Calcium-binding protein A

Overview
NameCalcium-binding protein A
Smed IDSMED30011700
Length (bp)350
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 Calcium-binding protein A (SMED30011700) t-SNE clustered cells

Violin plots show distribution of expression levels for Calcium-binding protein A (SMED30011700) 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 Calcium-binding protein A (SMED30011700) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Calcium-binding protein A (SMED30011700) 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




SMED30011700

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30011700SMESG000048475.1 SmedASXL_018792SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v4_605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v4_605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v4_605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v4_605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v4_605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v4_605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v4_605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v4_605_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011700SMESG000048475.1 Contig52181newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011700SMESG000048475.1 Contig52181uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Category 3 cellSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v6_605_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30011700SMESG000052083.1 SMESG000048475.1 dd_Smed_v4_605_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 Calcium-binding protein A vs. TrEMBL
Match: A0A1I8FHH7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 55.0694 bits (131), Expect = 2.548e-6
Identity = 24/67 (35.82%), Postives = 44/67 (65.67%), Query Frame = 2
Query:   68 KMFLAVDINKNGIISIEELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLA 268
            K FL++D + +G I+++EL+ +C K +  +  V+K+L  FD +++  ITY E+ +ALG P  +  +A
Sbjct:   13 KAFLSIDTDHSGEITVDELQSYCRKMNYQETFVQKWLMLFDADQNGRITYDEYCNALGLPPKKDVIA 79          
BLAST of Calcium-binding protein A vs. TrEMBL
Match: A0A267FI43 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig004334g1 PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 6.158e-6
Identity = 24/67 (35.82%), Postives = 45/67 (67.16%), Query Frame = 2
Query:   68 KMFLAVDINKNGIISIEELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLA 268
            K FL++D +++G I+++EL+ +C K +  +  V+K+L  FD +++  ITY E+ +ALG P  +  +A
Sbjct:   13 KAFLSIDTDQSGEITVDELQSYCRKMNYQETFVQKWLMLFDADQNGRITYDEYCNALGLPPKKDVVA 79          
BLAST of Calcium-binding protein A vs. TrEMBL
Match: A0A1I8IIW6 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 6.262e-6
Identity = 24/67 (35.82%), Postives = 45/67 (67.16%), Query Frame = 2
Query:   68 KMFLAVDINKNGIISIEELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLA 268
            K FL++D +++G I+++EL+ +C K +  +  V+K+L  FD +++  ITY E+ +ALG P  +  +A
Sbjct:   13 KAFLSIDTDQSGEITVDELQSYCRKMNYQETFVQKWLMLFDADQNGRITYDEYCNALGLPPKKDVVA 79          
BLAST of Calcium-binding protein A vs. TrEMBL
Match: A0A267GN94 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig004334g2 PE=4 SV=1)

HSP 1 Score: 53.5286 bits (127), Expect = 8.003e-6
Identity = 24/67 (35.82%), Postives = 44/67 (65.67%), Query Frame = 2
Query:   68 KMFLAVDINKNGIISIEELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLA 268
            K FL++D + +G I+++EL+ +C K +  +  V+K+L  FD +++  ITY E+ +ALG P  +  +A
Sbjct:   13 KAFLSIDTDHSGEITVDELQSYCRKMNYQETFVQKWLMLFDADQNGRITYDEYCNALGLPPKKDVIA 79          
BLAST of Calcium-binding protein A vs. Planmine SMEST
Match: SMESG000048475.1 (SMESG000048475.1)

HSP 1 Score: 162.155 bits (409), Expect = 1.845e-53
Identity = 77/78 (98.72%), Postives = 78/78 (100.00%), Query Frame = 2
Query:   47 MGDDMASKMFLAVDINKNGIISIEELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLALFQK 280
            MGDDMASKMFLAVDINKNGIIS+EELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLALFQK
Sbjct:    1 MGDDMASKMFLAVDINKNGIISVEELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLALFQK 78          
BLAST of Calcium-binding protein A vs. Planmine SMEST
Match: SMESG000002907.1 (SMESG000002907.1)

HSP 1 Score: 119.013 bits (297), Expect = 2.546e-36
Identity = 51/78 (65.38%), Postives = 70/78 (89.74%), Query Frame = 2
Query:   47 MGDDMASKMFLAVDINKNGIISIEELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLALFQK 280
            MGDD+ASKMFL +D NKNG+ISI+EL++HCSK +NVDEA++ FLKNFD ++D+ +TY+EFA ALG P++EKTL++F+K
Sbjct:    1 MGDDIASKMFLKIDTNKNGVISIDELKQHCSKTANVDEAIKTFLKNFDKDKDKNVTYEEFAKALGIPVSEKTLSVFKK 78          
BLAST of Calcium-binding protein A vs. Planmine SMEST
Match: SMESG000045893.1 (SMESG000045893.1)

