epiregulin-1

Overview
Nameepiregulin-1 (AFJ24829.1)
Smed IDSMED30030413
Length (bp)845
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 epiregulin-1 (SMED30030413) t-SNE clustered cells

Violin plots show distribution of expression levels for epiregulin-1 (SMED30030413) 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 epiregulin-1 (SMED30030413) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for epiregulin-1 (SMED30030413) 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



SMED30030413

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
gutSMED30030413h1SMcG0022114 dd_Smed_v4_10923_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
[Close]
BLAST of epiregulin-1 vs. TrEMBL
Match: A0A1B1ACX1 (Epidermal growth factor Smed-egf-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 311.612 bits (797), Expect = 1.004e-104
Identity = 182/182 (100.00%), Postives = 182/182 (100.00%), Query Frame = 3 
Query:   48 MITTFSSVTNCFDLTYCVHGVCTLRQLSRNSMPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYSEXXXXXXXXXXXXXXXXXXXXXXXXXXXRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITYSLSWN 593
            MITTFSSVTNCFDLTYCVHGVCTLRQLSRNSMPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYSEIILLIISAILVLLIIIAILLIYCCILYRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITYSLSWN
Sbjct:    1 MITTFSSVTNCFDLTYCVHGVCTLRQLSRNSMPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYSEIILLIISAILVLLIIIAILLIYCCILYRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITYSLSWN 182
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BLAST of epiregulin-1 vs. TrEMBL
Match: I1ZIH5 (Epiregulin-1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 301.597 bits (771), Expect = 8.966e-101
Identity = 177/178 (99.44%), Postives = 178/178 (100.00%), Query Frame = 3 
Query:   60 FSSVTNCFDLTYCVHGVCTLRQLSRNSMPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYSEXXXXXXXXXXXXXXXXXXXXXXXXXXXRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITYSLSWN 593
            FSSVTNCFDLTYCVHGVCTLRQLSRNSMPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYS+IILLIISAILVLLIIIAILLIYCCILYRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITYSLSWN
Sbjct:    1 FSSVTNCFDLTYCVHGVCTLRQLSRNSMPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYSQIILLIISAILVLLIIIAILLIYCCILYRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITYSLSWN 178
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BLAST of epiregulin-1 vs. TrEMBL
Match: A0A1B1ACX5 (Epidermal growth factor Smed-egf-2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 129.028 bits (323), Expect = 4.085e-33
Identity = 90/177 (50.85%), Postives = 115/177 (64.97%), Query Frame = 3 
Query:   48 MITTFSSVTNCFDLTYCVHGVCTLRQLSRNSMPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYSEXXXXXXXXXXXXXXXXXXXXXXXXXXXRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITY 578
            M+T+  S   C D +YCVHG+CT+RQLS +S+P R+C C +PY G RCN KNFSVFK + E D YS   L IISAI +LLIII I+LIYC ILY++ +++  N            E+ PQ+I I+CNE  VQSPM       ++  R S+DD     PLNDEF+NIK PRK+SD  Y
Sbjct:    1 MLTSTLSSLICADTSYCVHGICTIRQLSESSLPSRFCACFYPYIGPRCNKKNFSVFKRIMEGDEYSLAALSIISAIFILLIIIIIVLIYCLILYKRKRNNPINV-----QGKTFMESCPQQIQIVCNEAHVQSPMMGTPSFPERKFRTSFDDF-KFFPLNDEFQNIKIPRKYSDRNY 171
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BLAST of epiregulin-1 vs. Planmine SMEST
Match: SMESG000022749.1 (SMESG000022749.1)

HSP 1 Score: 245.358 bits (625), Expect = 1.295e-82
Identity = 150/151 (99.34%), Postives = 151/151 (100.00%), Query Frame = 3 
Query:  141 MPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYSEXXXXXXXXXXXXXXXXXXXXXXXXXXXRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITYSLSWN 593
            MPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYS+IILLIISAILVLLIIIAILLIYCCILYRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITYSLSWN
Sbjct:    1 MPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYSQIILLIISAILVLLIIIAILLIYCCILYRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITYSLSWN 151
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BLAST of epiregulin-1 vs. Planmine SMEST
Match: SMESG000022750.1 (SMESG000022750.1)

