HTH CENPB-type domain-containing protein

Overview
NameHTH CENPB-type domain-containing protein
Smed IDSMED30001882
Length (bp)642
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 HTH CENPB-type domain-containing protein (SMED30001882) t-SNE clustered cells

Violin plots show distribution of expression levels for HTH CENPB-type domain-containing protein (SMED30001882) 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 HTH CENPB-type domain-containing protein (SMED30001882) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for HTH CENPB-type domain-containing protein (SMED30001882) 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.
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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




SMED30001882

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
X2 cellSMED30001882 SmedASXL_070434SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of HTH CENPB-type domain-containing protein vs. Ensembl Zebrafish
Match: CR354398.1 (pep chromosome:GRCz11:7:64150332:64152087:-1 gene:ENSDARG00000101994.2 transcript:ENSDART00000165234.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:CR354398.1)

HSP 1 Score: 116.701 bits (291), Expect = 1.899e-30
Identity = 72/119 (60.50%), Postives = 84/119 (70.59%), Query Frame = 1
Query:  199 PLDIGVLTGRLKVKLRAAWEL*MTEGEHTFTKTGRQHRASYDTICQQIVDAWVEVSVSSAI*ALRKAGIITEQLSNCNETXXXXXXXXXXXXXXXXAEITQLLNSNTEDEEFDGFLVEE 555
            PLDIGV     KVKLRAAWE  MT+GEHTFTKTGRQ RASY TIC+ IVDAW +VS  + + A  KAGII EQ    NETDSDND+ +    +    E  QL NS+TEDE+FDGF+ E+
Sbjct:  312 PLDIGVNRA-FKVKLRAAWEQWMTDGEHTFTKTGRQRRASYATICEWIVDAWAKVSALTVVRAFAKAGIIAEQPPG-NETDSDNDEREPGVFDD---ETAQLFNSDTEDEDFDGFVGED 425          

HSP 2 Score: 69.3218 bits (168), Expect = 1.626e-13
Identity = 33/49 (67.35%), Postives = 37/49 (75.51%), Query Frame = 3
Query:    3 EVSLTFDIPVNRTIEKTGTSMVSIRTTRNEKSSFTVVLGCQANG*NYHP 149
            EV LTFDIPVN T+EK G S VSIRTT +EKS+FTVVLGC  +G    P
Sbjct:  171 EVPLTFDIPVNHTVEKKGASTVSIRTTGHEKSAFTVVLGCHGDGQKLPP 219          
BLAST of HTH CENPB-type domain-containing protein vs. Ensembl Zebrafish
Match: BX914205.2 (pep chromosome:GRCz11:4:64121772:64123545:-1 gene:ENSDARG00000099590.2 transcript:ENSDART00000170040.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:BX914205.2)

HSP 1 Score: 97.4413 bits (241), Expect = 1.945e-23
Identity = 53/80 (66.25%), Postives = 58/80 (72.50%), Query Frame = 1
Query:  199 PLDIGVLTGRLKVKLRAAWEL*MTEGEHTFTKTGRQHRASYDTICQQIVDAWVEVSVSSAI*ALRKAGIITEQLSNCNET 438
            PLDIGV     KVKLRAAWE  MT+GEHTFTKTGRQ RASY TIC+ IVDAW +VS  + + A  KAGII EQ    NET
Sbjct:  312 PLDIGVNRA-FKVKLRAAWEQWMTDGEHTFTKTGRQRRASYATICEWIVDAWAKVSALTVVRAFAKAGIIAEQPPG-NET 389          

HSP 2 Score: 69.3218 bits (168), Expect = 1.463e-13
Identity = 33/49 (67.35%), Postives = 37/49 (75.51%), Query Frame = 3
Query:    3 EVSLTFDIPVNRTIEKTGTSMVSIRTTRNEKSSFTVVLGCQANG*NYHP 149
            EV LTFDIPVN T+EK G S VSIRTT +EKS+FTVVLGC  +G    P
Sbjct:  171 EVPLTFDIPVNHTVEKKGASTVSIRTTGHEKSAFTVVLGCHGDGQKLPP 219          
BLAST of HTH CENPB-type domain-containing protein vs. Ensembl Zebrafish
Match: CR352209.1 (pep chromosome:GRCz11:24:26088143:26089609:1 gene:ENSDARG00000103972.2 transcript:ENSDART00000171129.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:CR352209.1)

