Nuclear transcription factor Y subunit alpha

Overview
NameNuclear transcription factor Y subunit alpha
Smed IDSMED30007328
Length (bp)666
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 Nuclear transcription factor Y subunit alpha (SMED30007328) t-SNE clustered cells

Violin plots show distribution of expression levels for Nuclear transcription factor Y subunit alpha (SMED30007328) 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 Nuclear transcription factor Y subunit alpha (SMED30007328) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Nuclear transcription factor Y subunit alpha (SMED30007328) 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



SMED30007328

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30007328h1SMcG0001084 SmedASXL_001620SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30007328h1SMcG0001084 dd_Smed_v4_9452_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007328h1SMcG0001084 dd_Smed_v4_9452_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30007328h1SMcG0001084 dd_Smed_v4_9452_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007328h1SMcG0001084 dd_Smed_v4_9452_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
whole organismSMED30007328h1SMcG0001084 Contig32998uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30007328h1SMcG0001084 Contig32998newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
reproductive organSMED30007328h1SMcG0001084 Contig32998uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30007328h1SMcG0001084 Contig32998newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
zeta neoblastSMED30007328h1SMcG0001084 dd_Smed_v4_18122_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007328h1SMcG0001084 SMED_11577_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30007328h1SMcG0001084 SMED_11577_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Nuclear transcription factor Y subunit alpha vs. Planmine SMEST
Match: SMESG000031441.1 (SMESG000031441.1)

HSP 1 Score: 243.817 bits (621), Expect = 6.607e-83
Identity = 155/160 (96.88%), Postives = 155/160 (96.88%), Query Frame = 3 
Query:   54 MNENVKLNLVSSNADQSIKTDDKVLFITTPEGYIRQFRINNLNQIYEPIQQKLDXXXXXXXXXXXXXXXXXXQTYGMPQEYLNINQNDPPVLFVNPKQYNXXXXXXXXXXXXXXXTGERSRYMYESRRKHALNRARSIGGQFTKKNSANTLENNQSFSII 533
            MNENVKLNLVSSNADQSIKTDDKVLFITTPEGYIRQFRINNLNQIYEPIQQKLDMNLNNIVIHNNMN     QTYGMPQEYLNINQNDPPVLFVNPKQYNRILKRRVARAKLKLRTGERSRYMYESRRKHALNRARSIGGQFTKKNSANTLENNQSFSII
Sbjct:    1 MNENVKLNLVSSNADQSIKTDDKVLFITTPEGYIRQFRINNLNQIYEPIQQKLDMNLNNIVIHNNMN-----QTYGMPQEYLNINQNDPPVLFVNPKQYNRILKRRVARAKLKLRTGERSRYMYESRRKHALNRARSIGGQFTKKNSANTLENNQSFSII 155
The following BLAST results are available for this feature:
BLAST of Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha 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 Nuclear transcription factor Y subunit alpha vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000031441.16.607e-8396.88SMESG000031441.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007328 ID=SMED30007328|Name=Nuclear transcription factor Y subunit alpha|organism=Schmidtea mediterranea sexual|type=transcript|length=666bp
CTTATATTTGTTTTAATAAAATATAATTATATGACAATTAGATTAAATTG
AAAATGAATGAAAATGTTAAATTAAATCTAGTTAGTTCAAATGCAGATCA
ATCGATAAAAACTGATGATAAAGTATTATTTATCACAACACCTGAAGGGT
ATATTCGACAATTTCGCATCAACAATTTAAATCAGATTTATGAGCCTATT
CAACAAAAACTGGATATGAATCTTAACAATATTGTAATTCATAATAATAT
GAATCATACCAATATGAATCAAACTTACGGAATGCCACAAGAGTATCTTA
ATATTAATCAAAATGATCCTCCAGTGTTGTTCGTTAATCCTAAGCAGTAT
AATAGAATTTTGAAACGAAGAGTTGCAAGAGCCAAGCTTAAATTAAGAAC
CGGTGAAAGATCTAGATATATGTATGAATCAAGAAGGAAGCATGCTCTTA
ATCGTGCAAGAAGCATTGGTGGTCAATTTACCAAAAAGAATTCTGCAAAT
ACACTGGAGAATAATCAATCATTTTCTATAATTTGATAAATTTTTCTATA
ATTTTTAAATTTCTTATTTTTATTAGAAAAATAATGTAATAGTTTTCACT
ACATTTTATACTAATTTCACAGTTCCTATTGGCCAATAATAAATATTTGT
TTAATGTCAAAAAAAA
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protein sequence of SMED30007328-orf-1

>SMED30007328-orf-1 ID=SMED30007328-orf-1|Name=SMED30007328-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=161bp
MNENVKLNLVSSNADQSIKTDDKVLFITTPEGYIRQFRINNLNQIYEPIQ
QKLDMNLNNIVIHNNMNHTNMNQTYGMPQEYLNINQNDPPVLFVNPKQYN
RILKRRVARAKLKLRTGERSRYMYESRRKHALNRARSIGGQFTKKNSANT
LENNQSFSII*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
GO:0003700transcription factor activity, sequence-specific DNA binding
Vocabulary: cellular component
TermDefinition
GO:0016602CCAAT-binding factor complex
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000136whole organism
PLANA:0000429neoblast
PLANA:0002089reproductive organ
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR001289NFYA
Vocabulary: biological process
TermDefinition
GO:0006355regulation of transcription, DNA-templated
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001289Nuclear transcription factor Y subunit ASMARTSM00521cbf3coord: 80..140
e-value: 2.3E-18
score: 77.0
IPR001289Nuclear transcription factor Y subunit APFAMPF02045CBFB_NFYAcoord: 87..137
e-value: 8.4E-18
score: 64.7
IPR001289Nuclear transcription factor Y subunit APANTHERPTHR12632TRANSCRIPTION FACTOR NF-Y ALPHA-RELATEDcoord: 38..144
IPR001289Nuclear transcription factor Y subunit APROSITEPS51152NFYA_HAP2_2coord: 83..140
score: 20.531
NoneNo IPR availablePANTHERPTHR12632:SF6NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHAcoord: 38..144