Cysteine-rich protein

Overview
NameCysteine-rich protein
Smed IDSMED30016045
Length (bp)530
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 Cysteine-rich protein (SMED30016045) t-SNE clustered cells

Violin plots show distribution of expression levels for Cysteine-rich protein (SMED30016045) 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 Cysteine-rich protein (SMED30016045) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Cysteine-rich protein (SMED30016045) 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




SMED30016045

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



PAGE Curations: 18

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30016045SMESG000044206.1 Contig353uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30016045SMESG000044206.1 Contig353uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
central nervous systemSMED30016045SMESG000044206.1 Contig353uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30016045SMESG000044206.1 Contig353newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30016045SMESG000044206.1 Contig353newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
central nervous systemSMED30016045SMESG000044206.1 Contig353newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30016045SMESG000003375.1 Contig353uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30016045SMESG000003375.1 Contig353uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
central nervous systemSMED30016045SMESG000003375.1 Contig353uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30016045SMESG000003375.1 Contig353newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30016045SMESG000003375.1 Contig353newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
central nervous systemSMED30016045SMESG000003375.1 Contig353newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
nervous systemSMED30016045SMESG000044206.1 dd_Smed_v4_1185_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30016045SMESG000044206.1 dd_Smed_v4_1185_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30016045SMESG000044206.1 dd_Smed_v4_1185_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30016045SMESG000044206.1 dd_Smed_v4_1185_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30016045SMESG000044206.1 dd_Smed_v4_1185_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30016045SMESG000044206.1 dd_Smed_v4_1185_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Cysteine-rich protein vs. TrEMBL
Match: A0A168HU39 (Uncharacterized protein OS=Mucor circinelloides f. lusitanicus CBS 277.49 OX=747725 GN=MUCCIDRAFT_114366 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 1.028e-8
Identity = 40/79 (50.63%), Postives = 49/79 (62.03%), Query Frame = 2
Query:   20 REFQIINYIQMKIFIFALWISFISCVISGPLXXXXXXXXXXXXVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 256
              FQ    ++  ++   L + F+S V +GPL+  IC   C A  V CYSAAGF FGTVTAGA  PAVI+ CNAA G CM
Sbjct:   12 NPFQSSAMLKTVVYCLVL-LGFLSYVSAGPLAYGICQTGCNALAVACYSAAGFTFGTVTAGAGVPAVILACNAAQGFCM 89          
BLAST of Cysteine-rich protein vs. TrEMBL
Match: A0A0B7NXC5 (Uncharacterized protein OS=Parasitella parasitica OX=35722 GN=PARPA_14131.1 scaffold 48034 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.256e-8
Identity = 37/70 (52.86%), Postives = 46/70 (65.71%), Query Frame = 2
Query:   47 QMKIFIFALWISFISCVISGPLXXXXXXXXXXXXVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 256
            ++   IF L   FIS   +GPL+  IC   C A  V+CY+AAGF FGT+TAGA+ PA I+ CNAA G CM
Sbjct:    3 KLYFSIFVLLTFFISNSNAGPLAYGICQTGCNALAVSCYAAAGFTFGTITAGAAIPAAIVSCNAALGVCM 72          
BLAST of Cysteine-rich protein vs. TrEMBL
Match: A0A2J7ZU87 (Uncharacterized protein OS=Tetrabaena socialis OX=47790 GN=TSOC_010074 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 4.172e-8
Identity = 36/53 (67.92%), Postives = 40/53 (75.47%), Query Frame = 2
Query:   98 ISGPLXXXXXXXXXXXXVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 256
            ++GPLS  IC   C A VV+CY+AAGF FGTVTAGA  PAVIIGCNA  G CM
Sbjct:   25 VAGPLSYGICQTGCNALVVSCYTAAGFTFGTVTAGAGIPAVIIGCNAGLGFCM 77          
BLAST of Cysteine-rich protein vs. TrEMBL
Match: A0A1J1HFI7 (CLUMA_CG000612, isoform A OS=Clunio marinus OX=568069 GN=CLUMA_CG000612 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 1.280e-7
Identity = 37/71 (52.11%), Postives = 45/71 (63.38%), Query Frame = 2
Query:   44 IQMKIFIFALWISFISCVISGPLXXXXXXXXXXXXVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 256
            ++  IFI  + +   S + +GPL+  IC   C A VV CY+AAGF FGTVTAGA  PA II CN A G CM
Sbjct:    1 MRNVIFICIVLLLSASSIKAGPLAYGICQTGCNAMVVACYAAAGFTFGTVTAGAGVPAAIIACNVALGTCM 71          
BLAST of Cysteine-rich protein vs. TrEMBL
Match: A0A0C9N468 (Zygote-specific protein OS=Mucor ambiguus OX=91626 GN=MAM1_0415c10407 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 1.321e-7
Identity = 34/62 (54.84%), Postives = 42/62 (67.74%), Query Frame = 2
Query:   71 LWISFISCVISGPLXXXXXXXXXXXXVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 256
            L +  IS   +GPL+  IC   C A VV+CY+AAGF FGT+TAGA  PAV++ CNA  G CM
Sbjct:   10 LVLGLISSSYAGPLAYGICQTGCNALVVSCYAAAGFTFGTITAGAGLPAVLVSCNAGLGVCM 71          
BLAST of Cysteine-rich protein vs. Planmine SMEST
Match: SMESG000044206.1 (SMESG000044206.1)