HSP 1 Score: 97.4413 bits (241), Expect = 1.972e-23
Identity = 53/80 (66.25%), Postives = 58/80 (72.50%), Query Frame = 1
Query:  199 PLDIGVLTGRLKVKLRAAWEL*MTEGEHTFTKTGRQHRASYDTICQQIVDAWVEVSVSSAI*ALRKAGIITEQLSNCNET 438
            PLDIGV     KVKLRAAWE  MT+GEHTFTKTGRQ RASY TIC+ IVDAW +VS  + + A  KAGII EQ    NET
Sbjct:  312 PLDIGVNRA-FKVKLRAAWEQWMTDGEHTFTKTGRQRRASYATICEWIVDAWAKVSALTVVRAFAKAGIIAEQPPG-NET 389          

HSP 2 Score: 69.3218 bits (168), Expect = 1.452e-13
Identity = 33/49 (67.35%), Postives = 37/49 (75.51%), Query Frame = 3
Query:    3 EVSLTFDIPVNRTIEKTGTSMVSIRTTRNEKSSFTVVLGCQANG*NYHP 149
            EV LTFDIPVN T+EK G S VSIRTT +EKS+FTVVLGC  +G    P
Sbjct:  171 EVPLTFDIPVNHTVEKKGASTVSIRTTGHEKSAFTVVLGCHGDGQKLPP 219          
BLAST of HTH CENPB-type domain-containing protein vs. TrEMBL
Match: A0A2D4IZV1 (DDE-1 domain-containing protein (Fragment) OS=Micrurus lemniscatus lemniscatus OX=129467 PE=4 SV=1)

HSP 1 Score: 131.724 bits (330), Expect = 6.901e-35
Identity = 79/119 (66.39%), Postives = 90/119 (75.63%), Query Frame = 1
Query:  199 PLDIGVLTGRLKVKLRAAWEL*MTEGEHTFTKTGRQHRASYDTICQQIVDAWVEVSVSSAI*ALRKAGIITEQLSNCNETXXXXXXXXXXXXXXXXAEITQLLNSNTEDEEFDGFLVEE 555
            PLDI +     KVKLRAAWE  MTEG+HTFT TGRQ  ASY T+CQ IVDAW +VSVSS I A RKAGI TE+ S+ NET    D D+D++   LDAEI QLLNS+TEDEEFDGFLVE+
Sbjct:   72 PLDISI-NRSFKVKLRAAWEHWMTEGDHTFTNTGRQRCASYATMCQWIVDAWKKVSVSSVIRAFRKAGITTEEPSSSNET----DSDNDEEDPRLDAEIAQLLNSDTEDEEFDGFLVED 185          
BLAST of HTH CENPB-type domain-containing protein vs. TrEMBL
Match: A0A5J5DCQ1 (DDE-1 domain-containing protein OS=Etheostoma spectabile OX=54343 GN=FQN60_013136 PE=4 SV=1)

HSP 1 Score: 118.627 bits (296), Expect = 3.000e-30
Identity = 71/118 (60.17%), Postives = 90/118 (76.27%), Query Frame = 1
Query:  199 PLDIGVLTGRLKVKLRAAWEL*MTEGEHTFTKTGRQHRASYDTICQQIVDAWVEVSVSSAI*ALRKAGIITEQLSNCNETXXXXXXXXXXXXXXXXAEITQLLNSNTEDEEFDGFLVE 552
            PLDIGV    + VKLR+AWE  MTEGEHTFT TGRQ RA+Y TICQ IVDAW +VSVS+ + A  KAG+ITE  +N N+T   + D+D++D ++L A I QLLNS+T+DEEF+GF+ E
Sbjct:   33 PLDIGVNRAFI-VKLRSAWEQWMTEGEHTFTNTGRQRRATYATICQWIVDAWAKVSVSTVVRASTKAGMITELPANSNDT---DSDNDERDSDILFAIIAQLLNSDTKDEEFEGFVDE 146          
BLAST of HTH CENPB-type domain-containing protein vs. TrEMBL
Match: A0A5C6PH34 (DDE-1 domain-containing protein OS=Takifugu flavidus OX=433684 GN=D4764_11G0002920 PE=4 SV=1)

