C-type lectin domain-containing protein

Overview
NameC-type lectin domain-containing protein
Smed IDSMED30019646
Length (bp)755
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 C-type lectin domain-containing protein (SMED30019646) t-SNE clustered cells

Violin plots show distribution of expression levels for C-type lectin domain-containing protein (SMED30019646) 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



SMED30019646

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30019646SMESG000015726.1 SmedASXL_005587SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
reproductive organSMED30019646SMESG000015726.1 Contig50510newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30019646SMESG000015726.1 Contig50510uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
ovarySMED30019646SMESG000015726.1 Contig2421_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
early male germ cellSMED30019646SMESG000015726.1 Contig2421_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30019646SMESG000015726.1 SMED_06720_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30019646SMESG000015726.1 SMED_06720_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of C-type lectin domain-containing protein vs. TrEMBL
Match: A0A183WIW1 (C-type lectin domain-containing protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS12064 PE=4 SV=1)

HSP 1 Score: 139.428 bits (350), Expect = 8.166e-37
Identity = 72/199 (36.18%), Postives = 106/199 (53.27%), Query Frame = 2 
Query:  173 INASMKISEGHISDKMFAFIHGGEDARMNFTDAEEFCSN-----------FTFHRNNSDSHL-------------------ASIQNLKEVKLIQNWILNLERKSFWIGGEIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVDLQDGRWGVHHCSEKKYFLCLTKNQLVTEKDVVVDNNFITS 679
            +  +++ S G +  ++F F+HG E A++NF+ AE++C N           FTF    S +HL                   ASI +  E   I  WI   E+ SFWIGG++  +MN  L  +++LHWI+  + +F+  ++PN  +  M V E RC+SVD   G+WGVH CSEKKYF+CLT         V+  NN +TS
Sbjct:   14 VAYAIEKSRGALGPRIFTFVHGDEAAKLNFSAAEDYCRNSIGKDSDSADQFTFTERKSSNHLSAHALSKNKDGELVLETSLASIHSYPENTAIIKWISQKEKNSFWIGGQVTKTMNDFLRSIYVLHWIDGSRSDFSLLRLPNPELTTMLVGEHRCISVDYSSGQWGVHLCSEKKYFICLT-------VPVLYSNNTVTS 205
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BLAST of C-type lectin domain-containing protein vs. TrEMBL
Match: A0A4Z2D460 (Bone marrow proteoglycan OS=Schistosoma japonicum OX=6182 GN=EWB00_004736 PE=4 SV=1)

HSP 1 Score: 136.346 bits (342), Expect = 1.037e-35
Identity = 66/198 (33.33%), Postives = 110/198 (55.56%), Query Frame = 2 
Query:  182 SMKISEGHISDKMFAFIHGGEDARMNFTDAEEFCSNFTFHRNNSD----------------------------SHLASIQNLKEVKLIQNWILNLERKSFWIGGEIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVDLQDGRWGVHHCSEKKYFLCLTKNQLVTEKDVVVDNNFITSSSVP 691
            +++ S G +  ++F F+HG E+A++NF++AE +C       +N+D                            + LASI +  E   + NWI   E+ SFWIGG+I  ++N  +  +++LHW++  K +F+  ++PN  + ++ V E+RCVSVD   G+WGVH CSEK+YF+CLT   L T+  ++      +S +VP
Sbjct:   17 AIEKSRGALGSRVFTFVHGDENAKLNFSEAENYCKFVGQQSDNNDMLDSLNKHDRQHVSSQAPQNSKEKMVLQTALASIHSYPENLALVNWISKQEKHSFWIGGKITKTVNEFMRPLYVLHWVDGSKSDFSLLRLPNPEMTSISVGEQRCVSVDYSSGQWGVHLCSEKRYFVCLTVPVLSTDNQMISKQKEQSSLTVP 214
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BLAST of C-type lectin domain-containing protein vs. TrEMBL
Match: A0A183MZ91 (C-type lectin domain-containing protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS21366 PE=4 SV=1)

