SMED30032329
Overview
Neoblast Clusters
Zeng et. al., 2018
Overview
Single cell RNA-seq of pluripotent neoblasts and its early progeniesWe 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 AppEmbryonic Expression
Davies et. al., 2017
Hover the mouse over a column in the graph to view average RPKM values per sample. Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult. back to top Anatomical Expression
PAGE et. al., 2020SMED30032329 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 13Note: Hover over icons to view figure legend
Alignments
SMED30032329 aligns in the following genomic locations:
Homology
BLAST of SMED30032329 vs. Ensembl Human
Match: GCHFR (GTP cyclohydrolase I feedback regulator [Source:HGNC Symbol;Acc:HGNC:4194]) HSP 1 Score: 64.3142 bits (155), Expect = 1.535e-15 Identity = 28/42 (66.67%), Postives = 35/42 (83.33%), Query Frame = -1 Query: 50 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL 175 ++LISTQ+R+ GPT VGDE+SDPELM +L A K +ALGNNL Sbjct: 3 YLLISTQIRMEVGPTMVGDEQSDPELMQHLGASKRRALGNNL 44
BLAST of SMED30032329 vs. Ensembl Human
Match: GCHFR (GTP cyclohydrolase I feedback regulator [Source:HGNC Symbol;Acc:HGNC:4194]) HSP 1 Score: 63.1586 bits (152), Expect = 1.082e-14 Identity = 28/44 (63.64%), Postives = 35/44 (79.55%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 ++LISTQ+R+ GPT VGDE+SDPELM +L A K +ALGNN E Sbjct: 3 YLLISTQIRMEVGPTMVGDEQSDPELMQHLGASKRRALGNNFYE 46
BLAST of SMED30032329 vs. Ensembl Human
Match: GCHFR (GTP cyclohydrolase I feedback regulator [Source:HGNC Symbol;Acc:HGNC:4194]) HSP 1 Score: 43.1282 bits (100), Expect = 5.628e-7 Identity = 19/28 (67.86%), Postives = 22/28 (78.57%), Query Frame = -1 Query: 44 VGDEESDPELMTYLNAEKIKALGNNL*E 127 VGDE+SDPELM +L A K +ALGNN E Sbjct: 2 VGDEQSDPELMQHLGASKRRALGNNFYE 29
BLAST of SMED30032329 vs. Ensembl Human
Match: GCHFR (GTP cyclohydrolase I feedback regulator [Source:HGNC Symbol;Acc:HGNC:4194]) HSP 1 Score: 43.1282 bits (100), Expect = 5.628e-7 Identity = 19/28 (67.86%), Postives = 22/28 (78.57%), Query Frame = -1 Query: 44 VGDEESDPELMTYLNAEKIKALGNNL*E 127 VGDE+SDPELM +L A K +ALGNN E Sbjct: 2 VGDEQSDPELMQHLGASKRRALGNNFYE 29
BLAST of SMED30032329 vs. Ensembl Celegans
Match: gfrp-1 (GTP cyclohydrolase I Feedback Regulatory Protein homolog [Source:UniProtKB/TrEMBL;Acc:D6RYD9]) HSP 1 Score: 52.7582 bits (125), Expect = 6.182e-11 Identity = 25/46 (54.35%), Postives = 32/46 (69.57%), Query Frame = -1 Query: 38 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*ELL 175 ++LISTQ+R+ GPT VGD ESDP+LM L A+ K LGN E + Sbjct: 3 YILISTQIRMECGPTMVGDGESDPKLMGTLEAKLTKQLGNEFQEYI 48
BLAST of SMED30032329 vs. Ensembl Zebrafish
Match: gchfr (GTP cyclohydrolase I feedback regulator [Source:NCBI gene;Acc:393735]) HSP 1 Score: 62.3882 bits (150), Expect = 1.502e-14 Identity = 29/44 (65.91%), Postives = 33/44 (75.00%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 ++LISTQ+RL TGPT VGDE SDP +M YL A KI LGNN E Sbjct: 3 YILISTQIRLETGPTMVGDEYSDPSIMNYLGARKITVLGNNFSE 46
BLAST of SMED30032329 vs. Ensembl Xenopus
Match: eci2 (enoyl-CoA delta isomerase 2 [Source:Xenbase;Acc:XB-GENE-961246]) HSP 1 Score: 54.6842 bits (130), Expect = 2.200e-11 Identity = 27/44 (61.36%), Postives = 32/44 (72.73%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 +VLISTQ+R+ TGPT VGDE SD +LM L A+K LGNN E Sbjct: 3 YVLISTQIRMETGPTIVGDEFSDTQLMAQLEADKRTVLGNNFSE 46
BLAST of SMED30032329 vs. Ensembl Mouse
Match: Gchfr (GTP cyclohydrolase I feedback regulator [Source:MGI Symbol;Acc:MGI:2443977]) HSP 1 Score: 59.3066 bits (142), Expect = 2.568e-13 Identity = 27/44 (61.36%), Postives = 32/44 (72.73%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 ++LISTQ+R+ GPT VGDE SDPELM +L A K LGNN E Sbjct: 3 YLLISTQIRMEVGPTMVGDEHSDPELMQHLGASKRSVLGNNFYE 46