HSP 1 Score: 107.842 bits (268), Expect = 6.643e-31
Identity = 69/69 (100.00%), Postives = 69/69 (100.00%), Query Frame = 2
Query:   50 MKIFIFALWISFISCVISGPLXXXXXXXXXXXXVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 256
            MKIFIFALWISFISCVISGPLSGAICSACCAAGVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM
Sbjct:    1 MKIFIFALWISFISCVISGPLSGAICSACCAAGVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 69          
BLAST of Cysteine-rich protein vs. Planmine SMEST
Match: SMESG000044193.1 (SMESG000044193.1)

HSP 1 Score: 95.5153 bits (236), Expect = 4.346e-26
Identity = 58/71 (81.69%), Postives = 64/71 (90.14%), Query Frame = 2
Query:   44 IQMKIFIFALWISFISCVISGPLXXXXXXXXXXXXVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 256
            +QMKIFIFALW+S ISCVISGP+SG +CSACCAAGVV CYSAAGF+FGT+  G  TPAVIIGCNAAFGKCM
Sbjct:    1 MQMKIFIFALWLSLISCVISGPISGGVCSACCAAGVVACYSAAGFVFGTIITGPLTPAVIIGCNAAFGKCM 71          
BLAST of Cysteine-rich protein vs. Planmine SMEST
Match: SMESG000044193.1 (SMESG000044193.1)

HSP 1 Score: 92.0485 bits (227), Expect = 8.095e-25
Identity = 57/69 (82.61%), Postives = 62/69 (89.86%), Query Frame = 2
Query:   50 MKIFIFALWISFISCVISGPLXXXXXXXXXXXXVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 256
            MKIFIFALW+S ISCVISGP+SG +CSACCAAGVV CYSAAGF+FGT+  G  TPAVIIGCNAAFGKCM
Sbjct:    1 MKIFIFALWLSLISCVISGPISGGVCSACCAAGVVACYSAAGFVFGTIITGPLTPAVIIGCNAAFGKCM 69          
BLAST of Cysteine-rich protein vs. Planmine SMEST
Match: SMESG000044191.1 (SMESG000044191.1)

HSP 1 Score: 57.3806 bits (137), Expect = 1.752e-11
Identity = 44/69 (63.77%), Postives = 48/69 (69.57%), Query Frame = 2
Query:   50 MKIFIFALWISFISCVISGPLXXXXXXXXXXXXVVTCYSAAGFIFGTVTAGASTPAVIIGCNAAFGKCM 256
            M I  F + I F S V  G +S A CSACCA GVV CYSAAGF+FGT+  G  T AVIIGCNAAF KCM
Sbjct:    1 MHIQFFLIIILFRSSVKCGLISVAKCSACCAEGVVKCYSAAGFVFGTIIVGPLTSAVIIGCNAAFRKCM 69          
The following BLAST results are available for this feature:
BLAST of Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A168HU391.028e-850.63Uncharacterized protein OS=Mucor circinelloides f.... [more]
A0A0B7NXC51.256e-852.86Uncharacterized protein OS=Parasitella parasitica ... [more]
A0A2J7ZU874.172e-867.92Uncharacterized protein OS=Tetrabaena socialis OX=... [more]
A0A1J1HFI71.280e-752.11CLUMA_CG000612, isoform A OS=Clunio marinus OX=568... [more]
A0A0C9N4681.321e-754.84Zygote-specific protein OS=Mucor ambiguus OX=91626... [more]
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BLAST of Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich 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 Cysteine-rich protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000044206.16.643e-31100.00SMESG000044206.1[more]
SMESG000044193.14.346e-2681.69SMESG000044193.1[more]
SMESG000044193.18.095e-2582.61SMESG000044193.1[more]
SMESG000044191.11.752e-1163.77SMESG000044191.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016045 ID=SMED30016045|Name=Cysteine-rich protein|organism=Schmidtea mediterranea sexual|type=transcript|length=530bp
AAATTAATAAACAAAGTCACGGGAATTCCAAATAATTAATTATATACAAA
TGAAAATTTTTATTTTTGCATTATGGATATCATTTATTTCCTGTGTAATT
AGTGGGCCCTTAAGTGGAGCTATATGTTCAGCTTGTTGTGCTGCAGGAGT
GGTTACATGTTATTCAGCCGCAGGATTTATATTTGGTACAGTAACTGCGG
GGGCTTCAACGCCTGCAGTTATTATAGGATGTAATGCAGCTTTTGGAAAA
TGTATGGCTGCTTGTGCAGTTGCCACTGTTGTCCCAGCGCCTTAAAAATT
AATGAAAAAAGTTGCTCTTTTAAGTAATGTTTTGAATTTTAGCTTTGAAA
TGAGCTTCGACTACATTCATAACTTTCAAACTTCATAATCCATAAATTTA
GTTTCATCACTTGTACATAAAAATCACTATAATATATTTTAGATATGCCG
CGTAGATAATAATTTGTAATTTTAACTTGGCTTCAAAAATATGAATTTCA
ACAATTTTATTTAAAAAAAATTTGGTAAGG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000103central nervous system
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePANTHERPTHR37475FAMILY NOT NAMEDcoord: 5..81
NoneNo IPR availablePROSITEPS51257PROKAR_LIPOPROTEINcoord: 1..15
score: 5.0
NoneNo IPR availableSIGNALP_EUKSignalP-TMSignalP-TMcoord: 1..18
score: 0.806
NoneNo IPR availableTMHMMTMhelixcoord: 40..62
NoneNo IPR availableTMHMMTMhelixcoord: 3..25