C2H2-type domain-containing protein

Overview
NameC2H2-type domain-containing protein
Smed IDSMED30009039
Length (bp)895
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 (SMED30009039) t-SNE clustered cells

Violin plots show distribution of expression levels for C2H2-type domain-containing protein (SMED30009039) 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 (SMED30009039) 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 (SMED30009039) 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



SMED30009039

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 regionSMED30009039h1SMcG0017168 SmedASXL_000456SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30009039h1SMcG0017168 SmedASXL_007136SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30009039h1SMcG0017168 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 regionSMED30009039h1SMcG0017168 dd_Smed_v6_38033_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30009039h1SMcG0017168 dd_Smed_v6_48354_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
oocyteSMED30009039h1SMcG0017168 Contig3164GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30009039h1SMcG0017168 Contig3164GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30009039h1SMcG0016229 Contig3164GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30009039h1SMcG0016229 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: A0A5K3F917 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 134.035 bits (336), Expect = 2.474e-31
Identity = 63/147 (42.86%), Postives = 89/147 (60.54%), Query Frame = 3 
Query:   30 ALINTLWLINRVLFHIGGVHKHKNLLWGQFN-LTQVFGQTCLQYY----PNKVNFVGASMKDLDMELFSNKESDTPVSIGRGDSRLPVDAIEIFQIYANMRPVECRNMTDPFYLCPDPIWKKGGSWFKPINAGFQYISKIPRLMGFK 455
            AL+N++WLI R  F++ G  KH+ L WGQF  +T V  Q  L++     P +V F         + LF  +ES++  +  R    LP D ++IF  YA +RP EC    +P YLCPDP+W++GG WFKP+ AG Q +S+IPRL+G K
Sbjct:  634 ALLNSVWLIVRTQFNVVGTQKHRTLTWGQFQCVTNVNSQEILRFTARSNPQEVRFCHGHGGPHGVRLFDGQESNSSGNTKR--QTLPFDCVDIFNFYARLRPAECHGPDEPLYLCPDPVWERGGPWFKPVVAGAQLLSRIPRLLGMK 778
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A0R3ULP6 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS8612 PE=4 SV=2)

HSP 1 Score: 134.035 bits (336), Expect = 2.736e-31
Identity = 63/147 (42.86%), Postives = 89/147 (60.54%), Query Frame = 3 
Query:   30 ALINTLWLINRVLFHIGGVHKHKNLLWGQFN-LTQVFGQTCLQYY----PNKVNFVGASMKDLDMELFSNKESDTPVSIGRGDSRLPVDAIEIFQIYANMRPVECRNMTDPFYLCPDPIWKKGGSWFKPINAGFQYISKIPRLMGFK 455
            AL+N++WLI R  F++ G  KH+ L WGQF  +T V  Q  L++     P +V F         + LF  +ES++  +  R    LP D ++IF  YA +RP EC    +P YLCPDP+W++GG WFKP+ AG Q +S+IPRL+G K
Sbjct:  648 ALLNSVWLIVRTQFNVVGTQKHRTLTWGQFQCVTNVNSQEILRFTARSNPQEVRFCHGHGGPHGVRLFDGQESNSSGNTKR--QTLPFDCVDIFNFYARLRPAECHGPDEPLYLCPDPVWERGGPWFKPVVAGAQLLSRIPRLLGMK 792
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A1S8X6Q6 (DUF3504 domain-containing protein OS=Opisthorchis viverrini OX=6198 GN=X801_01752 PE=4 SV=1)

HSP 1 Score: 130.954 bits (328), Expect = 3.327e-30
Identity = 64/151 (42.38%), Postives = 95/151 (62.91%), Query Frame = 3 
Query:   30 ALINTLWLINRVLFHIGGVHKHKNLLWGQFNL-TQVFGQTCLQYYP----NKVNFV---GASMKDLDMELFSNKESDTPVSIGRGDSR-LPVDAIEIFQIYANMRPVECRNMTDPFYLCPDPIWKKGGSWFKPINAGFQYISKIPRLMGFK 455
            A++N+LWLINR  F+IGG  +H+NL+WGQF L T   G   +++ P     +V +    G S K  D+   S+  + T    G    + LP + +E+F++YAN+RP E R +++PFYLCPDP W++  +WFK   AG Q +S+IPRL+G K
Sbjct:  379 AILNSLWLINRTQFNIGGTQRHRNLVWGQFQLITDDAGAKAIKFTPLFESAEVRYCRGYGGS-KGADVTCRSSSSAQTLSCTGAAKRQPLPFNCVELFELYANLRPPEARGVSEPFYLCPDPGWEQNRTWFKTNAAGSQLLSRIPRLLGLK 528
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A183ABF2 (DUF3504 domain-containing protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS4287 PE=4 SV=1)

