NeuroD-2 protein

Overview
NameNeuroD-2 protein
Smed IDSMED30004868
Length (bp)718
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 NeuroD-2 protein (SMED30004868) t-SNE clustered cells

Violin plots show distribution of expression levels for NeuroD-2 protein (SMED30004868) 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 NeuroD-2 protein (SMED30004868) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for NeuroD-2 protein (SMED30004868) 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



SMED30004868

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30004868h1SMcG0001067 Contig3403newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004868h1SMcG0001067 Contig3403uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004868h1SMcG0021898 Contig3403newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004868h1SMcG0021898 Contig3403uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
parapharyngeal regionSMED30004868h1SMcG0021898 SmedASXL_000384SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
muscle cellSMED30004868h1SMcG0021898 dd_Smed_v4_9906_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
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BLAST of NeuroD-2 protein vs. TrEMBL
Match: U5YTP2 (NeuroD-2 protein (Fragment) OS=Schmidtea mediterranea OX=79327 GN=neuroD-2 PE=2 SV=1)

HSP 1 Score: 324.324 bits (830), Expect = 1.703e-110
Identity = 178/195 (91.28%), Postives = 178/195 (91.28%), Query Frame = 3 
Query:   99 PYAINGIIKAKDSFGNFY*KKMPDKYLKHEIVSDKINGTNFKRVXXXXXXXXXXXXXXMQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHSAGFVETESDPIHYSTVGDHVSYPSNNYRLNSLGSNVVYYQCMNSKNKNGSLVNCRDNGYLFDANSSNNGCNSLEIYSEKYSSNSLK 683
            PYAINGIIKAKDSF                 VSDKINGTNFKRVRSRRPRATQRERQRMQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHSAGFVETESDPIHYSTVGDHVSYPSNNYRLNSLGSNVVYYQCMNSKNKNGSLVNCRDNGYLFDANSSNNGCNSLEIYSEKYSSNSLK
Sbjct:    1 PYAINGIIKAKDSF-----------------VSDKINGTNFKRVRSRRPRATQRERQRMQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHSAGFVETESDPIHYSTVGDHVSYPSNNYRLNSLGSNVVYYQCMNSKNKNGSLVNCRDNGYLFDANSSNNGCNSLEIYSEKYSSNSLK 178
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BLAST of NeuroD-2 protein vs. TrEMBL
Match: A0A183B099 (BHLH domain-containing protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS12635 PE=4 SV=1)

HSP 1 Score: 79.7221 bits (195), Expect = 8.789e-14
Identity = 36/51 (70.59%), Postives = 43/51 (84.31%), Query Frame = 3 
Query:  273 MQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHS 425
            M  +NQAFDNLR VVPR H+ +YQ+LSKIATLRLAIQYIRAM + LG +H+
Sbjct:   56 MAQVNQAFDNLRRVVPRGHMTEYQRLSKIATLRLAIQYIRAMNRILGKSHT 106
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BLAST of NeuroD-2 protein vs. TrEMBL
Match: A0A504YL56 (BHLH domain-containing protein OS=Fasciola gigantica OX=46835 GN=FGIG_08234 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.610e-13
Identity = 35/47 (74.47%), Postives = 40/47 (85.11%), Query Frame = 3 
Query:  273 MQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLG 413
            M  +NQAFDNLR VVPR H+ +YQ+LSKIATLRLAIQYIRAM + LG
Sbjct:   48 MAQVNQAFDNLRRVVPRGHMTEYQRLSKIATLRLAIQYIRAMNRILG 94
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BLAST of NeuroD-2 protein vs. TrEMBL
Match: A0A1S8WLA2 (Helix-loop-helix DNA-binding domain protein (Fragment) OS=Opisthorchis viverrini OX=6198 GN=X801_09072 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 5.844e-13
Identity = 39/77 (50.65%), Postives = 48/77 (62.34%), Query Frame = 3 
Query:  273 MQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHSAGFVETESDPIHYSTVGDHVSYPSNN 503
            M  +NQAFD LR VVPR H+ +YQ+LSKIATLRLAIQYIRAM + LG         T + P+  S        P++N
Sbjct:   58 MAQVNQAFDGLRKVVPRGHMTEYQRLSKIATLRLAIQYIRAMNRILGRTVYVSMEPTLNVPLEESMWERTTEKPTDN 134
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BLAST of NeuroD-2 protein vs. TrEMBL
Match: A0A074ZKE5 (BHLH domain-containing protein OS=Opisthorchis viverrini OX=6198 GN=T265_06501 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 5.890e-13
Identity = 39/77 (50.65%), Postives = 48/77 (62.34%), Query Frame = 3 
Query:  273 MQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHSAGFVETESDPIHYSTVGDHVSYPSNN 503
            M  +NQAFD LR VVPR H+ +YQ+LSKIATLRLAIQYIRAM + LG         T + P+  S        P++N
Sbjct:   58 MAQVNQAFDGLRKVVPRGHMTEYQRLSKIATLRLAIQYIRAMNRILGRTVYVSMEPTLNVPLEESMWERTTEKPTDN 134
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BLAST of NeuroD-2 protein vs. Ensembl Nematostella
Match: EDO36265 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SJ29])