HSP 1 Score: 134.806 bits (338), Expect = 5.147e-35
Identity = 69/207 (33.33%), Postives = 108/207 (52.17%), Query Frame = 2 
Query:  170 SINASMKI--SEGHISDKMFAFIHGGEDARMNFTDAEEFCSNFT-------------------FHRNNSDSH---------LASIQNLKEVKLIQNWILNLERKSFWIGGEIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVDLQDGRWGVHHCSEKKYFLCLTKNQLVTEKDVVVDNNFITSSSVPKTT 700
            S NA+  +  S+G +  ++F F+HGG DA++NF+ AE +C +                        N S SH         LAS+ +  E   +  W+   E+ SFWIGG+I  +MN     +++LHW++  K +F+  ++PN  + +M++ E+RC SVD   G+WGVH CSEK+YF+CLT   L  E          +S S+ K +
Sbjct:   11 SYNAAYALEKSQGALGPRIFTFVHGGADAKLNFSAAEHYCKSVGELGDTNNMDDSKDKQDRQHLFFNPSQSHKDGMILRTSLASVHSYPENLALVKWVAKQEKHSFWIGGKITKTMNEFTRPIYVLHWVDGSKSDFSLIRLPNPEITSMRIGEQRCTSVDYSSGQWGVHLCSEKRYFVCLTVPVLNIENQETTKQKEKSSPSLQKKS 217
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BLAST of C-type lectin domain-containing protein vs. TrEMBL
Match: A0A183NE71 (C-type lectin domain-containing protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS407 PE=4 SV=1)

HSP 1 Score: 131.724 bits (330), Expect = 6.235e-34
Identity = 68/207 (32.85%), Postives = 108/207 (52.17%), Query Frame = 2 
Query:  170 SINASMKI--SEGHISDKMFAFIHGGEDARMNFTDAEEFCSNFT-------------------FHRNNSDSH---------LASIQNLKEVKLIQNWILNLERKSFWIGGEIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVDLQDGRWGVHHCSEKKYFLCLTKNQLVTEKDVVVDNNFITSSSVPKTT 700
            S NA+  +  S+G +  ++F F+HG  DA++NF+ AE +C +                        N S S+         LAS+ +  E   +  W+   E+ SFWIGG+I  +MN     +++LHW++  K +F+  ++PN  + +M++ E+RC SVD   G+WGVH CSEK+YF+CLT   L TE          +S S+ K +
Sbjct:   11 SYNAAYALEKSQGALGPRIFTFVHGDVDAKLNFSAAEHYCKSVGGLSDTNNMDDPKDKQDRQHLFSNPSQSYKDGMVLRTSLASVHSYPENLALVKWVAKQEKHSFWIGGKITKTMNEFTRPIYVLHWVDGSKSDFSLIRLPNPEITSMRIGEQRCTSVDYSSGQWGVHLCSEKRYFVCLTVPVLNTENQETTKQKKKSSPSLQKKS 217
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BLAST of C-type lectin domain-containing protein vs. TrEMBL
Match: A0A095A1N6 (Bone marrow proteoglycan OS=Schistosoma haematobium OX=6185 GN=MS3_09684 PE=4 SV=1)

HSP 1 Score: 131.724 bits (330), Expect = 6.793e-34
Identity = 68/207 (32.85%), Postives = 108/207 (52.17%), Query Frame = 2 
Query:  170 SINASMKI--SEGHISDKMFAFIHGGEDARMNFTDAEEFCSNFT-------------------FHRNNSDSH---------LASIQNLKEVKLIQNWILNLERKSFWIGGEIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVDLQDGRWGVHHCSEKKYFLCLTKNQLVTEKDVVVDNNFITSSSVPKTT 700
            S NA+  +  S+G +  ++F F+HG  DA++NF+ AE +C +                        N S S+         LAS+ +  E   +  W+   E+ SFWIGG+I  +MN     +++LHW++  K +F+  ++PN  + +M++ E+RC SVD   G+WGVH CSEK+YF+CLT   L TE          +S S+ K +
Sbjct:   11 SYNAAYALEKSQGALGPRIFTFVHGDVDAKLNFSAAEHYCKSVGGLSDTNNMDDSKDKQDRQHLFSNPSQSYKDGMVLRTSLASVHSYPENLALVKWVAKQEKHSFWIGGKITKTMNEFTRPIYVLHWVDGSKSDFSLIRLPNPEITSMRIGEQRCTSVDYSSGQWGVHLCSEKRYFVCLTVPVLNTENQETTKQKEKSSPSLQKKS 217
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BLAST of C-type lectin domain-containing protein vs. Ensembl Nematostella
Match: EDO49509 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RGD7])

