C2H2-type domain-containing protein

Overview
NameC2H2-type domain-containing protein
Smed IDSMED30000026
Length (bp)870
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 C2H2-type domain-containing protein (SMED30000026) t-SNE clustered cells

Violin plots show distribution of expression levels for C2H2-type domain-containing protein (SMED30000026) 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 C2H2-type domain-containing protein (SMED30000026) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for C2H2-type domain-containing protein (SMED30000026) 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



SMED30000026

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30000026h1SMcG0017168 SmedASXL_000456SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30000026h1SMcG0017168 SmedASXL_007136SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30000026h1SMcG0017168 dd_Smed_v4_38033_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30000026h1SMcG0017168 dd_Smed_v6_38033_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30000026h1SMcG0017168 dd_Smed_v6_48354_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
oocyteSMED30000026h1SMcG0017168 Contig3164GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30000026h1SMcG0017168 Contig3164GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30000026h1SMcG0016229 Contig3164GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30000026h1SMcG0016229 Contig3164GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A1I8IEF5 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 74.3294 bits (181), Expect = 4.100e-11
Identity = 28/61 (45.90%), Postives = 42/61 (68.85%), Query Frame = 1 
Query:  259 VHILRCFECGFESVDRFKFDTHLPCILKDPPIGYTIYKCCICSTISTNKSIMDEHKQIYHE 441
            VH +RC EC + +++  KF+TH PC L+D P  Y  Y C +C  IST++ IM++H++IYH 
Sbjct:  108 VHFVRCPECAYTTLNLHKFETHFPCSLRDEPPKYFTYVCSVCQAISTSREIMEDHREIYHR 168
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A267E6A4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig004103g1 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 6.903e-11
Identity = 28/61 (45.90%), Postives = 42/61 (68.85%), Query Frame = 1 
Query:  259 VHILRCFECGFESVDRFKFDTHLPCILKDPPIGYTIYKCCICSTISTNKSIMDEHKQIYHE 441
            VH +RC EC + +++  KF+TH PC L+D P  Y  Y C +C  IST++ IM++H++IYH 
Sbjct:   37 VHFVRCPECAYTTLNLHKFETHFPCSLRDEPPKYFTYVCSVCQAISTSREIMEDHREIYHR 97
[Close]
BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A267G2P0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig004103g3 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 6.906e-11
Identity = 28/61 (45.90%), Postives = 42/61 (68.85%), Query Frame = 1 
Query:  259 VHILRCFECGFESVDRFKFDTHLPCILKDPPIGYTIYKCCICSTISTNKSIMDEHKQIYHE 441
            VH +RC EC + +++  KF+TH PC L+D P  Y  Y C +C  IST++ IM++H++IYH 
Sbjct:   38 VHFVRCPECAYTTLNLHKFETHFPCSLRDEPPKYFTYVCSVCQAISTSREIMEDHREIYHR 98
[Close]
BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A1I8JJ09 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=3 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 9.372e-11
Identity = 28/72 (38.89%), Postives = 45/72 (62.50%), Query Frame = 1 
Query:  259 VHILRCFECGFESVDRFKFDTHLPCILKDPPIGYTIYKCCICSTISTNKSIMDEHKQIYHEGDETIIINEIQ 474
            VH +RC ECG+ +++  KF+TH PC  +  P  Y  Y C +C  +ST++ IM++H++IYH   +  II   +
Sbjct: 2726 VHFVRCPECGYTTLNLQKFETHFPCSQRTEPPKYFTYVCSLCQAVSTSRDIMEDHREIYHRRAKASIIESCE 2797
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A183A7N8 (C2H2-type domain-containing protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS2973 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.190e-10
Identity = 31/63 (49.21%), Postives = 40/63 (63.49%), Query Frame = 1 
Query:  256 KVHILRCFECGFESVDRFKFDTHLPCILKDPPIGYTIYKCCICSTISTNKSIMDEHKQIYHEG 444
             VH+LRC ECGFES+ R +F  H+PC  K     Y IY C  CS  ST++S+M EH ++ H G
Sbjct:   36 AVHVLRCVECGFESLVRHRFAAHVPCATKHE--SYLIYACSQCSAYSTSQSLMQEHGELCHAG 96
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BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000061450.1 (SMESG000061450.1)