HSP 1 Score: 54.299 bits (129), Expect = 4.104e-9
Identity = 26/47 (55.32%), Postives = 32/47 (68.09%), Query Frame = 3 
Query:  273 MQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLG 413
            M  LN AFD+LR  +P+T+    +K SKIATLRLAI YI A+   LG
Sbjct:   80 MHSLNDAFDSLRKAIPKTNYNQEEKPSKIATLRLAIHYIAALSDILG 126
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BLAST of NeuroD-2 protein vs. Ensembl Nematostella
Match: TWIST (Predicted protein; Twist family bHLH transcription factor [Source:UniProtKB/TrEMBL;Acc:Q6S5G7])

HSP 1 Score: 44.2838 bits (103), Expect = 4.065e-6
Identity = 26/49 (53.06%), Postives = 34/49 (69.39%), Query Frame = 3 
Query:  276 QMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNH 422
            Q LN+AF+ LR ++P T  +D  KLSKI TLRLA +YI  + Q LG+N 
Sbjct:   50 QALNEAFNKLRKIIP-TLPSD--KLSKIQTLRLASRYIDFLCQVLGNNE 95
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BLAST of NeuroD-2 protein vs. Planmine SMEST
Match: SMESG000081091.1 (SMESG000081091.1)

HSP 1 Score: 281.567 bits (719), Expect = 8.995e-98
Identity = 136/137 (99.27%), Postives = 137/137 (100.00%), Query Frame = 3 
Query:  273 MQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHSAGFVETESDPIHYSTVGDHVSYPSNNYRLNSLGSNVVYYQCMNSKNKNGSLVNCRDNGYLFDANSSNNGCNSLEIYSEKYSSNSLK 683
            MQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHSAGFVETESDPIHYSTVGDHV+YPSNNYRLNSLGSNVVYYQCMNSKNKNGSLVNCRDNGYLFDANSSNNGCNSLEIYSEKYSSNSLK
Sbjct:    1 MQMLNQAFDNLRIVVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHSAGFVETESDPIHYSTVGDHVNYPSNNYRLNSLGSNVVYYQCMNSKNKNGSLVNCRDNGYLFDANSSNNGCNSLEIYSEKYSSNSLK 137
The following BLAST results are available for this feature:
BLAST of NeuroD-2 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 NeuroD-2 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 NeuroD-2 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 NeuroD-2 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 NeuroD-2 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 NeuroD-2 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 NeuroD-2 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 NeuroD-2 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
U5YTP21.703e-11091.28NeuroD-2 protein (Fragment) OS=Schmidtea mediterra... [more]
A0A183B0998.789e-1470.59BHLH domain-containing protein OS=Echinostoma capr... [more]
A0A504YL561.610e-1374.47BHLH domain-containing protein OS=Fasciola giganti... [more]
A0A1S8WLA25.844e-1350.65Helix-loop-helix DNA-binding domain protein (Fragm... [more]
A0A074ZKE55.890e-1350.65BHLH domain-containing protein OS=Opisthorchis viv... [more]
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BLAST of NeuroD-2 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 NeuroD-2 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 NeuroD-2 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 NeuroD-2 protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 2