HSP 1 Score: 130.568 bits (327), Expect = 3.458e-30
Identity = 64/163 (39.26%), Postives = 92/163 (56.44%), Query Frame = 3 
Query:   30 ALINTLWLINRVLFHIGGVHKHKNLLWGQFNL-TQVFGQTCLQYYP------------------NKVNFVGASMKDLDMELFSNKESDTPVSIGRGDSRLPVDAIEIFQIYANMRPVECRNMTDPFYLCPDPIWKKGGSWFKPINAGFQYISKIPRLMGFKTS 461
            A++N+LWLINR  F+IGG  +H+NL+WGQF L T   G   +++ P                     +F G S+  +     SN     P         LP + +E+F++YAN+RPVE R +++PFYLCP+  W++ GSWFK   AG Q +S+IPRL+G K S
Sbjct:  423 AVLNSLWLINRTQFNIGGTQRHRNLVWGQFQLITDDHGVKSIKFTPLFESAEVRYCRGHGGGKNTATDFSGRSVSGMQTLTGSNLSKRQP---------LPFNCVELFELYANLRPVEARGVSEPFYLCPESAWEQSGSWFKTSAAGSQLLSRIPRLLGLKPS 576
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: H2KUJ5 (DUF3504 domain-containing protein OS=Clonorchis sinensis OX=79923 GN=CLF_109209 PE=4 SV=1)

HSP 1 Score: 130.568 bits (327), Expect = 4.348e-30
Identity = 64/151 (42.38%), Postives = 95/151 (62.91%), Query Frame = 3 
Query:   30 ALINTLWLINRVLFHIGGVHKHKNLLWGQFNL-TQVFGQTCLQYYP----NKVNFV---GASMKDLDMELFSNKESDTPVSIGRGDSR-LPVDAIEIFQIYANMRPVECRNMTDPFYLCPDPIWKKGGSWFKPINAGFQYISKIPRLMGFK 455
            A++N+LWLINR  F+IGG  +H+NL+WGQF L T   G   +++ P     +V +    G S K  D+   S+  + T    G    + LP + +E+F++YAN+RP E R +++PFYLCPDP W++  +WFK   AG Q +S+IPRL+G K
Sbjct:  384 AILNSLWLINRTQFNIGGTQRHRNLVWGQFQLITDDAGAKAIKFTPLFESAEVRYCRGYGGS-KGADVTCRSSSSAQTLSCTGAAKRQPLPFNCVELFELYANLRPPEARGVSEPFYLCPDPGWEQNRTWFKTNAAGSQLLSRIPRLLGLK 533
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000061450.1 (SMESG000061450.1)