HSP 1 Score: 429.098 bits (1102), Expect = 6.540e-145
Identity = 205/207 (99.03%), Postives = 206/207 (99.52%), Query Frame = 1 
Query:  118 MNQIDFLTKPKEHDQSMGCKINEEFDRVISNSNSKSDEAIDEEIVMKVHILRCFECGFESVDRFKFDTHLPCILKDPPIGYTIYKCCICSTISTNKSIMDEHKQIYHEGDETIIINEIQDRLKPHLLINDSKDGDQKKQTHSSINFSTNNNQKKYLNSNIQSALDFSKKISKPIPSHFEYPCRVQNVELTNGASKPLIDCLINSWQK 738
            MNQIDFLTKPKEHDQSMGCKINEE DRVISNSNSKSDEAIDEEIVMKVHILRCFECGFESVDRFKFDTHLPCILKDPPIGYTIYKCCICSTISTNKSIMDEHKQIYHEGDETIIINEIQDRLKPHLLINDSKDGDQKKQTHSSINFSTNNNQKKYLNSNIQSALDFSKKISKPIPSHFEYPCRVQN+ELTNGASKPLIDCLINSWQK
Sbjct:    1 MNQIDFLTKPKEHDQSMGCKINEELDRVISNSNSKSDEAIDEEIVMKVHILRCFECGFESVDRFKFDTHLPCILKDPPIGYTIYKCCICSTISTNKSIMDEHKQIYHEGDETIIINEIQDRLKPHLLINDSKDGDQKKQTHSSINFSTNNNQKKYLNSNIQSALDFSKKISKPIPSHFEYPCRVQNIELTNGASKPLIDCLINSWQK 207

HSP 2 Score: 68.9366 bits (167), Expect = 8.983e-13
Identity = 32/33 (96.97%), Postives = 33/33 (100.00%), Query Frame = 2 
Query:  734 KKTPSNNHTSIPYSKRDPLIPNLYNFAMISSML 832
            +KTPSNNHTSIPYSKRDPLIPNLYNFAMISSML
Sbjct:  206 QKTPSNNHTSIPYSKRDPLIPNLYNFAMISSML 238
The following BLAST results are available for this feature:
BLAST of C2H2-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 C2H2-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 C2H2-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 C2H2-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 C2H2-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 C2H2-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 C2H2-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 C2H2-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
A0A1I8IEF54.100e-1145.90Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267E6A46.903e-1145.90Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267G2P06.906e-1145.90Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8JJ099.372e-1138.89Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A183A7N81.190e-1049.21C2H2-type domain-containing protein OS=Echinostoma... [more]
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BLAST of C2H2-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 C2H2-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 C2H2-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 C2H2-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 C2H2-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 C2H2-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
SMESG000061450.16.540e-14599.03SMESG000061450.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000026 ID=SMED30000026|Name=C2H2-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=870bp
GTCGATTTGATTTAAATTTTTTTCCAAGTTTAATTTCCATTTTATTATCT
AATTCACTTGTTAAGAATTGGAAAACAACAGCAACAAAAAGAACTCACAA
AAATAAATATTCCTTCAATGAATCAAATCGACTTCCTTACCAAACCGAAA
GAGCACGATCAATCGATGGGTTGCAAAATCAATGAAGAATTTGATCGGGT
CATCAGCAATTCAAATTCGAAATCCGATGAGGCAATTGACGAAGAAATCG
TCATGAAAGTTCACATTCTTCGATGCTTTGAATGCGGTTTTGAAAGCGTA
GATCGTTTCAAGTTTGACACCCATTTGCCGTGTATTTTAAAAGATCCCCC
AATTGGTTATACGATTTACAAATGTTGTATTTGTTCGACAATTTCAACAA
ACAAATCCATTATGGATGAACACAAACAAATCTATCACGAAGGAGACGAG
ACTATAATTATCAATGAAATCCAAGATCGATTAAAGCCTCATTTATTGAT
CAATGATTCGAAAGATGGCGATCAGAAAAAACAGACTCATTCCTCAATTA
ATTTTTCCACAAATAATAACCAAAAGAAATATCTCAACTCCAATATTCAA
AGCGCGTTAGATTTCTCTAAGAAAATATCGAAGCCAATTCCTTCACATTT
TGAATATCCGTGTCGAGTCCAGAATGTTGAACTAACCAATGGCGCATCAA
AGCCTTTGATCGATTGTTTGATCAACAGTTGGCAAAAAAACTCCATCCAA
TAATCATACTAGTATACCATATTCAAAGCGAGATCCATTAATTCCGAATT
TGTACAATTTCGCGATGATATCCTCGATGCTTCAAAAACAACAAACCCAG
CAACAACAACAACAACAACA
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protein sequence of SMED30000026-orf-1

>SMED30000026-orf-1 ID=SMED30000026-orf-1|Name=SMED30000026-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=212bp
MNQIDFLTKPKEHDQSMGCKINEEFDRVISNSNSKSDEAIDEEIVMKVHI
LRCFECGFESVDRFKFDTHLPCILKDPPIGYTIYKCCICSTISTNKSIMD
EHKQIYHEGDETIIINEIQDRLKPHLLINDSKDGDQKKQTHSSINFSTNN
NQKKYLNSNIQSALDFSKKISKPIPSHFEYPCRVQNVELTNGASKPLIDC
LINSWQKNSIQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0046872metal ion binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR013087Znf_C2H2_type
IPR007087Znf_C2H2
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013087Zinc finger C2H2-typePROSITEPS50157ZINC_FINGER_C2H2_2coord: 84..112
score: 8.808