CHHC U11-48K-type domain-containing protein

Overview
NameCHHC U11-48K-type domain-containing protein
Smed IDSMED30025085
Length (bp)976
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 CHHC U11-48K-type domain-containing protein (SMED30025085) t-SNE clustered cells

Violin plots show distribution of expression levels for CHHC U11-48K-type domain-containing protein (SMED30025085) 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 CHHC U11-48K-type domain-containing protein (SMED30025085) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for CHHC U11-48K-type domain-containing protein (SMED30025085) 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



SMED30025085

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30025085SMESG000009746.1 SmedASXL_010098SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30025085SMESG000009746.1 SmedASXL_010098SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30025085SMESG000009746.1 dd_Smed_v4_4174_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30025085SMESG000009746.1 dd_Smed_v4_4174_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of CHHC U11-48K-type domain-containing protein vs. Ensembl Fly
Match: CG14321 (gene:FBgn0038540 transcript:FBtr0083511)

HSP 1 Score: 46.9802 bits (110), Expect = 1.693e-6
Identity = 20/31 (64.52%), Postives = 24/31 (77.42%), Query Frame = 2 
Query:  158 QCMNNKCYQEIYQMNELEEGEIDRRYYSFRG 250
            QC++  CYQ+IY  NELEEGEID R  SF+G
Sbjct:   85 QCISPSCYQDIYAFNELEEGEIDARLNSFKG 115
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BLAST of CHHC U11-48K-type domain-containing protein vs. TrEMBL
Match: W4YCH2 (CHHC U11-48K-type domain-containing protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 9.249e-7
Identity = 42/145 (28.97%), Postives = 70/145 (48.28%), Query Frame = 3 
Query:  318 IDNILSQINWSKESIENTEIKEICKYNCCHSISLSSKSNHESKCLMLNNGWNKKEYESIPKIQLKPVIGDGLGGVHKLELNH-LEERLQSRINQSDDNTDLLSSKGRNRREKELELLAEVRDIKRKRQSYR---VYKEIKSQTEV 740
            +D IL +I WS E +++ E    C  N  H +  SS   H  +C    +G+ ++E E    ++      +    VH +EL+   +  + SR   +DD  +   +          E LAE+RD +R+RQSYR   V+   +S+T+V
Sbjct:   33 LDGILKEIGWSFEDLQSKEALVTCPINPQHRVVESSLQCHIDRCKWARDGYTREEQEEAASLEANRFFYENKKDVHAVELDADCQREITSRFVDNDDKKETTQTHA--------EALAEMRDYRRRRQSYRAKNVHITKRSKTDV 169
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BLAST of CHHC U11-48K-type domain-containing protein vs. Planmine SMEST
Match: SMESG000009746.1 (SMESG000009746.1)

