord: 168..190
NoneNo IPR availableTMHMMTMhelixcoord: 126..148
NoneNo IPR availableTMHMMTMhelixcoord: 285..307
NoneNo IPR availableTMHMMTMhelixcoord: 6..28