GCR134

Overview
NameGCR134
Smed IDSMED30004869
Length (bp)981
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



SMED30004869

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30004869SMESG000037700.1 GCR134smed_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
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BLAST of GCR134 vs. TrEMBL
Match: A0A193KUE8 (GCR134 OS=Schmidtea mediterranea OX=79327 GN=gcr134 PE=2 SV=1)

HSP 1 Score: 618.231 bits (1593), Expect = 0.000e+0
Identity = 310/310 (100.00%), Postives = 310/310 (100.00%), Query Frame = 3 
Query:   24 MQLDLKSILVIIFALIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDCITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGFRTVFFLFRSFMLIYQRILIFYNIYVSIIVMAVFIVFLCSYHIPVLVNHKPLKEVPSELVTIFRLIFLFLSDVCILFSSIYLIYFLMIQVKPVLLRIEALFEYHLTQEEIQENHQRNLYGSTKRTILWTSAMGIVWVLCNLPFIAINILMLNTTDSNLDVYYYSFNDDMMLVMLFPLSISWLFTIILSQPLRQEMVVKLQLLKFQTLGTFRYISSVVRSGDEN 953
            MQLDLKSILVIIFALIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDCITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGFRTVFFLFRSFMLIYQRILIFYNIYVSIIVMAVFIVFLCSYHIPVLVNHKPLKEVPSELVTIFRLIFLFLSDVCILFSSIYLIYFLMIQVKPVLLRIEALFEYHLTQEEIQENHQRNLYGSTKRTILWTSAMGIVWVLCNLPFIAINILMLNTTDSNLDVYYYSFNDDMMLVMLFPLSISWLFTIILSQPLRQEMVVKLQLLKFQTLGTFRYISSVVRSGDEN
Sbjct:    1 MQLDLKSILVIIFALIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDCITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGFRTVFFLFRSFMLIYQRILIFYNIYVSIIVMAVFIVFLCSYHIPVLVNHKPLKEVPSELVTIFRLIFLFLSDVCILFSSIYLIYFLMIQVKPVLLRIEALFEYHLTQEEIQENHQRNLYGSTKRTILWTSAMGIVWVLCNLPFIAINILMLNTTDSNLDVYYYSFNDDMMLVMLFPLSISWLFTIILSQPLRQEMVVKLQLLKFQTLGTFRYISSVVRSGDEN 310
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BLAST of GCR134 vs. TrEMBL
Match: A0A193KUP5 (GCR133 OS=Schmidtea mediterranea OX=79327 GN=gcr133 PE=2 SV=1)

HSP 1 Score: 79.7221 bits (195), Expect = 5.622e-13
Identity = 74/284 (26.06%), Postives = 132/284 (46.48%), Query Frame = 3 
Query:   66 LIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDCITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGF-RTVFFLFRSFMLIYQRILIF-YNIYVSIIVMAV----------FIVFLCSYHIPVLVNHKPLKEVPSELVTIFRLIFLFLSDVCILFSSIYLIYFLMIQVKPVLLRIEALFEYHLTQEEIQENHQ----RNLYGSTKRTILWTSAMGIVWVLCNLPFIAINILMLNTTDSNLDVYYYSFNDDMMLVMLFPLSISWLFTIILSQPLRQEM 869
            +IG  SS+ + ++L  ++I++ +I FW+R+ICG D   +TC I  +FF       F   V+Y     L    G+ R  F L R  MLI  + + F +++Y+S+ + ++          F  +LC            +      ++ +   + L +  V +LFSS + +YFL   + P+  ++E   E  +    I  N         Y   KR I W+S + I+WV+   P++ +    L    +N  +      +    ++L PLS++WLF +++   L QEM
Sbjct:   31 VIGLGSSIFASFLLTGERIHNAIIVFWLRAICGTD---VTCLI--YFFLDELLFNFPCKVDYYFSHILLTLSGYTRCAFSLARVIMLITGKCVTFRFHLYISLFIASIILIIYIPTFYFFDYLC-----------VIDRFHETILLLIESVTLLIGIVVMLFSSSFFLYFLSTTITPLFYKVE---ETEVVNRIINVNFHCKTWSEFYKCVKRGIFWSSIINIIWVVACSPYLIMCFWYL----ANRSILVQYIKEKTSTLILIPLSLNWLFAVVIDHMLFQEM 291
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BLAST of GCR134 vs. Planmine SMEST
Match: SMESG000037700.1 (SMESG000037700.1)

