Expressed conserved protein

Overview
NameExpressed conserved protein
Smed IDSMED30022790
Length (bp)671
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 Expressed conserved protein (SMED30022790) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Expressed conserved protein (SMED30022790) 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.
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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



SMED30022790

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
Smed sexual biotypeSMED30022790h1SMcG0008136 Contig10252newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022790h1SMcG0008136 Contig10252uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022790h1SMcG0008136 Contig26960newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022790h1SMcG0008136 Contig26960uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022790h1SMcG0008136 Contig4077uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022790h1SMcG0008136 Contig4077newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
cephalic gangliaSMED30022790h1SMcG0008136 dd_Smed_v4_2516_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30022790h1SMcG0008136 dd_Smed_v4_2516_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022790h1SMcG0022503 Contig4077uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022790h1SMcG0022503 Contig4077newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30022790h1SMcG0008136 dd_Smed_v6_2516_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
pigment cellSMED30022790h1SMcG0008136 dd_Smed_v6_2516_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30022790h1SMcG0008136 dd_Smed_v6_2516_0dd_Smed_v6PMID:29674432
Plass 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 Expressed conserved protein vs. TrEMBL
Match: W6U553 (Uncharacterized protein OS=Echinococcus granulosus OX=6210 GN=EGR_08875 PE=4 SV=1)

HSP 1 Score: 78.5666 bits (192), Expect = 1.701e-14
Identity = 44/119 (36.97%), Postives = 65/119 (54.62%), Query Frame = 2 
Query:  146 ERKFLPLLN-ISCYVCE-TSQKTKNMNPIEWKVKNDECTTKPEIFKKICDPA--MRPRGCGKIFTRTVDQLPFAKKRVVELISRFCSSA--DETENGCNEMESHGGIQTYCLCSGDFCN 484
            ER F P  N +SCYVCE  S    N   ++WK++N  C    E   ++C+     +PRGCGK+ T++  Q+ F  +R V+L+ RFC+S+  +  E  C    S G     C+C G+ CN
Sbjct:   28 ERSFTPYSNNLSCYVCEPGSMNLTNRTYVQWKIENMRCEEPTEDLLQLCEETEIFKPRGCGKLVTKSYQQINFGGEREVKLVRRFCASSGMNLDEQKCVMTMSQGRWTEMCVCGGEACN 146
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BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A0X3NUI8 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=TR154307 PE=4 SV=1)

HSP 1 Score: 77.411 bits (189), Expect = 3.784e-14
Identity = 44/147 (29.93%), Postives = 70/147 (47.62%), Query Frame = 2 
Query:  125 LNAANPEERKFLPLLNISCYVCETSQKT--KNMNPIEWKVKNDECTTKPEIFKKIC--DPAMRPRGCGKIFTRTVDQLPFAKKRVVELISRFCSS--ADETENGCNEMESHGGIQTYCLCSGDFCNYSSKIYLNKYFLFFMASIFYV 547
            + A    ER F P  NI+C  C++  +   K  +  EW++ N  C   PE F K C      +PRGCGK+ TR+         R + ++ RFC+S  A + E  C+   S G +   C+C  D CN ++ +       F +A+ + +
Sbjct:   21 VGAITSLERSFTPSRNITCAQCQSESRAAYKTTSHAEWRMANLRCLNYPEQFYKPCVETETFKPRGCGKLVTRSYLYFGVHDDREITIVRRFCASEGASKDEVRCDTTLSQGRVTERCICGSDRCNGAASLSFLPSSAFLLAAAWLM 167
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BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A068WLV4 (Expressed conserved protein OS=Echinococcus granulosus OX=6210 GN=EgrG_000097200 PE=4 SV=1)

HSP 1 Score: 78.1814 bits (191), Expect = 4.796e-14
Identity = 44/119 (36.97%), Postives = 65/119 (54.62%), Query Frame = 2 
Query:  146 ERKFLPLLN-ISCYVCE-TSQKTKNMNPIEWKVKNDECTTKPEIFKKICDPA--MRPRGCGKIFTRTVDQLPFAKKRVVELISRFCSSA--DETENGCNEMESHGGIQTYCLCSGDFCN 484
            ER F P  N +SCYVCE  S    N   ++WK++N  C    E   ++C+     +PRGCGK+ T++  Q+ F  +R V+L+ RFC+S+  +  E  C    S G     C+C G+ CN
Sbjct:   24 ERSFTPYSNNLSCYVCEPGSMNLTNRTYVQWKIENMRCEEPTEDLLQLCEETEIFKPRGCGKLVTKSYQQINFGGEREVKLVRRFCASSGMNLDEQKCVMTMSQGRWTEMCVCGGEACN 142
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BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A0X3NM49 (Uncharacterized protein (Fragment) OS=Schistocephalus solidus OX=70667 GN=TR154307 PE=4 SV=1)

