Epidermal growth factor Smed-egf-6

Overview
NameEpidermal growth factor Smed-egf-6
Smed IDSMED30027364
Length (bp)1110
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-6 (SMED30027364) t-SNE clustered cells

Violin plots show distribution of expression levels for Epidermal growth factor Smed-egf-6 (SMED30027364) 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-6 (SMED30027364) 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-6 (SMED30027364) 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



SMED30027364

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
head regionSMED30027364SMESG000029319.1 SmedASXL_006878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30027364SMESG000029319.1 dd_Smed_v4_6222_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30027364SMESG000029319.1 dd_Smed_v4_6222_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30027364SMESG000029319.1 dd_Smed_v4_6222_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30027364SMESG000029319.1 dd_Smed_v4_6222_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30027364SMESG000029319.1 dd_Smed_v6_6222_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-6 vs. TrEMBL
Match: A0A1B1ACY1 (Epidermal growth factor Smed-egf-6 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 488.034 bits (1255), Expect = 7.999e-172
Identity = 253/253 (100.00%), Postives = 253/253 (100.00%), Query Frame = 3 
Query:  276 MYSDVQLFKLTXXXXXXXXXXXXXXXXXVPQLNPKSGNINETIVAMIRNHYFDLMSKKNDWLMKILEVVKVELTFRQIVWRCGKNNSCLYSIQLFHPISESRNRRSIAEQIFKDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPTKPIANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNVISKDILQSKPLDN 1034
            MYSDVQLFKLTHAHLLKVFFLLLLVAIIVPQLNPKSGNINETIVAMIRNHYFDLMSKKNDWLMKILEVVKVELTFRQIVWRCGKNNSCLYSIQLFHPISESRNRRSIAEQIFKDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPTKPIANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNVISKDILQSKPLDN
Sbjct:    1 MYSDVQLFKLTHAHLLKVFFLLLLVAIIVPQLNPKSGNINETIVAMIRNHYFDLMSKKNDWLMKILEVVKVELTFRQIVWRCGKNNSCLYSIQLFHPISESRNRRSIAEQIFKDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPTKPIANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNVISKDILQSKPLDN 253
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BLAST of Epidermal growth factor Smed-egf-6 vs. TrEMBL
Match: A0A4E0RD62 (EGF region OS=Fasciola hepatica OX=6192 GN=D915_004892 PE=4 SV=1)

HSP 1 Score: 89.7373 bits (221), Expect = 9.671e-16
Identity = 51/152 (33.55%), Postives = 79/152 (51.97%), Query Frame = 3 
Query:  564 PISESRNRRSIAEQIFKDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPTKPIANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNVISKDILQS 1019
            P SE+     +      DN    E  L++ PR     +++     +     KP  N    C GRF +YC N  KC++I +L+ A C C  GY G+RC+ F+L  T+  L  ++ + +DV +L Q N   + SVV+ATAR+T N + ++ L S
Sbjct:  380 PTSEAPTLGELTPDEESDNSWNREDSLDNNPRLNVDLSVQAIPFGQNEFVGKPYEN----CTGRFENYCYNALKCVYISVLETAACYCRTGYTGVRCDMFNLPQTLDILKSFKEEIIDVSSLRQTNAVTLYSVVEATARYTVNAVLEENLIS 527
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BLAST of Epidermal growth factor Smed-egf-6 vs. TrEMBL
Match: A0A504YKB4 (EGF region OS=Fasciola gigantica OX=46835 GN=FGIG_03728 PE=4 SV=1)

HSP 1 Score: 87.8113 bits (216), Expect = 3.783e-15
Identity = 48/137 (35.04%), Postives = 75/137 (54.74%), Query Frame = 3 
Query:  612 KDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPTKPIANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNVISKDILQSK 1022
             DN    E  L++ PR     +++     +     KP  N    C GRF +YC N  KC++I +L+ A C C  GY G+RC+ F+L  T+  L  ++ + +DV +L Q N   + SVV+ATAR+T N + ++ L S+
Sbjct:  396 SDNSWNREDSLDNNPRLNVDLSVQAIPFGQNEFVGKPYEN----CTGRFENYCYNALKCVYISVLETAACYCRTGYTGVRCDMFNLPQTLDILKSFKEEIIDVSSLRQTNAVTLYSVVEATARYTVNAVLEENLISE 528
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BLAST of Epidermal growth factor Smed-egf-6 vs. TrEMBL
Match: A0A5J4NNB0 (EGF-like domain-containing protein OS=Paragonimus westermani OX=34504 GN=DEA37_0012545 PE=4 SV=1)

