Homeobox protein Hox-B13a

Overview
NameHomeobox protein Hox-B13a
Smed IDSMED30028426
Length (bp)688
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 Homeobox protein Hox-B13a (SMED30028426) t-SNE clustered cells

Violin plots show distribution of expression levels for Homeobox protein Hox-B13a (SMED30028426) 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 Homeobox protein Hox-B13a (SMED30028426) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Homeobox protein Hox-B13a (SMED30028426) 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




SMED30028426

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
headSMED30028426SMESG000045930.1 dd_Smed_v6_17797_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Homeobox protein Hox-B13a vs. Planmine SMEST
Match: SMESG000045930.1 (SMESG000045930.1)

HSP 1 Score: 264.618 bits (675), Expect = 7.326e-91
Identity = 144/145 (99.31%), Postives = 145/145 (100.00%), Query Frame = 2
Query:  119 MDGNPSKCFHIKENEKENSDQTVLLNKLNNQTKPLDLSLKSNQSEDESMFYEENNKMHVFREVNFEKSDIFYCYCCNNIMRKGNIYRAPIVDCAVGKRASRFQFTNDQLXXXXXXXXXXXXXXXXQRALLSTDLNIPEKQIMFWW 553
            MDGNPSKCFHIK+NEKENSDQTVLLNKLNNQTKPLDLSLKSNQSEDESMFYEENNKMHVFREVNFEKSDIFYCYCCNNIMRKGNIYRAPIVDCAVGKRASRFQFTNDQLKILKDNFNKNIKINKIQRALLSTDLNIPEKQIMFWW
Sbjct:    1 MDGNPSKCFHIKQNEKENSDQTVLLNKLNNQTKPLDLSLKSNQSEDESMFYEENNKMHVFREVNFEKSDIFYCYCCNNIMRKGNIYRAPIVDCAVGKRASRFQFTNDQLKILKDNFNKNIKINKIQRALLSTDLNIPEKQIMFWW 145          
The following BLAST results are available for this feature:
BLAST of Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a 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 Homeobox protein Hox-B13a vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000045930.17.326e-9199.31SMESG000045930.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028426 ID=SMED30028426|Name=Homeobox protein Hox-B13a|organism=Schmidtea mediterranea sexual|type=transcript|length=688bp
GAAATATATTTTTATCGATATTAATCCAGTTTTAATTTATTTTAAGCTGA
AGTTTATATTATTTATTCAAATATCTTTATGTATAAATTCGAGAAATCAT
GTTAATCCTTTAAATTAAATGGATGGCAATCCCTCAAAGTGTTTTCACAT
TAAAGAAAATGAAAAAGAAAATTCAGATCAAACTGTTCTTTTAAATAAAC
TTAATAATCAGACTAAACCTCTTGATCTAAGTTTAAAATCAAATCAATCT
GAGGATGAATCAATGTTTTACGAAGAAAATAATAAAATGCATGTATTTCG
TGAAGTAAATTTCGAAAAATCTGATATTTTCTATTGTTATTGTTGTAATA
ATATAATGAGAAAAGGAAATATTTACCGAGCACCAATTGTAGACTGTGCT
GTTGGTAAAAGAGCTTCGAGATTTCAATTTACCAATGATCAACTGAAAAT
ATTGAAAGATAACTTCAATAAAAATATCAAAATAAATAAAATCCAAAGGG
CTTTGCTGTCAACAGATTTAAATATACCTGAAAAACAAATAATGTTTTGG
TGGCAAAATCAACGAGCAAGGCAGAAACGAAATCAAAATTGAAATATTTT
AATAGAAATGTCGTATTATTAATTTTTATATTATTATTGTTCTTTTTAAT
TGTAATAATTTTTATTAAAATATAATTTTTTATCTGTG
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protein sequence of SMED30028426-orf-1

>SMED30028426-orf-1 ID=SMED30028426-orf-1|Name=SMED30028426-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=158bp
MDGNPSKCFHIKENEKENSDQTVLLNKLNNQTKPLDLSLKSNQSEDESMF
YEENNKMHVFREVNFEKSDIFYCYCCNNIMRKGNIYRAPIVDCAVGKRAS
RFQFTNDQLKILKDNFNKNIKINKIQRALLSTDLNIPEKQIMFWWQNQRA
RQKRNQN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR001356Homeobox_dom
IPR009057Homeobox-like_sf
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 11..31
NoneNo IPR availableGENE3DG3DSA:1.10.10.60coord: 94..157
e-value: 5.7E-14
score: 53.5
IPR001356Homeobox domainSMARTSM00389HOX_1coord: 97..157
e-value: 2.6E-5
score: 33.7
IPR001356Homeobox domainPFAMPF00046Homeodomaincoord: 98..154
e-value: 2.0E-13
score: 50.0
IPR001356Homeobox domainPROSITEPS50071HOMEOBOX_2coord: 95..155
score: 14.754
IPR001356Homeobox domainCDDcd00086homeodomaincoord: 98..156
e-value: 1.49598E-10
score: 51.8605
IPR009057Homeobox-like domain superfamilySUPERFAMILYSSF46689Homeodomain-likecoord: 89..156