BLAST of SMED30032329 vs. UniProt/SwissProt
Match: sp|P30047|GFRP_HUMAN (GTP cyclohydrolase 1 feedback regulatory protein OS=Homo sapiens OX=9606 GN=GCHFR PE=1 SV=3) HSP 1 Score: 63.1586 bits (152), Expect = 5.198e-14 Identity = 28/44 (63.64%), Postives = 35/44 (79.55%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 ++LISTQ+R+ GPT VGDE+SDPELM +L A K +ALGNN E Sbjct: 3 YLLISTQIRMEVGPTMVGDEQSDPELMQHLGASKRRALGNNFYE 46
BLAST of SMED30032329 vs. UniProt/SwissProt
Match: sp|Q6PBT6|GFRP_DANRE (GTP cyclohydrolase 1 feedback regulatory protein OS=Danio rerio OX=7955 GN=gchfr PE=3 SV=1) HSP 1 Score: 62.3882 bits (150), Expect = 1.134e-13 Identity = 29/44 (65.91%), Postives = 33/44 (75.00%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 ++LISTQ+RL TGPT VGDE SDP +M YL A KI LGNN E Sbjct: 3 YILISTQIRLETGPTMVGDEYSDPSIMNYLGARKITVLGNNFSE 46
BLAST of SMED30032329 vs. UniProt/SwissProt
Match: sp|Q32L41|GFRP_BOVIN (GTP cyclohydrolase 1 feedback regulatory protein OS=Bos taurus OX=9913 GN=GCHFR PE=3 SV=1) HSP 1 Score: 59.3066 bits (142), Expect = 1.558e-12 Identity = 27/44 (61.36%), Postives = 32/44 (72.73%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 ++LISTQ+R+ GPT VGDE SDPELM +L A K LGNN E Sbjct: 3 YLLISTQIRMEVGPTVVGDEHSDPELMQHLGASKRSVLGNNFSE 46
BLAST of SMED30032329 vs. UniProt/SwissProt
Match: sp|P99025|GFRP_MOUSE (GTP cyclohydrolase 1 feedback regulatory protein OS=Mus musculus OX=10090 GN=Gchfr PE=1 SV=3) HSP 1 Score: 59.3066 bits (142), Expect = 1.796e-12 Identity = 27/44 (61.36%), Postives = 32/44 (72.73%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 ++LISTQ+R+ GPT VGDE SDPELM +L A K LGNN E Sbjct: 3 YLLISTQIRMEVGPTMVGDEHSDPELMQHLGASKRSVLGNNFYE 46
BLAST of SMED30032329 vs. UniProt/SwissProt
Match: sp|P70552|GFRP_RAT (GTP cyclohydrolase 1 feedback regulatory protein OS=Rattus norvegicus OX=10116 GN=Gchfr PE=1 SV=3) HSP 1 Score: 58.9214 bits (141), Expect = 2.310e-12 Identity = 27/44 (61.36%), Postives = 32/44 (72.73%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 ++LISTQ+R+ GPT VGDE SDPELM L A K + LGNN E Sbjct: 3 YLLISTQIRMEVGPTMVGDEHSDPELMQQLGASKRRVLGNNFYE 46
BLAST of SMED30032329 vs. TrEMBL
Match: A0A2J8QDM2 (GCHFR isoform 2 OS=Pan troglodytes OX=9598 GN=CK820_G0033505 PE=4 SV=1) HSP 1 Score: 64.3142 bits (155), Expect = 2.185e-12 Identity = 28/42 (66.67%), Postives = 35/42 (83.33%), Query Frame = -1 Query: 50 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL 175 ++LISTQ+R+ GPT VGDE+SDPELM +L A K +ALGNNL Sbjct: 3 YLLISTQIRMEVGPTMVGDEQSDPELMQHLGASKRRALGNNL 44
BLAST of SMED30032329 vs. TrEMBL
Match: H0YNM1 (GTP cyclohydrolase 1 feedback regulatory protein OS=Homo sapiens OX=9606 GN=GCHFR PE=1 SV=1) HSP 1 Score: 64.3142 bits (155), Expect = 2.185e-12 Identity = 28/42 (66.67%), Postives = 35/42 (83.33%), Query Frame = -1 Query: 50 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL 175 ++LISTQ+R+ GPT VGDE+SDPELM +L A K +ALGNNL Sbjct: 3 YLLISTQIRMEVGPTMVGDEQSDPELMQHLGASKRRALGNNL 44
BLAST of SMED30032329 vs. TrEMBL
Match: A0A401P3Z4 (Uncharacterized protein OS=Scyliorhinus torazame OX=75743 GN=scyTo_0013745 PE=4 SV=1) HSP 1 Score: 65.0846 bits (157), Expect = 2.771e-12 Identity = 32/44 (72.73%), Postives = 34/44 (77.27%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 +VLISTQ+RL TGPT VGDE SD ELM YL AEK ALGNN E Sbjct: 3 YVLISTQIRLETGPTIVGDEHSDEELMRYLGAEKTTALGNNFSE 46
BLAST of SMED30032329 vs. TrEMBL