HSP 1 Score: 85.8853 bits (211), Expect = 1.540e-14
Identity = 40/91 (43.96%), Postives = 59/91 (64.84%), Query Frame = 3 
Query:  744 CEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYN-VISKDIL 1013
            C GRF +YC N  KCL+I +L+ A C C  GY G+RC+ F+L  T+  L  ++ + + V +L Q N   + SVV+ATAR+T N V+ +D+L
Sbjct:  439 CTGRFENYCYNALKCLYISVLETAACYCRTGYTGVRCDMFNLPQTLDILKSFREEVIHVPSLRQPNAVTLYSVVEATARYTVNAVLEEDLL 529
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BLAST of Epidermal growth factor Smed-egf-6 vs. TrEMBL
Match: A0A068WBS7 (EGF region OS=Echinococcus granulosus OX=6210 GN=EgrG_000753300 PE=4 SV=1)

HSP 1 Score: 80.4925 bits (197), Expect = 2.509e-13
Identity = 54/206 (26.21%), Postives = 100/206 (48.54%), Query Frame = 3 
Query:  384 GNINETIVAMIRNHYFDLMSKKNDWLMKILEVVKVELTFRQIVWRCGKNNSCLYSIQLFHPISESRNRRSIAEQIFKDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPT--KPIANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNV 995
             NI E I     N + + +     W + +L  ++ E   R+    C +   C+Y I  +  +S+S     +  ++ K   + E   L S+ R +    +++    +  + +   P+ N    C G F +YC N   C+++ +L+ A C C  GY G+RC+ + LS T+  L  ++  T+D+  L  ++   + SV+DATAR+TY+ 
Sbjct:   97 SNIREII-----NTFVEALKHDKSWFVSLLFQIRKEQKRRE-SESCSEAE-CIYKIPCY--LSQSFRSVPMYSEMLKRARVREGFDLLSR-RRRSLDGLEMDAEFKSLISSGKAPVTN----CTGIFANYCYNSISCIYVSVLESAACSCMPGYTGLRCDLYDLSITLATLSQFRTTTVDIEALRPEDSATMYSVLDATARYTYSA 288
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BLAST of Epidermal growth factor Smed-egf-6 vs. Planmine SMEST
Match: SMESG000029319.1 (SMESG000029319.1)