HSP 1 Score: 129.028 bits (323), Expect = 1.136e-36
Identity = 90/177 (50.85%), Postives = 115/177 (64.97%), Query Frame = 3 
Query:   48 MITTFSSVTNCFDLTYCVHGVCTLRQLSRNSMPIRYCICSFPYSGNRCNHKNFSVFKPVQEEDTYSEXXXXXXXXXXXXXXXXXXXXXXXXXXXRKNKHSYTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSYDDLINIAPLNDEFKNIKFPRKHSDITY 578
            M+T+  S   C D +YCVHG+CT+RQLS +S+P R+C C +PY G RCN KNFSVFK + E D YS   L IISAI +LLIII I+LIYC ILY++ +++  N            E+ PQ+I I+CNE  VQSPM       ++  R S+DD     PLNDEF+NIK PRK+SD  Y
Sbjct:    1 MLTSTLSSLICADTSYCVHGICTIRQLSESSLPSRFCACFYPYIGPRCNKKNFSVFKRIMEGDEYSLAALSIISAIFILLIIIIIVLIYCLILYKRKRNNPINV-----QGKTFMESCPQQIQIVCNEAHVQSPMMGTPSFPERKFRTSFDDF-KFFPLNDEFQNIKIPRKYSDRNY 171
The following BLAST results are available for this feature:
BLAST of epiregulin-1 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 epiregulin-1 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 epiregulin-1 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 epiregulin-1 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 epiregulin-1 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 epiregulin-1 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 epiregulin-1 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 epiregulin-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A1B1ACX11.004e-104100.00Epidermal growth factor Smed-egf-1 OS=Schmidtea me... [more]
I1ZIH58.966e-10199.44Epiregulin-1 (Fragment) OS=Schmidtea mediterranea ... [more]
A0A1B1ACX54.085e-3350.85Epidermal growth factor Smed-egf-2 OS=Schmidtea me... [more]
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BLAST of epiregulin-1 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 epiregulin-1 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 epiregulin-1 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 epiregulin-1 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 epiregulin-1 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 epiregulin-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000022749.11.295e-8299.34SMESG000022749.1[more]
SMESG000022750.11.136e-3650.85SMESG000022750.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30030413
GenBankAFJ24829.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030413 ID=SMED30030413|Name=epiregulin-1|organism=Schmidtea mediterranea sexual|type=transcript|length=845bp
CTTGAGATTATTTTATTAAATTCATTTTTAAAATTGAATATCAAAAAATG
ATAACAACCTTTTCTTCAGTTACTAATTGTTTTGACTTGACCTATTGTGT
CCACGGGGTTTGCACCTTAAGACAATTGTCAAGGAACAGCATGCCTATCA
GATATTGCATATGCAGTTTTCCGTACAGTGGGAATCGGTGCAATCATAAA
AATTTTAGTGTATTTAAACCGGTTCAAGAAGAAGATACATATTCAGAAAT
AATTTTGCTTATCATTTCAGCCATTTTAGTTTTATTAATCATTATTGCAA
TACTGCTCATTTACTGTTGCATTTTATATAGAAAGAATAAACACAGTTAC
ACCAATTCTGTTTCTCAAAACCACAACAGTGCCAATGTCAAAGAAAACCT
TCCACAAAAAATTCATATTCTCTGCAACGAGACCCTTGTCCAATCTCCAA
TGTTCAATGGAATCCCCGCAACAGACAAGTGGCGCCGAAACAGTTATGAT
GATTTAATAAACATAGCCCCATTAAATGACGAATTTAAAAATATCAAATT
CCCTAGAAAACATTCTGACATTACCTATAGTTTGAGTTGGAATTGAAACG
GTCTGGCATTTGATCCCAATTGGCAGACTTCTAGAATTATCCTCAGATCT
ACCGGATGTAGAAGTCTCGAATTTACTTTGTAGATAATAAGTAATATTTT
ATATTCCCTGTTCTGCCATAGTCGCGAAGTAATAGCCTTTTAATTATCAA
TCTTGAATGTCCAGGGAAAGTGAATGAAGTTTATTGTTTAAATGAAAGTC
ATGAAAAAGCTGATTTTTATTTTGATTCTTTTGTTTTTATTTTCA
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protein sequence of SMED30030413-orf-1

>SMED30030413-orf-1 ID=SMED30030413-orf-1|Name=SMED30030413-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=183bp
MITTFSSVTNCFDLTYCVHGVCTLRQLSRNSMPIRYCICSFPYSGNRCNH
KNFSVFKPVQEEDTYSEIILLIISAILVLLIIIAILLIYCCILYRKNKHS
YTNSVSQNHNSANVKENLPQKIHILCNETLVQSPMFNGIPATDKWRRNSY
DDLINIAPLNDEFKNIKFPRKHSDITYSLSWN*
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Aliases
The feature 'epiregulin-1' has the following synonyms
Synonym
epiregulin-1
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR011759Cyt_c_oxidase_su2_TM_dom
IPR013032EGF-like_CS
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
GO:0016020membrane
Vocabulary: biological process
TermDefinition
GO:0022900electron transport chain
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: 13..51
e-value: 2.2E-5
score: 26.5
NoneNo IPR availablePANTHERPTHR10740:SF11PROEPIREGULINcoord: 15..105
NoneNo IPR availablePANTHERPTHR10740TRANSFORMING GROWTH FACTOR ALPHAcoord: 15..105
NoneNo IPR availableSUPERFAMILYSSF57196EGF/Laminincoord: 14..53
NoneNo IPR availableTMHMMTMhelixcoord: 68..90
IPR013032EGF-like, conserved sitePROSITEPS00022EGF_1coord: 37..48
IPR013032EGF-like, conserved sitePROSITEPS01186EGF_2coord: 37..48