Match: M1ERP8 (GTP cyclohydrolase I feedback regulator (Fragment) OS=Mustela putorius furo OX=9669 PE=2 SV=1) HSP 1 Score: 64.3142 bits (155), Expect = 5.032e-12 Identity = 30/44 (68.18%), Postives = 33/44 (75.00%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 +VLISTQ+R+ GPT VGDE SDPELM YL A K ALGNN E Sbjct: 3 YVLISTQIRMEVGPTMVGDEHSDPELMQYLGASKRSALGNNFYE 46
BLAST of SMED30032329 vs. TrEMBL
Match: M3YBF3 (GTP cyclohydrolase I feedback regulator OS=Mustela putorius furo OX=9669 GN=GCHFR PE=4 SV=1) HSP 1 Score: 64.3142 bits (155), Expect = 5.949e-12 Identity = 30/44 (68.18%), Postives = 33/44 (75.00%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 +VLISTQ+R+ GPT VGDE SDPELM YL A K ALGNN E Sbjct: 3 YVLISTQIRMEVGPTMVGDEHSDPELMQYLGASKRSALGNNFYE 46
BLAST of SMED30032329 vs. Ensembl Nematostella
Match: EDO32067 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SW52]) HSP 1 Score: 55.0694 bits (131), Expect = 3.542e-12 Identity = 26/46 (56.52%), Postives = 32/46 (69.57%), Query Frame = -1 Query: 38 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*ELL 175 ++LIST++RL GPT GDE SDPELM L+AE + GNN E L Sbjct: 3 YILISTRIRLELGPTQCGDEWSDPELMALLDAELVHQFGNNFKEYL 48
BLAST of SMED30032329 vs. Ensembl Medaka
Match: gchfr (GTP cyclohydrolase I feedback regulator [Source:NCBI gene;Acc:101171044]) HSP 1 Score: 58.9214 bits (141), Expect = 3.186e-13 Identity = 28/44 (63.64%), Postives = 32/44 (72.73%), Query Frame = -1 Query: 44 FVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 175 ++LISTQ+RL TGPT VGDE SDP +M YL A K LGNN E Sbjct: 3 YILISTQIRLETGPTNVGDEFSDPAVMNYLGARKTTVLGNNFSE 46
BLAST of SMED30032329 vs. Ensembl Medaka
Match: gchfr (GTP cyclohydrolase I feedback regulator [Source:NCBI gene;Acc:101171044]) HSP 1 Score: 44.669 bits (104), Expect = 1.242e-7 Identity = 21/33 (63.64%), Postives = 22/33 (66.67%), Query Frame = -1 Query: 44 TGPTYVGDEESDPELMTYLNAEKIKALGNNL*E 142 TGPT VGDE SDP +M YL A K LGNN E Sbjct: 27 TGPTNVGDEFSDPAVMNYLGARKTTVLGNNFSE 59
BLAST of SMED30032329 vs. Planmine SMEST
Match: SMESG000042387.1 (SMESG000042387.1) HSP 1 Score: 85.5001 bits (210), Expect = 5.388e-24 Identity = 40/43 (93.02%), Postives = 41/43 (95.35%), Query Frame = -1 Query: 50 MFVLISTQVRLVTGPTYVGDEESDPELMTYLNAEKIKALGNNL 178 MFVLISTQVRL +GPTYVGDEESDPELMTYLNAEKIKALGNN Sbjct: 1 MFVLISTQVRLESGPTYVGDEESDPELMTYLNAEKIKALGNNF 43 The following BLAST results are available for this feature:
BLAST of SMED30032329 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 4
BLAST of SMED30032329 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 1
BLAST of SMED30032329 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30032329 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 1
BLAST of SMED30032329 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 1
BLAST of SMED30032329 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 1
BLAST of SMED30032329 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 5
BLAST of SMED30032329 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30032329 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30032329 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30032329 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30032329 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 1
BLAST of SMED30032329 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 2
BLAST of SMED30032329 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30032329 ID=SMED30032329|Name=SMED30032329|organism=Schmidtea mediterranea sexual|type=transcript|length=184bpback to top Annotated Terms
The following terms have been associated with this transcript:
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
|