C2H2-type domain-containing protein

Overview
NameC2H2-type domain-containing protein
Smed IDSMED30022979
Length (bp)327
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 (SMED30022979) t-SNE clustered cells

Violin plots show distribution of expression levels for C2H2-type domain-containing protein (SMED30022979) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30022979

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
oocyteSMED30022979 Contig19737uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30022979 Contig19737newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30022979 Contig19737uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30022979 Contig19737newmark_estsPMID: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: A0A443S1W5 (Uncharacterized protein (Fragment) OS=Leptotrombidium deliense OX=299467 GN=B4U80_06898 PE=4 SV=1)

HSP 1 Score: 68.5514 bits (166), Expect = 1.699e-12
Identity = 40/100 (40.00%), Postives = 55/100 (55.00%), Query Frame = 3 
Query:   45 EFLGVFPLDKIPYIDINKA-FIVNTQSCNLNGEHWIAVYV-KPEKIYAFDLMGFYYPPLLVSKLQSLLMP-----IEYNKIRYQNPMTKTCGQYCLAWLK 323
            EF+G FP D IP      A FIVNT S N  GEHW+A+Y+ K  K   FD  G    P L   L   +       ++YN I  Q+P++ TCG++CL +++
Sbjct:    3 EFVGTFPRDNIPTTTRRPASFIVNTDSSNEPGEHWVAIYLTKNNKAEYFDSFGL---PPLHRDLTEFIHEHAKNGVKYNNICIQHPLSTTCGKFCLKYVQ 99
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A443S0V0 (Uncharacterized protein OS=Leptotrombidium deliense OX=299467 GN=B4U80_07887 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 4.418e-10
Identity = 34/96 (35.42%), Postives = 50/96 (52.08%), Query Frame = 3 
Query:   45 EFLGVFPLDKIPYIDINKAFIVNTQSCNLNGEHWIAVYVKPEKIYAFDLMGFYYPPL---LVSKLQSLLMPIEYNKIRYQNPMTKTCGQYCLAWLK 323
             + GV P + +P    N  F+ NT +C   G HW+A+YVK      FD  G   PPL    VS L +  +   YN +  Q+  +K CG +C+A++K
Sbjct:   15 HYAGVHPRNHLPEAQRNITFVANTDTCLEKGTHWVAIYVKNNTAEYFDSFGL--PPLTKDFVSFLNNYAL-WSYNTVTIQDVDSKKCGDFCIAFVK 107
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A1I8B7D9 (Uncharacterized protein OS=Meloidogyne hapla OX=6305 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 9.419e-10
Identity = 36/109 (33.03%), Postives = 55/109 (50.46%), Query Frame = 3 
Query:    3 SIQIQKKCQKCLGSEFLGVFPLDKIPYIDINK--AFIVNTQSCNLNGEHWIAVYV-KPEKIYAFDLMGFYYPPLLVSKLQSLLMPIEYNKIRYQNPMTKTCGQYCLAWL 320
            S+QI+   +K L + F+GVF  + IPY + NK   F+ NT      GEHW+A Y   P  +  FD         +   +      ++ NK   Q+P++ TCG YC+ +L
Sbjct:    3 SLQIETILKKYLKNGFIGVFSSNNIPYREWNKPFCFVANTMRKGTVGEHWVACYSDNPTTVKYFDSFAEEPNCDMRQSMLGSFSKVKQNKFALQSPLSDTCGHYCIYFL 111
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A5H3CX07 (Adenain OS=Bos-associated insect adintovirus OX=2597806 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 4.978e-9
Identity = 35/94 (37.23%), Postives = 46/94 (48.94%), Query Frame = 3 
Query:   42 SEFLGVFPLDKIPYIDIN-KAFIVNTQSCNLNGEHWIAVYVKPEKIYAFDLMGFYYPPLLVSKLQSLLMPIEYNKIRYQNPMTKTCGQYCLAWL 320
            S F GVF  +++P      ++ IVN   CN  G HW+A   K  ++  FD  G   PPL + +       I YN  RYQN  T  CG  CL +L
Sbjct:   22 SNFRGVFMRNQLPTAPYKWESGIVNLDDCNGPGTHWVAYRKKGNQVEYFDSFGDLRPPLELQEYFGCNSKISYNYDRYQNYGTYNCGHLCLKFL 115
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A1I8BGG4 (Uncharacterized protein OS=Meloidogyne hapla OX=6305 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 8.078e-9
Identity = 35/100 (35.00%), Postives = 53/100 (53.00%), Query Frame = 3 
Query:   30 KCLGSEFLGVFPLDKIPYIDINK--AFIVNTQSCNLNGEHWIAVYV-KPEKIYAFDLMGFYYPPLLVSKLQSLLMPIEYNKIRYQNPMTKTCGQYCLAWL 320
            K L ++FLGVF  + IP ID +K   FI NT      GEHWIA Y  K + +  FD +G      +   + S    +  ++   Q+P++ TCG +C+ +L
Sbjct:   14 KPLKNKFLGVFSSNNIPDIDWHKPFCFIANTMRKGTVGEHWIACYSDKKDTLEYFDSLGDAPNCDMRQSMLSQFSIVRQSRFSLQSPLSDTCGHFCICFL 113
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BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000004406.1 (SMESG000004406.1)