HSP 1 Score: 618.231 bits (1593), Expect = 0.000e+0
Identity = 310/310 (100.00%), Postives = 310/310 (100.00%), Query Frame = 3 
Query:   24 MQLDLKSILVIIFALIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDCITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGFRTVFFLFRSFMLIYQRILIFYNIYVSIIVMAVFIVFLCSYHIPVLVNHKPLKEVPSELVTIFRLIFLFLSDVCILFSSIYLIYFLMIQVKPVLLRIEALFEYHLTQEEIQENHQRNLYGSTKRTILWTSAMGIVWVLCNLPFIAINILMLNTTDSNLDVYYYSFNDDMMLVMLFPLSISWLFTIILSQPLRQEMVVKLQLLKFQTLGTFRYISSVVRSGDEN 953
            MQLDLKSILVIIFALIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDCITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGFRTVFFLFRSFMLIYQRILIFYNIYVSIIVMAVFIVFLCSYHIPVLVNHKPLKEVPSELVTIFRLIFLFLSDVCILFSSIYLIYFLMIQVKPVLLRIEALFEYHLTQEEIQENHQRNLYGSTKRTILWTSAMGIVWVLCNLPFIAINILMLNTTDSNLDVYYYSFNDDMMLVMLFPLSISWLFTIILSQPLRQEMVVKLQLLKFQTLGTFRYISSVVRSGDEN
Sbjct:    1 MQLDLKSILVIIFALIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDCITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGFRTVFFLFRSFMLIYQRILIFYNIYVSIIVMAVFIVFLCSYHIPVLVNHKPLKEVPSELVTIFRLIFLFLSDVCILFSSIYLIYFLMIQVKPVLLRIEALFEYHLTQEEIQENHQRNLYGSTKRTILWTSAMGIVWVLCNLPFIAINILMLNTTDSNLDVYYYSFNDDMMLVMLFPLSISWLFTIILSQPLRQEMVVKLQLLKFQTLGTFRYISSVVRSGDEN 310
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BLAST of GCR134 vs. Planmine SMEST
Match: SMESG000037702.1 (SMESG000037702.1)