Match NameE-valueIdentityDescription
EDO362654.104e-955.32Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
TWIST4.065e-653.06Predicted protein; Twist family bHLH transcription... [more]
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BLAST of NeuroD-2 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 NeuroD-2 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000081091.18.995e-9899.27SMESG000081091.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004868 ID=SMED30004868|Name=NeuroD-2 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=718bp
AATATCTCTGTAAATGACATGTTCTAGATTCTTTGTTGATTTAGGGAAAC
TCATTGCCTACTTCCAAGAATTAAAACAACAGAATGATAAAAAGATAACC
ATATGCAATAAATGGAATTATAAAAGCCAAGGATTCATTCGGTAATTTCT
ATTGAAAGAAAATGCCAGATAAATATCTTAAACACGAAATAGTTTCTGAT
AAAATTAACGGAACAAATTTCAAGCGAGTTCGATCTCGAAGACCCAGAGC
AACTCAGAGAGAACGTCAAAGAATGCAGATGTTGAATCAAGCGTTTGACA
ATTTACGGATTGTCGTACCGAGAACGCATTTAGCTGACTATCAGAAATTA
TCGAAAATTGCTACGTTACGTTTGGCAATCCAGTACATACGAGCAATGAA
GCAAACGCTGGGTCACAATCACTCGGCTGGATTTGTCGAAACCGAATCCG
ATCCAATTCACTATTCGACAGTCGGAGACCATGTCAGCTACCCTTCTAAC
AATTATCGCTTGAATAGTTTAGGCTCAAATGTCGTTTATTATCAGTGTAT
GAATAGTAAGAATAAGAACGGATCTTTGGTTAATTGTCGGGACAATGGAT
ATTTATTCGATGCCAATTCCTCAAATAATGGTTGCAATAGTCTAGAAATT
TATTCAGAAAAATATTCAAGCAACTCCTTGAAATAGTTTTTAAATTTAGT
AAATAAAATTTTTTTTCT
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protein sequence of SMED30004868-orf-1

>SMED30004868-orf-1 ID=SMED30004868-orf-1|Name=SMED30004868-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=175bp
MPDKYLKHEIVSDKINGTNFKRVRSRRPRATQRERQRMQMLNQAFDNLRI
VVPRTHLADYQKLSKIATLRLAIQYIRAMKQTLGHNHSAGFVETESDPIH
YSTVGDHVSYPSNNYRLNSLGSNVVYYQCMNSKNKNGSLVNCRDNGYLFD
ANSSNNGCNSLEIYSEKYSSNSLK*
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Aliases
The feature 'NeuroD-2 protein' has the following synonyms
Synonym
neuroD-2
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000101muscle cell
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR036638HLH_DNA-bd_sf
IPR011598bHLH_dom
Vocabulary: molecular function
TermDefinition
GO:0046983protein dimerization activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR011598Myc-type, basic helix-loop-helix (bHLH) domainSMARTSM00353finuluscoord: 31..85
e-value: 1.2E-12
score: 58.0
IPR011598Myc-type, basic helix-loop-helix (bHLH) domainPFAMPF00010HLHcoord: 26..79
e-value: 9.7E-14
score: 51.1
IPR011598Myc-type, basic helix-loop-helix (bHLH) domainPROSITEPS50888BHLHcoord: 25..79
score: 15.32
IPR011598Myc-type, basic helix-loop-helix (bHLH) domainCDDcd00083HLHcoord: 24..83
e-value: 4.61797E-13
score: 58.7647
IPR036638Helix-loop-helix DNA-binding domain superfamilyGENE3DG3DSA:4.10.280.10coord: 25..84
e-value: 2.4E-19
score: 70.8
IPR036638Helix-loop-helix DNA-binding domain superfamilySUPERFAMILYSSF47459HLH, helix-loop-helix DNA-binding domaincoord: 24..85
NoneNo IPR availablePANTHERPTHR19290BASIC HELIX-LOOP-HELIX PROTEIN NEUROGENIN-RELATEDcoord: 22..96