HSP 1 Score: 353.599 bits (906), Expect = 4.172e-124
Identity = 177/180 (98.33%), Postives = 179/180 (99.44%), Query Frame = 3 
Query:  201 MNLKKVKSIDVIILFEDITDSDKNFVSNCQVFLSDSESLIDNILSQINWSKESIENTEIKEICKYNCCHSISLSSKSNHESKCLMLNNGWNKKEYESIPKIQLKPVIGDGLGGVHKLELNHLEERLQSRINQSDDNTDLLSSKGRNRREKELELLAEVRDIKRKRQSYRVYKEIKSQTEV 740
            MNLKKVKSIDVIILFEDITDSDKNFVSNCQVFLSDSESLI+NILSQINWSKESIENTEIKEICKYNCCHSISLSSKSNHESKCLMLNNGWNKKEYESIPKI LKPVIGDGLGGVHKLELNHLEERLQSRINQSDDNTDLLSSKGRNRREKELELLAEVRDIKRKRQSYRVYKEIKSQTE+
Sbjct:    1 MNLKKVKSIDVIILFEDITDSDKNFVSNCQVFLSDSESLIENILSQINWSKESIENTEIKEICKYNCCHSISLSSKSNHESKCLMLNNGWNKKEYESIPKIPLKPVIGDGLGGVHKLELNHLEERLQSRINQSDDNTDLLSSKGRNRREKELELLAEVRDIKRKRQSYRVYKEIKSQTEI 180
The following BLAST results are available for this feature:
BLAST of CHHC U11-48K-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 CHHC U11-48K-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 CHHC U11-48K-type domain-containing protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG143211.693e-664.52gene:FBgn0038540 transcript:FBtr0083511[more]
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BLAST of CHHC U11-48K-type domain-containing 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 CHHC U11-48K-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 CHHC U11-48K-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 CHHC U11-48K-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 CHHC U11-48K-type domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
W4YCH29.249e-728.97CHHC U11-48K-type domain-containing protein OS=Str... [more]
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BLAST of CHHC U11-48K-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 CHHC U11-48K-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 CHHC U11-48K-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 CHHC U11-48K-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 CHHC U11-48K-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 CHHC U11-48K-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
SMESG000009746.14.172e-12498.33SMESG000009746.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025085 ID=SMED30025085|Name=CHHC U11-48K-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=976bp
TGATTATTTCTAAAATATTTGTAATTTTATTTATTCTGTTTTTTATATTA
TTTTGTATTTCTGCACAATATTTAAATGTTCCACAATATAGTTTTCATAA
TAAAGGCAGGTCTAAACGAATTATATTAGATCTTGAACGTAAATGTATAC
AAACATGCAATGTATGAATAATAAATGTTATCAGGAAATATATCAAATGA
ATGAACTTGAAGAAGGTGAAATCGATCGACGTTATTATTCTTTTCGAGGA
TATAACAGACTCTGATAAAAATTTTGTAAGTAACTGTCAGGTATTTTTAT
CTGATTCTGAAAGCTTAATTGACAATATTTTATCACAAATCAATTGGAGC
AAAGAATCAATTGAAAATACTGAAATAAAAGAGATTTGTAAATATAATTG
TTGTCATTCTATTTCTTTATCAAGTAAAAGTAATCATGAATCAAAATGTC
TTATGTTGAATAATGGTTGGAATAAAAAAGAATATGAATCTATACCAAAA
ATACAATTGAAACCTGTTATAGGAGATGGGTTAGGAGGTGTTCATAAATT
AGAATTAAACCACTTAGAGGAGCGATTACAATCTCGAATAAATCAATCAG
ACGATAATACTGATTTGTTATCATCGAAAGGAAGGAATCGTAGAGAAAAA
GAATTGGAGTTATTGGCAGAAGTAAGAGATATCAAAAGGAAGCGGCAAAG
TTATCGAGTGTATAAGGAAATCAAAAGTCAAACAGAAGTAGGAAATCAGT
AATTGAAAATCAGAATAATTTGATGTAGATACACCGAGAAATAATTGCTC
ACCAAATGGAAATGTTGAACGAGTTAAACAAAGTTCAACTGCAAATTGAC
AGAATGTCGGATGATGATAGAAAGCATAGGAAAAAGCACTCGAAAAAAGG
AAAATACAAAAGTAAAAAAAGCAAACATACAAAATCGAAGAAAAAGAAAT
CGAAGCATAACGACAGATCGGAAGAG
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protein sequence of SMED30025085-orf-1

>SMED30025085-orf-1 ID=SMED30025085-orf-1|Name=SMED30025085-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=184bp
MNLKKVKSIDVIILFEDITDSDKNFVSNCQVFLSDSESLIDNILSQINWS
KESIENTEIKEICKYNCCHSISLSSKSNHESKCLMLNNGWNKKEYESIPK
IQLKPVIGDGLGGVHKLELNHLEERLQSRINQSDDNTDLLSSKGRNRREK
ELELLAEVRDIKRKRQSYRVYKEIKSQTEVGNQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR031985DUF4787