HSP 1 Score: 46.9802 bits (110), Expect = 5.022e-6
Identity = 43/176 (24.43%), Postives = 78/176 (44.32%), Query Frame = 2 
Query:  206 ISDKMFAF-IHGGEDARMNFTDAEEFCSNFTFHRNNSDSHLASIQNLKEVKLIQNWILNLERKSFWIGGEIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVDL--QDGRWGVHHCSEKKYFLCLTK-------NQLVTEKDVVVDNNFITSSSVPKTTP 703
            I D  F F  H  +  ++ ++ A++ C      R NS + LAS++ + E   I + + +   ++ WIG   I +     E +F+  W +  KV++TN+  P           K CV ++   Q+G W    C+ K  +LC  +       +    + +++ D+    SSS P   P
Sbjct:  317 IGDSCFEFNTHPAQ--KLTWSQAQDSC------RLNSGADLASVRTIDEQNAILSQLTDFGARNVWIGFNDIAT-----EGVFV--WSDRTKVDYTNWS-PREPGSGTLADSKDCVVLEAGSQNGTWSSTPCALKTTYLCRRRRGRDQCDSPFGMQNNMIDDSQITASSSKPSADP 476
[Close]
BLAST of C-type lectin domain-containing protein vs. Planmine SMEST
Match: SMESG000015726.1 (SMESG000015726.1)