HSP 1 Score: 56.9954 bits (136), Expect = 5.688e-9
Identity = 79/321 (24.61%), Postives = 144/321 (44.86%), Query Frame = 3 
Query:   33 DLKSILVIIFALIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDCITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGFRTVFFLF-----RSFMLIYQRILI-------FYNIYVSIIVMAVFIVFLCSYHIPVLVNHKPLKEVPSELVTIF-----RLIFL-------FLSDVCILFSSIYLI-YFLMIQVKPVLLRIEALFEYHLTQEEIQENHQRNLYG----STKRTILWTSAMGIVWVLCNLPFIAINI-LMLNTTDSNL----DVYYYSFNDDMMLVMLFPLSISWLFTIILSQPLRQEMVVKLQLLK 893
            D K+ + +   ++G +S ++ + IL  + I  + +S WMR  C  D + L   I+     K+  T++        ICS+     F  VF        RSF+ I Q IL+               ++M   I+ +     P L     ++ + +    +F     RLI L        L+ +  + S+ + + YF  IQ  P+L RI  + +   T E     + + ++     +T+ +I+     G +W   N+PF+ INI + +   D ++    +V YY       L +LFP S +W+FT+  + P+RQE+V+  ++L+
Sbjct:   17 DYKTYVALTLLILGLVSCVLIMVILSKKNILHHTLSIWMRFTCIIDIVFLVVVILAISINKTSLTRW--------ICSMK---EFFKVFSYLLATSSRSFIAIIQIILLKKPYLKRLNETKTYYLIMGFNIIIIGIVCTPSLFYAGEIRVINNVSQCVFHKDHVRLILLGEIFCLTILNTITYISSTYFAVCYFRTIQ--PMLNRILKVLQGVKTLEIGLFKYNKKIFKRVIYNTRHSIICILLNGYLWTTLNVPFLIINIEVAMGRMDMDVLLSTEVNYYE------LCVLFPPSANWIFTLTFNAPVRQELVMYFKILQ 318
The following BLAST results are available for this feature:
BLAST of GCR134 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 GCR134 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 GCR134 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 GCR134 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 GCR134 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 GCR134 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 GCR134 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 GCR134 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A193KUE80.000e+0100.00GCR134 OS=Schmidtea mediterranea OX=79327 GN=gcr13... [more]
A0A193KUP55.622e-1326.06GCR133 OS=Schmidtea mediterranea OX=79327 GN=gcr13... [more]
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BLAST of GCR134 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 GCR134 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 GCR134 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 GCR134 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 GCR134 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 GCR134 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000037700.10.000e+0100.00SMESG000037700.1[more]
SMESG000037702.15.688e-924.61SMESG000037702.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004869 ID=SMED30004869|Name=GCR134|organism=Schmidtea mediterranea sexual|type=transcript|length=981bp
GCCAAAGGTGAATTTCCCAGTAAATGCAATTGGATTTGAAGTCTATTTTA
GTTATAATATTCGCATTAATTGGATTTATCAGCTCATTGGTATCACTGTA
CATTTTGAAGAGTCAAAAGATCTACGACAATGTAATTTCGTTTTGGATGA
GATCAATCTGCGGATTTGACTGCATCACATTGACCTGTTTCATCGTCAAT
TTCTTTTTCGAGAAATCCCAGACAACGAAATTTGATTTCGTTGTAAACTA
TTTGCAGATTTGCTCTTTAAGTATCACCATTGGATTCCGAACCGTATTCT
TTCTCTTTAGATCCTTCATGCTCATCTATCAGAGAATATTAATATTTTAT
AATATTTACGTGAGCATTATTGTAATGGCGGTATTTATCGTATTTCTGTG
TTCGTATCACATCCCGGTGTTGGTAAATCACAAACCTCTCAAGGAAGTTC
CATCAGAACTCGTCACAATTTTCAGACTAATTTTCTTATTCTTGTCCGAC
GTTTGCATTTTGTTTTCGAGTATTTATCTCATTTACTTTCTTATGATTCA
AGTGAAACCGGTTCTGCTACGAATTGAGGCGTTATTTGAGTATCATTTGA
CCCAGGAGGAAATACAAGAGAATCATCAACGAAATTTATATGGATCGACA
AAGAGAACGATTCTTTGGACGTCTGCTATGGGAATCGTCTGGGTTCTCTG
TAATCTTCCTTTTATAGCGATTAATATTCTGATGCTTAATACAACTGATT
CGAATCTAGATGTTTATTATTATAGTTTCAATGATGACATGATGTTGGTC
ATGCTTTTTCCGTTATCCATTAGTTGGTTATTTACAATAATTTTGTCTCA
ACCTCTTCGACAAGAAATGGTGGTCAAACTGCAGTTACTAAAATTCCAAA
CTTTAGGAACTTTTAGATATATCAGTTCGGTAGTGAGAAGTGGAGATGAG
AATTGAAAATGAATTTAAGATTGAAAATATT
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protein sequence of SMED30004869-orf-1

>SMED30004869-orf-1 ID=SMED30004869-orf-1|Name=SMED30004869-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=311bp
MQLDLKSILVIIFALIGFISSLVSLYILKSQKIYDNVISFWMRSICGFDC
ITLTCFIVNFFFEKSQTTKFDFVVNYLQICSLSITIGFRTVFFLFRSFML
IYQRILIFYNIYVSIIVMAVFIVFLCSYHIPVLVNHKPLKEVPSELVTIF
RLIFLFLSDVCILFSSIYLIYFLMIQVKPVLLRIEALFEYHLTQEEIQEN
HQRNLYGSTKRTILWTSAMGIVWVLCNLPFIAINILMLNTTDSNLDVYYY
SFNDDMMLVMLFPLSISWLFTIILSQPLRQEMVVKLQLLKFQTLGTFRYI
SSVVRSGDEN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
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 availableTMHMMTMhelixcoord: 256..278
NoneNo IPR availableTMHMMTMhelixcoord: 214..236
NoneNo IPR availableTMHMMTMhelixcoord: 5..27
NoneNo IPR availableTMHMMTMhelixcoord: 148..170
NoneNo IPR availableTMHMMTMhelixcoord: 106..128
NoneNo IPR availableTMHMMTMhelixcoord: 72..94
NoneNo IPR availableTMHMMTMhelixcoord: 40..62