HSP 1 Score: 195.667 bits (496), Expect = 2.902e-60
Identity = 92/100 (92.00%), Postives = 95/100 (95.00%), Query Frame = 3 
Query:   15 QKKCQKCLGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLNGEHWIAVYVKPEKIYAFDLMGFYYPPLLVSKLQSLLMPIEYNKIRYQNPMTKTCGQYCLA 314
             KK +K LGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLN EHWIAVYVKPEKIYAFD MGFYYPPLLVSKLQSL+MPIEYNKIRYQNPMTKTCGQ+CLA
Sbjct:  180 SKKGRKWLGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLNEEHWIAVYVKPEKIYAFDPMGFYYPPLLVSKLQSLVMPIEYNKIRYQNPMTKTCGQHCLA 279
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000004406.1 (SMESG000004406.1)

HSP 1 Score: 195.667 bits (496), Expect = 1.192e-59
Identity = 92/99 (92.93%), Postives = 95/99 (95.96%), Query Frame = 3 
Query:   18 KKCQKCLGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLNGEHWIAVYVKPEKIYAFDLMGFYYPPLLVSKLQSLLMPIEYNKIRYQNPMTKTCGQYCLA 314
            KK +K LGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLN EHWIAVYVKPEKIYAFD MGFYYPPLLVSKLQSL+MPIEYNKIRYQNPMTKTCGQ+CLA
Sbjct:  181 KKGRKWLGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLNEEHWIAVYVKPEKIYAFDPMGFYYPPLLVSKLQSLVMPIEYNKIRYQNPMTKTCGQHCLA 279
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000004406.1 (SMESG000004406.1)

HSP 1 Score: 195.667 bits (496), Expect = 1.881e-59
Identity = 92/99 (92.93%), Postives = 95/99 (95.96%), Query Frame = 3 
Query:   18 KKCQKCLGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLNGEHWIAVYVKPEKIYAFDLMGFYYPPLLVSKLQSLLMPIEYNKIRYQNPMTKTCGQYCLA 314
            KK +K LGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLN EHWIAVYVKPEKIYAFD MGFYYPPLLVSKLQSL+MPIEYNKIRYQNPMTKTCGQ+CLA
Sbjct:  181 KKGRKWLGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLNEEHWIAVYVKPEKIYAFDPMGFYYPPLLVSKLQSLVMPIEYNKIRYQNPMTKTCGQHCLA 279
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000023200.1 (SMESG000023200.1)

