Epidermal growth factor Smed-egf-3

Overview
NameEpidermal growth factor Smed-egf-3
Smed IDSMED30033455
Length (bp)584
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 Epidermal growth factor Smed-egf-3 (SMED30033455) t-SNE clustered cells

Violin plots show distribution of expression levels for Epidermal growth factor Smed-egf-3 (SMED30033455) 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 Epidermal growth factor Smed-egf-3 (SMED30033455) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Epidermal growth factor Smed-egf-3 (SMED30033455) 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



SMED30033455

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30033455 SmedASXL_017568SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parenchymal cellSMED30033455 dd_Smed_v4_11286_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30033455 dd_Smed_v6_11286_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Epidermal growth factor Smed-egf-3 vs. TrEMBL
Match: A0A1B1ACW7 (Epidermal growth factor Smed-egf-3 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 175.637 bits (444), Expect = 2.023e-53
Identity = 117/117 (100.00%), Postives = 117/117 (100.00%), Query Frame = 3 
Query:   54 MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPFDIENXXXXXXXXXXXXXXXXXXXXXXXXXXXGKNSQLIREKLNNLCTKKNKMKYAKPQINM 404
            MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPFDIENASISIKAISIISIFIFLLILLLVFVKIGKNSQLIREKLNNLCTKKNKMKYAKPQINM
Sbjct:    1 MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPFDIENASISIKAISIISIFIFLLILLLVFVKIGKNSQLIREKLNNLCTKKNKMKYAKPQINM 117
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BLAST of Epidermal growth factor Smed-egf-3 vs. TrEMBL
Match: A0A1B1ACY0 (Epidermal growth factor Smed-egf-5 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 74.3294 bits (181), Expect = 9.062e-14
Identity = 58/108 (53.70%), Postives = 74/108 (68.52%), Query Frame = 3 
Query:   54 MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPFDIENXXXXXXXXXXXXXXXXXXXXXXXXXXXGKNSQLIREKLNNLCTKKNKM 377
            ME +C   E LY     +C +G C+M K SE+ + +RMC+CE +WHGKRC+Y+DP     +SISI A+S ISI I LLILL VFVK+ + S+ IREKLN    KKNKM
Sbjct:    1 MEVDCNPQESLYIDGGKYCMNGRCVMHKTSEILEAVRMCICENDWHGKRCSYFDPHHFFESSISISAMSAISILILLLILLFVFVKVEEKSKNIREKLNKFSFKKNKM 108
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BLAST of Epidermal growth factor Smed-egf-3 vs. TrEMBL
Match: A0A1B1ACX8 (Epidermal growth factor Smed-egf-4 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 4.966e-8
Identity = 25/56 (44.64%), Postives = 32/56 (57.14%), Query Frame = 3 
Query:   54 MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPF 221
            M +NC+  E L E  +  C +G+C+    S      + C C  NWHGKRCTYYDPF
Sbjct:    1 MYKNCSITESLDEFGEKLCLNGHCVWMNSSGTMTAAKQCFCNDNWHGKRCTYYDPF 56
[Close]
BLAST of Epidermal growth factor Smed-egf-3 vs. Planmine SMEST
Match: SMESG000063182.1 (SMESG000063182.1)

HSP 1 Score: 175.637 bits (444), Expect = 5.627e-57
Identity = 117/117 (100.00%), Postives = 117/117 (100.00%), Query Frame = 3 
Query:   54 MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPFDIENXXXXXXXXXXXXXXXXXXXXXXXXXXXGKNSQLIREKLNNLCTKKNKMKYAKPQINM 404
            MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPFDIENASISIKAISIISIFIFLLILLLVFVKIGKNSQLIREKLNNLCTKKNKMKYAKPQINM
Sbjct:    1 MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPFDIENASISIKAISIISIFIFLLILLLVFVKIGKNSQLIREKLNNLCTKKNKMKYAKPQINM 117
[Close]
BLAST of Epidermal growth factor Smed-egf-3 vs. Planmine SMEST
Match: SMESG000063361.1 (SMESG000063361.1)