HSP 1 Score: 487.649 bits (1254), Expect = 3.090e-175
Identity = 252/253 (99.60%), Postives = 253/253 (100.00%), Query Frame = 3 
Query:  276 MYSDVQLFKLTXXXXXXXXXXXXXXXXXVPQLNPKSGNINETIVAMIRNHYFDLMSKKNDWLMKILEVVKVELTFRQIVWRCGKNNSCLYSIQLFHPISESRNRRSIAEQIFKDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPTKPIANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNVISKDILQSKPLDN 1034
            MYSDVQLFKLTHAHLLKVFFLLLLVAIIVPQLNPKSGNINETIVAMIRNHYFDLMSKKNDWLMKILEVVK+ELTFRQIVWRCGKNNSCLYSIQLFHPISESRNRRSIAEQIFKDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPTKPIANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNVISKDILQSKPLDN
Sbjct:    1 MYSDVQLFKLTHAHLLKVFFLLLLVAIIVPQLNPKSGNINETIVAMIRNHYFDLMSKKNDWLMKILEVVKIELTFRQIVWRCGKNNSCLYSIQLFHPISESRNRRSIAEQIFKDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPTKPIANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSDTVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNVISKDILQSKPLDN 253
The following BLAST results are available for this feature:
BLAST of Epidermal growth factor Smed-egf-6 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-6 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-6 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-6 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-6 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-6 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-6 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-6 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1B1ACY17.999e-172100.00Epidermal growth factor Smed-egf-6 OS=Schmidtea me... [more]
A0A4E0RD629.671e-1633.55EGF region OS=Fasciola hepatica OX=6192 GN=D915_00... [more]
A0A504YKB43.783e-1535.04EGF region OS=Fasciola gigantica OX=46835 GN=FGIG_... [more]
A0A5J4NNB01.540e-1443.96EGF-like domain-containing protein OS=Paragonimus ... [more]
A0A068WBS72.509e-1326.21EGF region OS=Echinococcus granulosus OX=6210 GN=E... [more]
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BLAST of Epidermal growth factor Smed-egf-6 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-6 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-6 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-6 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-6 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-6 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000029319.13.090e-17599.60SMESG000029319.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027364 ID=SMED30027364|Name=Epidermal growth factor Smed-egf-6|organism=Schmidtea mediterranea sexual|type=transcript|length=1110bp
AATGTTGGAAAATTTCCCCATAATTGCAACGACGCCATCCACTCTTATCC
AGAGAAAGAATTATACAACTCCTTTACCATTGATTTGTTGACCAATCTTC
GGTGCCGATGAATTTGGTTTGCATCACGCCGCTTTGCAGTTGTGCCTATA
TTTAGCTGAATTCAGGTATTATCATTTCATTCAACAACACTTCCTGGATT
AAAATATTTTATTACAAACATATATTATTCCGTTTCAGAGAGATTGTTTA
TTTCATTTTGGCTCTCATATTCAATATGTATTCCGATGTACAACTGTTCA
AATTAACCCATGCTCACCTGTTGAAGGTATTCTTTCTACTCCTATTGGTC
GCGATAATTGTGCCGCAATTGAACCCAAAATCCGGAAACATTAACGAAAC
TATTGTTGCAATGATTCGAAATCATTATTTTGATTTGATGAGTAAAAAGA
ATGATTGGCTGATGAAAATTCTTGAGGTCGTGAAAGTCGAGTTGACCTTT
CGACAAATCGTTTGGAGGTGCGGAAAAAATAACAGTTGTCTTTATTCAAT
ACAATTGTTTCATCCGATCAGTGAGAGTAGGAATCGCAGATCTATTGCTG
AACAGATTTTCAAAGATAACCCGATTTTCGAAGAGAGGATTCTCAATTCA
AAGCCAAGATACAAACAATTTAAAAATATTAAGGTTCATAAAACGACTCG
AGAATACTTACCCACGAAACCCATTGCAAATCGCATGACAGCCTGTGAAG
GAAGATTTTTAGACTACTGCCAGAATGGAGCTAAATGTTTATTTATTGAT
ATGCTTAAACGAGCTGTGTGCTTATGCAATAAAGGATATGGTGGAATTCG
ATGCGAAGATTTCAGTCTTTCGGATACCGTGCAGTACCTAGGGGACTATC
AAATGAAAACTTTGGATGTTTATACTTTAAACCAGAAAAATCATGAAGAT
ATCTGTTCAGTTGTGGATGCTACTGCGAGATTCACTTACAATGTCATTTC
GAAAGATATTTTACAATCTAAGCCATTAGATAATTGAATGAGCCATTGCC
TGATATTGATATATTTTATTGTTATTTTTAGATATTTCATTTAATAATTT
TCATTTTTAA
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protein sequence of SMED30027364-orf-1

>SMED30027364-orf-1 ID=SMED30027364-orf-1|Name=SMED30027364-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=254bp
MYSDVQLFKLTHAHLLKVFFLLLLVAIIVPQLNPKSGNINETIVAMIRNH
YFDLMSKKNDWLMKILEVVKVELTFRQIVWRCGKNNSCLYSIQLFHPISE
SRNRRSIAEQIFKDNPIFEERILNSKPRYKQFKNIKVHKTTREYLPTKPI
ANRMTACEGRFLDYCQNGAKCLFIDMLKRAVCLCNKGYGGIRCEDFSLSD
TVQYLGDYQMKTLDVYTLNQKNHEDICSVVDATARFTYNVISKDILQSKP
LDN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
PLANA:0003001lateral region of the whole animal
Vocabulary: INTERPRO
TermDefinition
IPR000742EGF-like_dom
IPR013032EGF-like_CS
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
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
IPR000742EGF-like domainSMARTSM00181egf_5coord: 156..194
e-value: 0.0043
score: 26.3
IPR000742EGF-like domainPROSITEPS50026EGF_3coord: 153..194
score: 14.249
NoneNo IPR availableGENE3DG3DSA:2.10.25.10coord: 149..195
e-value: 2.8E-10
score: 42.1
NoneNo IPR availableCDDcd00054EGF_CAcoord: 165..194
e-value: 0.00470636
score: 32.2234
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..30
score: 0.685
NoneNo IPR availableSUPERFAMILYSSF57196EGF/Laminincoord: 152..195
NoneNo IPR availableTMHMMTMhelixcoord: 7..29
IPR013032EGF-like, conserved sitePROSITEPS00022EGF_1coord: 182..193
IPR013032EGF-like, conserved sitePROSITEPS01186EGF_2coord: 182..193