Calbindin-32-like protein

Overview
NameCalbindin-32-like protein
Smed IDSMED30006940
Length (bp)283
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 Calbindin-32-like protein (SMED30006940) t-SNE clustered cells

Violin plots show distribution of expression levels for Calbindin-32-like protein (SMED30006940) 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 Calbindin-32-like protein (SMED30006940) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Calbindin-32-like protein (SMED30006940) 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




SMED30006940

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30006940SMESG000043906.1 dd_Smed_v4_11287_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Calbindin-32-like protein vs. Ensembl Fly
Match: Cbp53E (gene:FBgn0004580 transcript:FBtr0340072)

HSP 1 Score: 46.595 bits (109), Expect = 4.132e-7
Identity = 18/45 (40.00%), Postives = 31/45 (68.89%), Query Frame = 1
Query:   82 NFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDGT-FASGIKVMGY 213
            NF+ Q+RD  +++L+  +A +F +VW HYDKDG  +  G ++ G+
Sbjct:   19 NFMRQYRDPESRELKKLSANQFMDVWAHYDKDGNGYIEGTELDGF 63          
BLAST of Calbindin-32-like protein vs. Ensembl Fly
Match: Cbp53E (gene:FBgn0004580 transcript:FBtr0087056)

HSP 1 Score: 46.595 bits (109), Expect = 4.132e-7
Identity = 18/45 (40.00%), Postives = 31/45 (68.89%), Query Frame = 1
Query:   82 NFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDGT-FASGIKVMGY 213
            NF+ Q+RD  +++L+  +A +F +VW HYDKDG  +  G ++ G+
Sbjct:   19 NFMRQYRDPESRELKKLSANQFMDVWAHYDKDGNGYIEGTELDGF 63          
BLAST of Calbindin-32-like protein vs. UniProt/SwissProt
Match: sp|P41044|CAB32_DROME (Calbindin-32 OS=Drosophila melanogaster OX=7227 GN=Cbp53E PE=2 SV=1)

HSP 1 Score: 46.595 bits (109), Expect = 4.142e-6
Identity = 18/45 (40.00%), Postives = 31/45 (68.89%), Query Frame = 1
Query:   82 NFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDGT-FASGIKVMGY 213
            NF+ Q+RD  +++L+  +A +F +VW HYDKDG  +  G ++ G+
Sbjct:   19 NFMRQYRDPESRELKKLSANQFMDVWAHYDKDGNGYIEGTELDGF 63          
BLAST of Calbindin-32-like protein vs. TrEMBL
Match: A0A1I8GC46 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.364e-11
Identity = 33/49 (67.35%), Postives = 40/49 (81.63%), Query Frame = 1
Query:   61 MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDGT-FASGIKV 204
            MS+ K  NFLSQFRDQ TKKL+NFTAT+FAEVW+HYD+DG  F  G ++
Sbjct:    1 MSHGKQKNFLSQFRDQGTKKLKNFTATQFAEVWSHYDQDGNGFIEGAEL 49          
BLAST of Calbindin-32-like protein vs. TrEMBL
Match: A0A267GD68 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig030011g2 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.832e-11
Identity = 33/49 (67.35%), Postives = 40/49 (81.63%), Query Frame = 1
Query:   61 MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDGT-FASGIKV 204
            MS+ K  NFLSQFRDQ TKKL+NFTAT+FAEVW+HYD+DG  F  G ++
Sbjct:    1 MSHGKQKNFLSQFRDQGTKKLKNFTATQFAEVWSHYDQDGNGFIEGAEL 49          
BLAST of Calbindin-32-like protein vs. TrEMBL
Match: A0A267GV22 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig030011g1 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.851e-11
Identity = 33/49 (67.35%), Postives = 40/49 (81.63%), Query Frame = 1
Query:   61 MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDGT-FASGIKV 204
            MS+ K  NFLSQFRDQ TKKL+NFTAT+FAEVW+HYD+DG  F  G ++
Sbjct:    1 MSHGKQKNFLSQFRDQGTKKLKNFTATQFAEVWSHYDQDGNGFIEGAEL 49          
BLAST of Calbindin-32-like protein vs. TrEMBL
Match: A0A267FNU4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig030011g3 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.851e-11
Identity = 31/40 (77.50%), Postives = 36/40 (90.00%), Query Frame = 1
Query:   61 MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDG 180
            MS+ K  NFLSQFRDQ TKKL+NFTAT+FAEVW+HYD+DG
Sbjct:    1 MSHGKQKNFLSQFRDQGTKKLKNFTATQFAEVWSHYDQDG 40          
BLAST of Calbindin-32-like protein vs. TrEMBL
Match: A0A1I8GV54 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig003004g1 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 9.532e-10
Identity = 27/37 (72.97%), Postives = 34/37 (91.89%), Query Frame = 1
Query:   70 NKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDG 180
            N+  NFL+QFRDQ T++L+NFTAT+FAEVW+HYDKDG
Sbjct:   11 NQRANFLAQFRDQNTRRLKNFTATQFAEVWSHYDKDG 47          
BLAST of Calbindin-32-like protein vs. Planmine SMEST
Match: SMESG000043906.1 (SMESG000043906.1)