HSP 1 Score: 419.468 bits (1077), Expect = 5.359e-141
Identity = 239/239 (100.00%), Postives = 239/239 (100.00%), Query Frame = 3 
Query:   30 ALINTLWLINRVLFHIGGVHKHKNLLWGQFNLTQVFGQTCLQYYPNKVNFVGASMKDLDMELFSNKESDTPVSIGRGDSRLPVDAIEIFQIYANMRPVECRNMTDPFYLCPDPIWKKGGSWFKPINAGFQYISKIPRLMGFKTSSALKGXXXXXXXXXXXXXXXXXXXXXXXKDNEMLDYXXXXXXXXXXXXXXEDNHSTGSSGSVSIYEQQKPNSKSGLTDFNCDEQSEAMDMSAKLY 746
            ALINTLWLINRVLFHIGGVHKHKNLLWGQFNLTQVFGQTCLQYYPNKVNFVGASMKDLDMELFSNKESDTPVSIGRGDSRLPVDAIEIFQIYANMRPVECRNMTDPFYLCPDPIWKKGGSWFKPINAGFQYISKIPRLMGFKTSSALKGSSQNSSILSSVLPSSTNSSLPVTKDNEMLDYDSSQIIDIDSQTIDEDNHSTGSSGSVSIYEQQKPNSKSGLTDFNCDEQSEAMDMSAKLY
Sbjct:  646 ALINTLWLINRVLFHIGGVHKHKNLLWGQFNLTQVFGQTCLQYYPNKVNFVGASMKDLDMELFSNKESDTPVSIGRGDSRLPVDAIEIFQIYANMRPVECRNMTDPFYLCPDPIWKKGGSWFKPINAGFQYISKIPRLMGFKTSSALKGSSQNSSILSSVLPSSTNSSLPVTKDNEMLDYDSSQIIDIDSQTIDEDNHSTGSSGSVSIYEQQKPNSKSGLTDFNCDEQSEAMDMSAKLY 884
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
A0A5K3F9172.474e-3142.86Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A0R3ULP62.736e-3142.86Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A1S8X6Q63.327e-3042.38DUF3504 domain-containing protein OS=Opisthorchis ... [more]
A0A183ABF23.458e-3039.26DUF3504 domain-containing protein OS=Echinostoma c... [more]
H2KUJ54.348e-3042.38DUF3504 domain-containing protein OS=Clonorchis si... [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
SMESG000061450.15.359e-141100.00SMESG000061450.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009039 ID=SMED30009039|Name=C2H2-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=895bp
TAATTAAAGTTATTTATTTATTTATTTAGGCCTTGATTAATACATTATGG
TTGATTAACCGAGTCCTTTTTCACATCGGTGGAGTTCATAAACACAAAAA
TCTCCTATGGGGTCAGTTTAACTTGACTCAAGTTTTCGGTCAAACCTGTC
TGCAGTATTATCCAAATAAAGTAAACTTTGTTGGGGCTTCAATGAAAGAT
TTGGACATGGAGTTATTCAGCAACAAAGAGAGCGACACCCCAGTTTCAAT
CGGTAGAGGTGATTCTCGTTTACCGGTGGATGCAATTGAAATATTTCAAA
TCTATGCTAATATGCGTCCAGTAGAATGCCGAAATATGACCGATCCGTTC
TATTTGTGTCCGGACCCTATTTGGAAAAAGGGTGGCAGTTGGTTCAAGCC
GATTAATGCTGGATTTCAATATATATCGAAAATTCCACGATTAATGGGAT
TTAAAACGTCTAGTGCTCTTAAAGGTTCCAGTCAAAATTCATCAATTCTT
TCATCGGTTTTACCTTCATCGACGAATTCTTCGCTCCCTGTCACCAAGGA
CAATGAAATGCTTGATTATGACAGTTCACAGATAATAGATATAGATTCTC
AGACAATAGACGAGGACAACCACAGCACAGGTTCCTCCGGAAGCGTCTCG
ATATATGAACAACAAAAGCCGAACAGTAAATCCGGGTTGACCGATTTCAA
TTGTGATGAACAGTCGGAAGCAATGGATATGTCCGCAAAACTGTATTAGT
AATTGTTATAATTTTTCAAAGAATATCAAAAATTTGTATAGTTTTCGTTT
CAATTTTTTTTTGGTCATGTTGTTCATATGTAATGCGTGCAAATACTGTC
GGTTGGATCGTGGCATTAACATATCACATTCAAAATATTCAGATA
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protein sequence of SMED30009039-orf-1

>SMED30009039-orf-1 ID=SMED30009039-orf-1|Name=SMED30009039-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=186bp
MKDLDMELFSNKESDTPVSIGRGDSRLPVDAIEIFQIYANMRPVECRNMT
DPFYLCPDPIWKKGGSWFKPINAGFQYISKIPRLMGFKTSSALKGSSQNS
SILSSVLPSSTNSSLPVTKDNEMLDYDSSQIIDIDSQTIDEDNHSTGSSG
SVSIYEQQKPNSKSGLTDFNCDEQSEAMDMSAKLY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000099neuron
PLANA:0000231vitelline gland
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR021893DUF3504
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 136..172
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 136..171