HSP 1 Score: 117.472 bits (293), Expect = 8.699e-30
Identity = 68/119 (57.14%), Postives = 84/119 (70.59%), Query Frame = 1
Query:  199 PLDIGVLTGRLKVKLRAAWEL*MTEGEHTFTKTGRQHRASYDTICQQIVDAWVEVSVSSAI*ALRKAGIITEQLSNCNETXXXXXXXXXXXXXXXXAEITQLLNSNTEDEEFDGFLVEE 555
            PLDIGV     K +LR AWE  M EGEHTFTKTGRQ RA+Y TICQ IV+AW ++SVS+ + A RKAGI+TE   N ++T   + D D+ +  MLDA   QL NS+ E+EEF+GFL EE
Sbjct:   37 PLDIGVNRA-FKARLRTAWEWWMMEGEHTFTKTGRQRRAAYATICQWIVNAWADISVSTVVRAFRKAGIVTEMPDNTSDT-DPDYDFDETEPAMLDAIFAQLFNSDIEEEEFEGFLDEE 153          
BLAST of HTH CENPB-type domain-containing protein vs. TrEMBL
Match: A0A5C6P1R6 (Uncharacterized protein OS=Takifugu flavidus OX=433684 GN=D4764_15G0008770 PE=4 SV=1)

HSP 1 Score: 118.242 bits (295), Expect = 1.238e-29
Identity = 70/119 (58.82%), Postives = 86/119 (72.27%), Query Frame = 1
Query:  199 PLDIGVLTGRLKVKLRAAWEL*MTEGEHTFTKTGRQHRASYDTICQQIVDAWVEVSVSSAI*ALRKAGIITEQLSNCNETXXXXXXXXXXXXXXXXAEITQLLNSNTEDEEFDGFLVEE 555
            PLDIGV     + +LR AWE  MTEGEHTFTKTGRQ RA+Y TICQ IV+AW ++SVS+ + A RKAGI+TE   N + T   +DD D+ +  MLDA   QL NS+TE+EEF+GFL EE
Sbjct:   75 PLDIGVNRA-FEARLRTAWERWMTEGEHTFTKTGRQRRATYVTICQWIVNAWADISVSTVVRAFRKAGIVTEMPDNTSNT-DPDDDFDETEPAMLDAVFAQLFNSDTEEEEFEGFLDEE 191          
BLAST of HTH CENPB-type domain-containing protein vs. TrEMBL
Match: A0A5J5D389 (DDE-1 domain-containing protein (Fragment) OS=Etheostoma spectabile OX=54343 GN=FQN60_010527 PE=4 SV=1)

HSP 1 Score: 117.472 bits (293), Expect = 1.013e-27
Identity = 72/115 (62.61%), Postives = 80/115 (69.57%), Query Frame = 1
Query:  199 PLDIGVLTGRLKVKLRAAWEL*MTEGEHTFTKTGRQHRASYDTICQQIVDAWVEVSVSSAI*ALRKAGIITEQLSNCNETXXXXXXXXXXXXXXXXAEITQLLNSNTEDEEFDGF 543
            PLDIGV     KVKLRAAWE  MTEG+HTFTKTGRQ  A+Y TICQ IVDAW +VSVS+ + A  KA IITE  +N N+TDSDND             I QLLNS+TEDEEF GF
Sbjct:   66 PLDIGV-NRAFKVKLRAAWEQWMTEGKHTFTKTGRQRPATYATICQWIVDAWAKVSVSTVVRAFTKARIITELPANSNDTDSDNDGFGHFGCV-----IAQLLNSDTEDEEFKGF 174          
BLAST of HTH CENPB-type domain-containing protein vs. Planmine SMEST
Match: SMESG000064663.1 (SMESG000064663.1)