HSP 1 Score: 185.652 bits (470), Expect = 1.291e-55
Identity = 81/108 (75.00%), Postives = 96/108 (88.89%), Query Frame = 3 
Query:    3 SIQIQKKCQKCLGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLNGEHWIAVYVKPEKIYAFDLMGFYYPPLLVSKLQSLLMPIEYNKIRYQNPMTKTCGQYCLAWLKS 326
            S+ IQ   +K +G  F+GVFPLDKIPYI+INKA IVNTQS NL GEHW+A+YVKP+KI+ FD MGFYYPPLL+SKL+S+LMPIEYN+IRYQNP+TKTCGQ+CLAWLKS
Sbjct: 1343 SVSIQTIAKKLIGKNFIGVFPLDKIPYININKALIVNTQSANLGGEHWLAIYVKPDKIHVFDPMGFYYPPLLISKLESMLMPIEYNRIRYQNPLTKTCGQHCLAWLKS 1450
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000054630.1 (SMESG000054630.1)

HSP 1 Score: 183.726 bits (465), Expect = 5.851e-55
Identity = 81/108 (75.00%), Postives = 95/108 (87.96%), Query Frame = 3 
Query:    3 SIQIQKKCQKCLGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLNGEHWIAVYVKPEKIYAFDLMGFYYPPLLVSKLQSLLMPIEYNKIRYQNPMTKTCGQYCLAWLKS 326
            S  IQ   +K +G  F+GVFPLDKIPYI+INKA IVNTQS NL GEHW+A+YVKP+KI+ FD MGFYYPPLL+SKL+S+LMPIEYN+IRYQNP+TKTCGQ+CLAWLKS
Sbjct: 1294 SRTIQTIAKKLIGKNFIGVFPLDKIPYININKALIVNTQSANLGGEHWLAIYVKPDKIHVFDPMGFYYPPLLISKLESMLMPIEYNRIRYQNPLTKTCGQHCLAWLKS 1401
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
A0A443S1W51.699e-1240.00Uncharacterized protein (Fragment) OS=Leptotrombid... [more]
A0A443S0V04.418e-1035.42Uncharacterized protein OS=Leptotrombidium deliens... [more]
A0A1I8B7D99.419e-1033.03Uncharacterized protein OS=Meloidogyne hapla OX=63... [more]
A0A5H3CX074.978e-937.23Adenain OS=Bos-associated insect adintovirus OX=25... [more]
A0A1I8BGG48.078e-935.00Uncharacterized protein OS=Meloidogyne hapla OX=63... [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: 5
Match NameE-valueIdentityDescription
SMESG000004406.12.902e-6092.00SMESG000004406.1[more]
SMESG000004406.11.192e-5992.93SMESG000004406.1[more]
SMESG000004406.11.881e-5992.93SMESG000004406.1[more]
SMESG000023200.11.291e-5575.00SMESG000023200.1[more]
SMESG000054630.15.851e-5575.00SMESG000054630.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022979 ID=SMED30022979|Name=C2H2-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=327bp
GTTCTATTCAGATTCAAAAAAAGTGTCAAAAATGTTTGGGATCAGAATTT
CTTGGAGTATTTCCCTTAGATAAAATACCATATATTGATATAAACAAGGC
ATTTATTGTAAATACTCAATCTTGTAATCTCAATGGAGAACATTGGATCG
CAGTCTATGTGAAACCTGAAAAAATATATGCATTTGATCTAATGGGTTTC
TATTACCCCCCTTTATTAGTATCAAAACTTCAATCATTGTTAATGCCTAT
TGAATACAATAAAATTCGGTATCAAAACCCGATGACAAAAACTTGTGGCC
AATATTGTTTAGCTTGGTTAAAATCAA
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protein sequence of SMED30022979-orf-1

>SMED30022979-orf-1 ID=SMED30022979-orf-1|Name=SMED30022979-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
SIQIQKKCQKCLGSEFLGVFPLDKIPYIDINKAFIVNTQSCNLNGEHWIA
VYVKPEKIYAFDLMGFYYPPLLVSKLQSLLMPIEYNKIRYQNPMTKTCGQ
YCLAWLKS
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0004197cysteine-type endopeptidase activity
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
Vocabulary: INTERPRO
TermDefinition
IPR000855Peptidase_C5
Vocabulary: biological process
TermDefinition
GO:0006508proteolysis