HSP 1 Score: 61.6178 bits (148), Expect = 1.176e-13
Identity = 33/82 (40.24%), Postives = 51/82 (62.20%), Query Frame = 2
Query:   47 MGDDMASKMFLAVDINKNGIISIEELRKHCSKCSNVDEAVEK----FLKNFDTNRDREITYKEFADALGYPLNEKTLALFQK 280
            M DD+ +K+F AVD NKNG IS +EL+++  K    D  +EK    ++  FDT+ ++ I+Y E    +G P N+ T A+F+K
Sbjct:    1 MDDDVVTKIFKAVDKNKNGEISQDELKEYFKKTKVADCDIEKRITDWMGKFDTDSNKSISYSEMCKVVGIPENQNTKAMFKK 82          
BLAST of Calcium-binding protein A vs. Planmine SMEST
Match: SMESG000019835.1 (SMESG000019835.1)

HSP 1 Score: 46.2098 bits (108), Expect = 8.504e-7
Identity = 24/70 (34.29%), Postives = 42/70 (60.00%), Query Frame = 2
Query:   68 KMFLAVDINKNGIISIEELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLALFQ 277
            K F A+D + +G I+++EL+ +  K +  D  V K+L  FD+N+  +ITYK + D LG    E+ + + +
Sbjct:    6 KAFEAIDEDGSGEITVDELQHYMIKNNYKDSFVSKWLTLFDSNQSGKITYKHYCDTLGLVPREREIPIVK 75          
BLAST of Calcium-binding protein A vs. Planmine SMEST
Match: SMESG000018598.1 (SMESG000018598.1)

HSP 1 Score: 43.1282 bits (100), Expect = 1.515e-6
Identity = 24/69 (34.78%), Postives = 35/69 (50.72%), Query Frame = 2
Query:   74 FLAVDINKNGIISIEELRKHCSKCSNVDEAVEKFLKNFDTNRDREITYKEFADALGYPLNEKTLALFQK 280
            FL +D NKNGII+++E           D   E   K F++N    ITY EF +  G   ++ T+  F+K
Sbjct:    7 FLKIDSNKNGIITLKEFEDAKKSIGKAD--AEAIRKQFESNSGNNITYAEFCNLFGIAPDDGTMKKFKK 73          
The following BLAST results are available for this feature:
BLAST of Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A1I8FHH72.548e-635.82Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FI436.158e-635.82Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8IIW66.262e-635.82Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267GN948.003e-635.82Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A 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 Calcium-binding protein A vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000048475.11.845e-5398.72SMESG000048475.1[more]
SMESG000002907.12.546e-3665.38SMESG000002907.1[more]
SMESG000045893.11.176e-1340.24SMESG000045893.1[more]
SMESG000019835.18.504e-734.29SMESG000019835.1[more]
SMESG000018598.11.515e-634.78SMESG000018598.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011700 ID=SMED30011700|Name=Calcium-binding protein A|organism=Schmidtea mediterranea sexual|type=transcript|length=350bp
TATACAAAGCGTCTTGCTTGATGAAGCATCAAAACAACTATTCAAAATGG
GCGATGATATGGCTTCAAAAATGTTTCTTGCTGTTGATATCAATAAAAAC
GGAATAATATCTATAGAAGAATTGAGGAAGCATTGTTCAAAATGTTCAAA
TGTTGATGAAGCCGTGGAAAAGTTTCTAAAAAATTTTGATACTAACAGAG
ATAGAGAAATTACGTATAAAGAGTTTGCTGATGCTTTGGGATATCCTCTA
AATGAGAAAACTTTGGCTTTGTTTCAAAAATGAACTAGTTTGATTCAATT
TTATGTTTTGTTTTTAGTTTGAATTATAAATTTTAGTTTATTTTTTACTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000035Category 3 cell
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR002048EF_hand_dom
IPR011992EF-hand-dom_pair
IPR018247EF_Hand_1_Ca_BS
Vocabulary: molecular function
TermDefinition
GO:0005509calcium ion binding
Vocabulary: biological process
TermDefinition
GO:0007017microtubule-based process
Vocabulary: cellular component
TermDefinition
GO:0030286dynein complex
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR002048EF-hand domainSMARTSM00054efh_1coord: 54..82
e-value: 4.4
score: 12.5
coord: 20..48
e-value: 0.89
score: 18.2
IPR002048EF-hand domainPFAMPF13499EF-hand_7coord: 24..78
e-value: 2.9E-9
score: 37.2
IPR002048EF-hand domainPROSITEPS50222EF_HAND_2coord: 16..46
score: 7.261
IPR002048EF-hand domainPROSITEPS50222EF_HAND_2coord: 50..85
score: 10.608
IPR002048EF-hand domainCDDcd00051EFhcoord: 23..79
e-value: 4.09424E-8
score: 43.6905
NoneNo IPR availableGENE3DG3DSA:1.10.238.10coord: 2..84
e-value: 1.4E-13
score: 53.2
IPR018247EF-Hand 1, calcium-binding sitePROSITEPS00018EF_HAND_1coord: 63..75
IPR011992EF-hand domain pairSUPERFAMILYSSF47473EF-handcoord: 12..79