HSP 1 Score: 44.669 bits (104), Expect = 3.531e-6
Identity = 29/94 (30.85%), Postives = 50/94 (53.19%), Query Frame = 1
Query:  265 MTEG-EHTFTKTGRQHRASYDTICQQIVDAWVEVSVSSAI*ALRKAGIITEQLSNCNETXXXXXXXXXXXXXXXXAEITQLLNSNTEDEEFDGF 543
            M +G +H+ T T R  RA++  + + +  AW  V+V + +    KA II +     +     +  +++  G+ +   I Q+ NS TEDE+FDGF
Sbjct:    1 MDDGRKHSLTATDRVRRATFGEVSEWVDTAWKAVTVRTIMVGFEKAKIIQKIGEEDDSEIEKDSYENEDIGDEILERIYQIFNSGTEDEDFDGF 94          
The following BLAST results are available for this feature:
BLAST of HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing protein vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 3
Match NameE-valueIdentityDescription
CR354398.11.899e-3060.50pep chromosome:GRCz11:7:64150332:64152087:-1 gene:... [more]
BX914205.21.945e-2366.25pep chromosome:GRCz11:4:64121772:64123545:-1 gene:... [more]
CR352209.11.972e-2366.25pep chromosome:GRCz11:24:26088143:26089609:1 gene:... [more]
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BLAST of HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2D4IZV16.901e-3566.39DDE-1 domain-containing protein (Fragment) OS=Micr... [more]
A0A5J5DCQ13.000e-3060.17DDE-1 domain-containing protein OS=Etheostoma spec... [more]
A0A5C6PH348.699e-3057.14DDE-1 domain-containing protein OS=Takifugu flavid... [more]
A0A5C6P1R61.238e-2958.82Uncharacterized protein OS=Takifugu flavidus OX=43... [more]
A0A5J5D3891.013e-2762.61DDE-1 domain-containing protein (Fragment) OS=Ethe... [more]
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BLAST of HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing 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 HTH CENPB-type domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000064663.13.531e-630.85SMESG000064663.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001882 ID=SMED30001882|Name=HTH CENPB-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=642bp
ACGAGGTCTCACTTACCTTTGATATCCCCGTAAATCGTACTATTGAGAAA
ACGGGGACCAGTATGGTATCTATACGTACTACAAGAAACGAGAAGTCATC
CTTCACTGTAGTTCTCGGTTGCCAGGCTAATGGCTAAAACTACCACCCAC
GGTAATTTTCAAGAGGAAGACTTTGCCAAAAGAAATGTTTCCGGTTGGCC
GCTAGATATTGGTGTTCTAACAGGTCGTTTAAAAGTTAAATTGCGAGCTG
CGTGGGAGCTTTAGATGACAGAAGGTGAACATACATTCACCAAGACAGGA
AGGCAACACCGTGCAAGTTACGATACTATCTGCCAGCAAATTGTGGATGC
CTGGGTAGAGGTATCAGTCTCCAGTGCCATCTGAGCTTTGAGGAAGGCCG
GAATCATCACTGAACAGCTAAGTAACTGCAACGAGACTGACTCTGATAAT
GATGATGATGATGATAAGGATGGGGAAATGCTTGATGCCGAAATCACCCA
ACTGTTAAACTCAAACACTGAAGATGAAGAATTTGATGGATTTTTGGTAG
AGGAATAGAATTTTATGTGTTTAACACTGAACAATGTTGATAGTTATTGT
GAAAGATTTCAATAGAGTTGAATAAAGCTTGACTTATTAGGA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0043565sequence-specific DNA binding
GO:0003676nucleic acid binding
GO:0003677DNA binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002056medial muscle cell
PLANA:0002111X2 cell