Protein SCAI homolog

Overview
NameProtein SCAI homolog
Smed IDSMED30030632
Length (bp)1669
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 Protein SCAI homolog (SMED30030632) t-SNE clustered cells

Violin plots show distribution of expression levels for Protein SCAI homolog (SMED30030632) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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




SMED30030632

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30030632SMESG000075968.1 SmedASXL_008686SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
parenchymaSMED30030632SMESG000075968.1 dd_Smed_v4_24482_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30030632SMESG000075968.1 dd_Smed_v4_24482_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 Protein SCAI homolog vs. UniProt/SwissProt
Match: sp|Q54YY1|SCAI_DICDI (Protein SCAI homolog OS=Dictyostelium discoideum OX=44689 GN=scai PE=3 SV=1)

HSP 1 Score: 52.373 bits (124), Expect = 8.774e-6
Identity = 38/119 (31.93%), Postives = 59/119 (49.58%), Query Frame = 1
Query:  148 WGKCYRECFLSMKELLDFQKSIKSEITD--------LEICRSAYYLSWLENANYCRTGDFIYLNNAKDFFHLVRKICHFKDKRKRFTMDEVDRISKYYSRFIWICMLVNDKILVRDLLE 480
            W   +++ F    +L  FQ+  +S + D         EI   A  +  L    Y RT D  YLN +  F+  +R   +FKD     T D + +  +YY+RFI +C+L+N K +V DL+E
Sbjct:   89 WQPFFQKTFELYTKLWKFQQQYRSILEDKSKYGLKRCEIGEIASKIGQLYYHYYLRTSDTNYLNESYIFYEAIRLRSYFKDVSLDKTPDMMVKQLRYYARFIVVCLLLNKKKVVFDLIE 207          
BLAST of Protein SCAI homolog vs. Planmine SMEST
Match: SMESG000075968.1 (SMESG000075968.1)