HSP 1 Score: 87.0409 bits (214), Expect = 1.289e-22
Identity = 40/40 (100.00%), Postives = 40/40 (100.00%), Query Frame = 1
Query:   61 MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDG 180
            MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDG
Sbjct:    1 MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDG 40          
BLAST of Calbindin-32-like protein vs. Planmine SMEST
Match: SMESG000043906.1 (SMESG000043906.1)

HSP 1 Score: 86.6557 bits (213), Expect = 1.311e-22
Identity = 40/40 (100.00%), Postives = 40/40 (100.00%), Query Frame = 1
Query:   61 MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDG 180
            MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDG
Sbjct:    1 MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDG 40          
BLAST of Calbindin-32-like protein vs. Planmine SMEST
Match: SMESG000055605.1 (SMESG000055605.1)

HSP 1 Score: 60.077 bits (144), Expect = 5.541e-12
Identity = 27/40 (67.50%), Postives = 33/40 (82.50%), Query Frame = 1
Query:   61 MSNNKDFNFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDG 180
            MS  K  NFL+Q++D  TKKL+NFTAT+FAEVW+HYD DG
Sbjct:    1 MSTTKFTNFLAQYKDNETKKLRNFTATQFAEVWSHYDADG 40          
BLAST of Calbindin-32-like protein vs. Planmine SMEST
Match: SMESG000023194.1 (SMESG000023194.1)

HSP 1 Score: 49.6766 bits (117), Expect = 2.836e-8
Identity = 23/45 (51.11%), Postives = 31/45 (68.89%), Query Frame = 1
Query:   82 NFLSQFRDQTTKKLQNFTATEFAEVWNHYDKDGT-FASGIKVMGY 213
            NFLS+FRD  T++  NFTA +F EVW HYD DG  +  G ++ G+
Sbjct:   10 NFLSKFRDSKTRRWTNFTAKQFLEVWCHYDTDGNGYIEGEELDGF 54          
The following BLAST results are available for this feature:
BLAST of Calbindin-32-like 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 Calbindin-32-like 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 Calbindin-32-like protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Cbp53E4.132e-740.00gene:FBgn0004580 transcript:FBtr0340072[more]
Cbp53E4.132e-740.00gene:FBgn0004580 transcript:FBtr0087056[more]
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BLAST of Calbindin-32-like 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 Calbindin-32-like 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 Calbindin-32-like 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 Calbindin-32-like protein vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|P41044|CAB32_DROME4.142e-640.00Calbindin-32 OS=Drosophila melanogaster OX=7227 GN... [more]
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BLAST of Calbindin-32-like protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8GC461.364e-1167.35Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267GD681.832e-1167.35Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267GV221.851e-1167.35Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FNU41.851e-1177.50Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8GV549.532e-1072.97Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of Calbindin-32-like 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 Calbindin-32-like 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 Calbindin-32-like 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 Calbindin-32-like 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 Calbindin-32-like 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 Calbindin-32-like protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000043906.11.289e-22100.00SMESG000043906.1[more]
SMESG000043906.11.311e-22100.00SMESG000043906.1[more]
SMESG000055605.15.541e-1267.50SMESG000055605.1[more]
SMESG000023194.12.836e-851.11SMESG000023194.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006940 ID=SMED30006940|Name=Calbindin-32-like protein|organism=Schmidtea mediterranea sexual|type=transcript|length=283bp
CATGTGTATTGAGTAAATCTTATCAACTCAATCAATCGCATTATTGTTTG
CAATATCGTCATGTCTAACAATAAAGATTTTAATTTTTTATCACAGTTTC
GCGATCAAACAACCAAAAAATTGCAAAATTTCACAGCTACCGAATTCGCC
GAAGTCTGGAATCATTATGACAAAGATGGTACGTTTGCTTCTGGTATAAA
GGTGATGGGATATGCGTAGATTAATACAGAGATTTTCAAGTTTTTTTGTT
GAATGGCATTGTTTTAAATTAATATTTTACAGG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003117parapharyngeal cell
Vocabulary: molecular function
TermDefinition
GO:0005509calcium ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.10.238.10coord: 11..41
e-value: 4.9E-5
score: 25.3