HSP 1 Score: 397.897 bits (1021), Expect = 1.254e-141
Identity = 196/212 (92.45%), Postives = 196/212 (92.45%), Query Frame = 2 
Query:   71 GNFSEHGNIYF*TMFVTSISVLVAVAFGFGSSNSINASMKISEGHISDKMFAFIHGGEDARMNFTDAEEFCSNFTFHRNNSDSHLASIQNLKEVKLIQNWILNLERKSFWIGGEIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVDLQDGRWGVHHCSEKKYFLCLTKNQLVTEKDVVVDNNFITSSSVPKTTPM 706
            GNFSEH                VAVAFGFGSSNSINASMKISEGHISDKMFAFIHGGEDARMNFTDAEEFCSNFTFHRNNSDSHLASIQNLKEVKLIQNWILNLERKSFWIGGEIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVDLQDGRWGVHHCSEKKYFLCLTKNQLVTEKDVVVDNNFITSSSVPKTTPM
Sbjct:   66 GNFSEH----------------VAVAFGFGSSNSINASMKISEGHISDKMFAFIHGGEDARMNFTDAEEFCSNFTFHRNNSDSHLASIQNLKEVKLIQNWILNLERKSFWIGGEIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVDLQDGRWGVHHCSEKKYFLCLTKNQLVTEKDVVVDNNFITSSSVPKTTPM 261
The following BLAST results are available for this feature:
BLAST of C-type lectin 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 C-type lectin 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 C-type lectin 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 C-type lectin 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 C-type lectin 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 C-type lectin 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 C-type lectin 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 C-type lectin domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183WIW18.166e-3736.18C-type lectin domain-containing protein OS=Trichob... [more]
A0A4Z2D4601.037e-3533.33Bone marrow proteoglycan OS=Schistosoma japonicum ... [more]
A0A183MZ915.147e-3533.33C-type lectin domain-containing protein OS=Schisto... [more]
A0A183NE716.235e-3432.85C-type lectin domain-containing protein OS=Schisto... [more]
A0A095A1N66.793e-3432.85Bone marrow proteoglycan OS=Schistosoma haematobiu... [more]
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BLAST of C-type lectin 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 C-type lectin 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 C-type lectin 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 C-type lectin domain-containing protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO495095.022e-624.43Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of C-type lectin 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 C-type lectin domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000015726.11.254e-14192.45SMESG000015726.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019646 ID=SMED30019646|Name=C-type lectin domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=755bp
GATTTATTGAGTTATCGTGTCATGTTGTTTTACTTTTGTAAAATATAAAA
TGCAATTAAATGCTATATAAGGAAATTTTTCCGAGCATGGTAACATTTAT
TTCTAAACAATGTTTGTTACTTCAATTTCCGTTTTAGTCGCAGTAGCTTT
CGGTTTCGGATCCTCAAATTCCATAAATGCATCTATGAAAATCAGTGAAG
GACATATTAGTGACAAAATGTTTGCTTTCATTCATGGTGGAGAAGACGCA
AGAATGAACTTTACTGATGCTGAAGAGTTCTGTTCAAATTTTACTTTCCA
TCGAAACAACAGTGACTCCCATCTTGCTTCAATTCAAAATTTGAAGGAAG
TGAAACTCATTCAAAACTGGATTTTAAACTTAGAAAGAAAATCCTTCTGG
ATTGGCGGTGAAATAATTTGCTCAATGAATGCACTATTAGAAAAAATGTT
TCTATTACATTGGATCAATAATGACAAAGTGGAGTTCACAAATTTCAAAG
TTCCCAATTACAATGTTAAAAACATGAAAGTAACAGAAAAACGATGCGTT
TCGGTTGACCTCCAAGATGGAAGATGGGGAGTTCATCATTGCTCAGAAAA
AAAATATTTTCTTTGCTTGACAAAAAATCAATTAGTCACTGAAAAGGATG
TTGTTGTTGATAACAATTTTATTACTTCATCTTCTGTTCCAAAAACCACG
CCCATGTTGGCTAAACTTGTTTAGTTTTTAAAAAATAAAAATTTGAATTA
TAAAA
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protein sequence of SMED30019646-orf-1

>SMED30019646-orf-1 ID=SMED30019646-orf-1|Name=SMED30019646-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=205bp
MFVTSISVLVAVAFGFGSSNSINASMKISEGHISDKMFAFIHGGEDARMN
FTDAEEFCSNFTFHRNNSDSHLASIQNLKEVKLIQNWILNLERKSFWIGG
EIICSMNALLEKMFLLHWINNDKVEFTNFKVPNYNVKNMKVTEKRCVSVD
LQDGRWGVHHCSEKKYFLCLTKNQLVTEKDVVVDNNFITSSSVPKTTPML
AKLV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000204ovary
PLANA:0000429neoblast
PLANA:0002030early male germ cell
PLANA:0002089reproductive organ
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR001304C-type_lectin-like
IPR016186C-type_lectin-like/link_sf
IPR016187CTDL_fold
Vocabulary: biological process
TermDefinition
GO:0006955immune response
Vocabulary: molecular function
TermDefinition
GO:0030246carbohydrate binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001304C-type lectin-likeSMARTSM00034CLECT_2coord: 28..170
e-value: 7.3E-7
score: 38.8
IPR001304C-type lectin-likePFAMPF00059Lectin_Ccoord: 48..169
e-value: 1.1E-11
score: 45.4
IPR001304C-type lectin-likePROSITEPS50041C_TYPE_LECTIN_2coord: 33..170
score: 13.709
IPR016186C-type lectin-like/link domain superfamilyGENE3DG3DSA:3.10.100.10coord: 30..171
e-value: 3.0E-17
score: 65.1
NoneNo IPR availableCDDcd00037CLECTcoord: 48..169
e-value: 6.6561E-15
score: 66.1041
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.58
IPR016187C-type lectin foldSUPERFAMILYSSF56436C-type lectin-likecoord: 47..169