HSP 1 Score: 306.99 bits (785), Expect = 4.813e-98
Identity = 148/148 (100.00%), Postives = 148/148 (100.00%), Query Frame = 1
Query:   37 MLNKESVDLTNFYKNLHKSAYTSLHHIKLISDFDDENWGKCYRECFLSMKELLDFQKSIKSEITDLEICRSAYYLSWLENANYCRTGDFIYLNNAKDFFHLVRKICHFKDKRKRFTMDEVDRISKYYSRFIWICMLVNDKILVRDLLE 480
            MLNKESVDLTNFYKNLHKSAYTSLHHIKLISDFDDENWGKCYRECFLSMKELLDFQKSIKSEITDLEICRSAYYLSWLENANYCRTGDFIYLNNAKDFFHLVRKICHFKDKRKRFTMDEVDRISKYYSRFIWICMLVNDKILVRDLLE
Sbjct:    1 MLNKESVDLTNFYKNLHKSAYTSLHHIKLISDFDDENWGKCYRECFLSMKELLDFQKSIKSEITDLEICRSAYYLSWLENANYCRTGDFIYLNNAKDFFHLVRKICHFKDKRKRFTMDEVDRISKYYSRFIWICMLVNDKILVRDLLE 148          
The following BLAST results are available for this feature:
BLAST of Protein SCAI homolog 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 Protein SCAI homolog 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 Protein SCAI homolog 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 Protein SCAI homolog 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 Protein SCAI homolog 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 Protein SCAI homolog 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 Protein SCAI homolog vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q54YY1|SCAI_DICDI8.774e-631.93Protein SCAI homolog OS=Dictyostelium discoideum O... [more]
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BLAST of Protein SCAI homolog vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Protein SCAI homolog 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 Protein SCAI homolog 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 Protein SCAI homolog 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 Protein SCAI homolog 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 Protein SCAI homolog 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 Protein SCAI homolog vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000075968.14.813e-98100.00SMESG000075968.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030632 ID=SMED30030632|Name=Protein SCAI homolog|organism=Schmidtea mediterranea sexual|type=transcript|length=1669bp
TCTTAATATTTTATTAAAATTAGTTTTGTAATTTCAATGTTAAATAAAGA
ATCTGTTGATTTAACAAATTTTTATAAGAATTTACACAAATCCGCATACA
CAAGCCTTCATCATATTAAATTGATATCGGATTTTGATGATGAAAACTGG
GGGAAATGTTATCGGGAATGTTTTCTTTCCATGAAGGAACTGTTAGACTT
TCAGAAATCCATTAAATCAGAAATAACTGATTTAGAAATATGTCGAAGTG
CATATTATTTGTCATGGCTTGAAAATGCAAATTACTGTCGAACTGGTGAT
TTTATATACCTCAATAATGCAAAAGATTTTTTTCATTTGGTTCGTAAAAT
ATGCCACTTTAAGGATAAAAGAAAAAGATTCACTATGGACGAAGTAGACA
GAATTAGCAAATATTATTCACGATTTATTTGGATATGTATGCTGGTGAAT
GACAAGATATTAGTGCGTGATTTACTAGAGGTAATGGATTTCGTTTTTTT
ATAACAATTCGACCATGTTGCGCGATTACGCAAACATCTCTCAATTGCCT
TGTGCCAGAGTGTTACACTTGTAAATGGAAAATGAATCTGAATTTCACAT
AGCAACCACATTCCCGTGACTGTAGAGAATATTAATTACTTTTCTCATGT
TTCAAATCACATTCTTTATTTGTCTATTAACTGTTACTGAAGTTTCTATC
ATTCGTATTAAATTCATTTTTTGTTAAGAATTATAAACAATCAGCACTTA
AAGTTCTGGATTTTTTTGGATGCTGACTGCTAAATGACTAAATAATAAAG
TCATATATATATATATATATAATATAGTTCCTGAAAAAATGCCGTGTTAT
AAAAAAAAGGGCTTATTATATATTTTATTAATTATTTGTGTGACTTTTTT
CTGCACCAGGAAACCATCGTCTTATATTAATATAAAAATGTAGGACAAAT
ATGTTTATTAAAACAATAATTTATCGAACGTTTTTTTAAATATTTTTTTC
TTAAGTGATCTTTTGTATTTTCTTAGATTCCTTATGCTAAATTCGCTTCT
ATTTTACTGAATGAATTTGTATTATCTCAGATGCTATTTCCACTGAAGGT
GCTTCGTATCTTGAATGTCTTCAAATCGTCAATCCTTACTATTCTTGTGA
TTTTACAAAAACTTTTACTATTGATTTTGTATTTTTTAAAAATGGTCTCT
GGGTAATTAATTTGTACCTGTTCTTTTAAAAACATCATAGCATTCAAATT
TGCGAGTTGTGACTCATGTAAGCTTTTAAAGTAACTATAAATCCCTGGTC
TGAATATTTCAGTAATAAAGTAGATGTCCAAACATTTAAATGCACCTATT
TTCTTAGATTAACGCCCTCTATAATGATAGATTCTACACTCACTTATAAG
TTGTTTAAAAGGTCTCATGTGTAAGTAATTTTTAAAAAGGTTACTTTTTT
TTGCTAAATTTTATTAAAAGATATTGATAATTATTGTAAGTCAGAATTTT
TTATTTGTAATGACTGTTAAAGGAAATTAAATGATTAATTTTTGTTTTAT
TATTTTCTGCATTTAGGTTTTCAATATCGATAATAATTACTAGTTAAAAT
ATTCATGGAAGTAAAATAAATTCCACATTTTTGAAAGAGCGTGAAATATA
AACTTATTAAGTTATCTGA
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protein sequence of SMED30030632-orf-1

>SMED30030632-orf-1 ID=SMED30030632-orf-1|Name=SMED30030632-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=156bp
MLNKESVDLTNFYKNLHKSAYTSLHHIKLISDFDDENWGKCYRECFLSMK
ELLDFQKSIKSEITDLEICRSAYYLSWLENANYCRTGDFIYLNNAKDFFH
LVRKICHFKDKRKRFTMDEVDRISKYYSRFIWICMLVNDKILVRDLLEVM
DFVFL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR011528NERD
IPR022709SCAI
IPR019774Aromatic-AA_hydroxylase_C
Vocabulary: biological process
TermDefinition
GO:0006351transcription, DNA-templated
GO:0055114oxidation-reduction process
GO:0006355regulation of transcription, DNA-templated
GO:1903507negative regulation of nucleic acid-templated transcription
Vocabulary: molecular function
TermDefinition
GO:0003714transcription corepressor activity
GO:0016714oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005737cytoplasm
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR022709Protein SCAIPFAMPF12070SCAIcoord: 32..150
e-value: 1.4E-9
score: 37.4