HSP 1 Score: 76.2554 bits (186), Expect = 3.952e-18
Identity = 59/108 (54.63%), Postives = 75/108 (69.44%), Query Frame = 3 
Query:   54 MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPFDIENXXXXXXXXXXXXXXXXXXXXXXXXXXXGKNSQLIREKLNNLCTKKNKM 377
            ME +C   E LY     +C +G C+M K SE+ + +RMC+CE +WHGKRC+Y+DP     +SISI A+S ISI I LLILL VFVK+ + S+ IREKLNN   KKNKM
Sbjct:    1 MEVDCNPQESLYIDGGKYCMNGRCVMHKTSEILEAVRMCICENDWHGKRCSYFDPHHFFESSISISAMSAISILILLLILLFVFVKVEEKSKNIREKLNNFSFKKNKM 108
[Close]
BLAST of Epidermal growth factor Smed-egf-3 vs. Planmine SMEST
Match: SMESG000037030.1 (SMESG000037030.1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.683e-11
Identity = 25/56 (44.64%), Postives = 32/56 (57.14%), Query Frame = 3 
Query:   54 MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRCTYYDPF 221
            M +NC+  E L E  +  C +G+C+    S      + C C  NWHGKRCTYYDPF
Sbjct:    1 MYKNCSITESLDEFGEKLCLNGHCVWMNSSGTMTAAKQCFCNDNWHGKRCTYYDPF 56
The following BLAST results are available for this feature:
BLAST of Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A1B1ACW72.023e-53100.00Epidermal growth factor Smed-egf-3 OS=Schmidtea me... [more]
A0A1B1ACY09.062e-1453.70Epidermal growth factor Smed-egf-5 OS=Schmidtea me... [more]
A0A1B1ACX84.966e-844.64Epidermal growth factor Smed-egf-4 OS=Schmidtea me... [more]
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BLAST of Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 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 Epidermal growth factor Smed-egf-3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000063182.15.627e-57100.00SMESG000063182.1[more]
SMESG000063361.13.952e-1854.63SMESG000063361.1[more]
SMESG000037030.11.683e-1144.64SMESG000037030.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033455 ID=SMED30033455|Name=Epidermal growth factor Smed-egf-3|organism=Schmidtea mediterranea sexual|type=transcript|length=584bp
CTAATATTTAAATAATTAAAAAATTTGACATTTTATTTCTTAGAATTAAA
ATAATGGAAAGAAATTGTACAGCGGACGAATTATTATATGAAAAAGACAA
AACATTCTGTTTTCATGGCAATTGCATTATGAAAAAAATGTCAGAAGTTT
ATAAAGAAATCAGAATGTGCTTGTGTGAAAAAAATTGGCATGGAAAAAGA
TGTACTTATTATGATCCATTTGATATTGAAAACGCAAGTATCTCAATTAA
AGCCATATCGATAATATCAATTTTTATTTTCCTTCTTATTTTACTATTAG
TTTTTGTAAAAATTGGAAAGAATTCTCAGCTTATAAGAGAAAAGTTGAAC
AATTTGTGCACAAAGAAAAATAAAATGAAATATGCAAAACCACAAATTAA
CATGTAATTTGGGGTAATAGGACAATCAAAAAGAATAAACTGGTTTAGGT
TGCTTCAATAAATGGTAATGGCAAATTCATTTTTCATTGAAATATTTTGT
AAAATTTTGTTTGTGATGAAAAACTAATATTTTGATGTATTTGAATTTGA
TTAAACTGTTTTCGATGAAACGTGAATATTGCCT
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protein sequence of SMED30033455-orf-1

>SMED30033455-orf-1 ID=SMED30033455-orf-1|Name=SMED30033455-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=118bp
MERNCTADELLYEKDKTFCFHGNCIMKKMSEVYKEIRMCLCEKNWHGKRC
TYYDPFDIENASISIKAISIISIFIFLLILLLVFVKIGKNSQLIREKLNN
LCTKKNKMKYAKPQINM*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
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 availableGENE3DG3DSA:2.10.25.10coord: 4..56
e-value: 7.2E-8
score: 34.2
NoneNo IPR availableSUPERFAMILYSSF57196EGF/Laminincoord: 14..53
NoneNo IPR availableTMHMMTMhelixcoord: 63..85