hypothetical protein

Overview
Namehypothetical protein (AFJ24736.1)
Smed IDSMED30002813
Length (bp)723
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 hypothetical protein (SMED30002813) t-SNE clustered cells

Violin plots show distribution of expression levels for hypothetical protein (SMED30002813) 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 hypothetical protein (SMED30002813) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for hypothetical protein (SMED30002813) 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




SMED30002813

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
epidermisSMED30002813SMESG000024478.1 SMESG000024473.1 dd_Smed_v4_574_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002813SMESG000024478.1 SMESG000024473.1 Contig46144newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002813SMESG000024478.1 SMESG000024473.1 Contig46144uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
tail regionSMED30002813SMESG000024478.1 SMESG000024473.1 dd_Smed_v6_574_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
whole organismSMED30002813SMESG000024478.1 SMESG000024473.1 Contig46144newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30002813SMESG000024478.1 SMESG000024473.1 Contig46144uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
Category 3 cellSMED30002813SMESG000024478.1 SMESG000024473.1 dd_Smed_v4_574_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of hypothetical protein vs. TrEMBL
Match: I1ZI82 (Uncharacterized protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 243.817 bits (621), Expect = 2.480e-79
Identity = 120/120 (100.00%), Postives = 120/120 (100.00%), Query Frame = 3
Query:  213 ILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 572
            ILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL
Sbjct:    1 ILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 120          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000024473.1 (SMESG000024473.1)

HSP 1 Score: 254.603 bits (649), Expect = 4.443e-87
Identity = 125/125 (100.00%), Postives = 125/125 (100.00%), Query Frame = 3
Query:  198 MNNIMILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 572
            MNNIMILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL
Sbjct:    1 MNNIMILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 125          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000024478.1 (SMESG000024478.1)

HSP 1 Score: 246.128 bits (627), Expect = 8.259e-84
Identity = 121/121 (100.00%), Postives = 121/121 (100.00%), Query Frame = 3
Query:  210 MILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 572
            MILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL
Sbjct:    1 MILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 121          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000024473.1 (SMESG000024473.1)

HSP 1 Score: 246.128 bits (627), Expect = 8.259e-84
Identity = 121/121 (100.00%), Postives = 121/121 (100.00%), Query Frame = 3
Query:  210 MILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 572
            MILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL
Sbjct:    1 MILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 121          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000024478.1 (SMESG000024478.1)

HSP 1 Score: 224.172 bits (570), Expect = 2.493e-75
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = 3
Query:  243 MLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 572
            MLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL
Sbjct:    1 MLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 110          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000024473.1 (SMESG000024473.1)

HSP 1 Score: 224.172 bits (570), Expect = 2.493e-75
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = 3
Query:  243 MLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 572
            MLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL
Sbjct:    1 MLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 110          
The following BLAST results are available for this feature:
BLAST of hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZI822.480e-79100.00Uncharacterized protein (Fragment) OS=Schmidtea me... [more]
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BLAST of hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000024473.14.443e-87100.00SMESG000024473.1[more]
SMESG000024478.18.259e-84100.00SMESG000024478.1[more]
SMESG000024473.18.259e-84100.00SMESG000024473.1[more]
SMESG000024478.12.493e-75100.00SMESG000024478.1[more]
SMESG000024473.12.493e-75100.00SMESG000024473.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30002813
GenBankAFJ24736.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002813 ID=SMED30002813|Name=hypothetical protein|organism=Schmidtea mediterranea sexual|type=transcript|length=723bp
TGAGAGAAAACAAAATTTAATCAGGGAAGAAGCAGAAAACAAAAGACTTA
TTGTTATTATTTATTAAAAATATGAAATGAGCCTACGTCAAAAGCAATTT
CTACCTTGCAAGATTGACCAACTCACCCACGAAAACATCACATTCAGATA
TAACTATAAATACTGAACATGATCAGATAGATAAATATAATCAACAAATG
AATAATATTATGATCTTATTCGCTGCAGTGCTGATTCAATCAATGCTGGT
GGTGCACTGTGCCAGTGTCAAGGCCGTGGAAAAGAAAGGATTTTGTAGTG
GAATTCTCCATAGAATCGACACGGAATGTGATGACAAATATCGGCGCCTG
GACAGGGAATGTGATCACAGCTATGAAAGTATTCATGAAGTATGCGACAT
CAAATATACGATGCTTAGTGGAAGGTGCAGGGTCAAGTTGACTGAGGACT
GTATCAAAAGATATGGAAATCTTGATCATTCTTGTCTCGAATCTCTTCGC
AATATCCAAGAGAAATGTCAAGAAAAATATAATCGAGTTGATGATCATTG
TGATGCATTATATAATCATTTATATTACTGTGATTATTACTATTACTGAT
GTCCTCGTTTTTTCACTCATGGACAGCCTTTTTAGATCCACTTAGTCCTT
CATCAATTTGTGCATTACTTGCTGGAAACATTTGTAGTTTTCATGAATAA
TTAATAAATGGTTTTGTAACTCT
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protein sequence of SMED30002813-orf-1

>SMED30002813-orf-1 ID=SMED30002813-orf-1|Name=SMED30002813-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=134bp
MNNIMILFAAVLIQSMLVVHCASVKAVEKKGFCSGILHRIDTECDDKYRR
LDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESL
RNIQEKCQEKYNRVDDHCDALYNHLYYCDYYYY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0000136whole organism
PLANA:0000421tail
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..21
score: 0.845