HSP 1 Score: 76.6406 bits (187), Expect = 6.322e-14
Identity = 46/160 (28.75%), Postives = 77/160 (48.12%), Query Frame = 2 
Query:   95 ILLVFFSNKFLNAANPEERK-FLPLLNISCYVCETSQKT--KNMNPIEWKVKNDECTTKPEIFKKIC--DPAMRPRGCGKIFTRTVDQLPFAKKRVVELISRFCSS--ADETENGCNEMESHGGIQTYCLCSGDFCNYSSKIYLNKYFLFFMASIFYVLL 553
            ++++FFS       +P  R  F P  NI+C  C++  +   K  +  EW++ N  C   PE F K C      +PRGCGK+ TR+         R + ++ RFC+S  A + E  C+   S G +   C+C  D CN ++ +       F +A+ + + +
Sbjct:    8 VIILFFS-----LTDPSSRAGFTPSRNITCAQCQSESRAAYKTTSHAEWRMANLRCLNYPEQFYKPCVETETFKPRGCGKLVTRSYLYFGVHDDREITIVRRFCASEGASKDEVRCDTTLSQGRVTERCICGSDRCNGAASLSFLPSSAFLLAAAWLMSM 162
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BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A5K3FB28 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 76.2554 bits (186), Expect = 1.342e-13
Identity = 48/147 (32.65%), Postives = 75/147 (51.02%), Query Frame = 2 
Query:   71 NMISKLVLILLVF-FSNKFLNAANPEERKFLPLL-NISCYVCET-SQKTKNMNPIEWKVKNDECTTKPEIFKKIC--DPAMRPRGCGKIFTRTVDQLPFAKKRVVELISRFCSSAD--ETENGCNEMESHGGIQTYCLCSGDFCNYS 490
            ++ ++ V +LL F        +    ER F P   N+SCYVCE  S        ++W+++N  C    E F + C      +PRGCGK+ T++  Q+ F  +R V+L+ RFC+S+   E E  C    S G     C+C G+ CN++
Sbjct:    2 DIYTRYVPVLLWFGLLAVHGQSLTSYERSFTPFHKNLSCYVCEPPSINLTGRTYVQWEMENRICEEPTEDFIQKCVETDTFKPRGCGKLVTKSYQQVNFGGEREVKLVRRFCASSGMKENEQKCQLTMSQGRWTEMCVCGGNACNHA 148
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BLAST of Expressed conserved protein vs. Planmine SMEST
Match: SMESG000079926.1 (SMESG000079926.1)

HSP 1 Score: 328.176 bits (840), Expect = 4.806e-116
Identity = 159/160 (99.38%), Postives = 159/160 (99.38%), Query Frame = 2 
Query:   74 MISKLVLILLVFFSNKFLNAANPEERKFLPLLNISCYVCETSQKTKNMNPIEWKVKNDECTTKPEIFKKICDPAMRPRGCGKIFTRTVDQLPFAKKRVVELISRFCSSADETENGCNEMESHGGIQTYCLCSGDFCNYSSKIYLNKYFLFFMASIFYVLL 553
            MISKLVLILLVFFSNKFL AANPEERKFLPLLNISCYVCETSQKTKNMNPIEWKVKNDECTTKPEIFKKICDPAMRPRGCGKIFTRTVDQLPFAKKRVVELISRFCSSADETENGCNEMESHGGIQTYCLCSGDFCNYSSKIYLNKYFLFFMASIFYVLL
Sbjct:    1 MISKLVLILLVFFSNKFLKAANPEERKFLPLLNISCYVCETSQKTKNMNPIEWKVKNDECTTKPEIFKKICDPAMRPRGCGKIFTRTVDQLPFAKKRVVELISRFCSSADETENGCNEMESHGGIQTYCLCSGDFCNYSSKIYLNKYFLFFMASIFYVLL 160
The following BLAST results are available for this feature:
BLAST of Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
W6U5531.701e-1436.97Uncharacterized protein OS=Echinococcus granulosus... [more]
A0A0X3NUI83.784e-1429.93Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A068WLV44.796e-1436.97Expressed conserved protein OS=Echinococcus granul... [more]
A0A0X3NM496.322e-1428.75Uncharacterized protein (Fragment) OS=Schistocepha... [more]
A0A5K3FB281.342e-1332.65Uncharacterized protein OS=Mesocestoides corti OX=... [more]
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BLAST of Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved protein 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 Expressed conserved 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 Expressed conserved protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000079926.14.806e-11699.38SMESG000079926.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022790 ID=SMED30022790|Name=Expressed conserved protein|organism=Schmidtea mediterranea sexual|type=transcript|length=671bp
GTTCAAATATGTTTATAATAATTCATTTTTGCATATATAAAATAAATTAA
TTTAATAATTAACGGTAAATAATATGATATCGAAGTTAGTGTTGATTCTT
TTGGTGTTCTTCAGTAATAAGTTTCTAAATGCTGCGAACCCTGAAGAAAG
AAAGTTTTTGCCGTTATTAAACATTTCTTGTTATGTCTGTGAGACATCAC
AGAAAACGAAAAACATGAATCCCATTGAATGGAAGGTAAAAAACGATGAA
TGCACGACGAAACCTGAAATCTTTAAAAAGATATGTGATCCTGCTATGCG
ACCGAGAGGATGCGGGAAGATATTTACACGAACTGTAGATCAGTTGCCAT
TTGCAAAAAAAAGAGTTGTTGAATTAATATCAAGATTTTGTTCGTCAGCA
GACGAAACAGAAAACGGATGCAACGAAATGGAGTCTCACGGAGGAATACA
AACGTATTGCTTGTGTTCGGGAGATTTTTGTAATTATTCTTCAAAAATTT
ATTTAAACAAATATTTTTTATTTTTCATGGCTTCGATTTTTTATGTTTTA
CTTTAAATAGACATGTAATAAAAATTCATATTATTTAACTATATATATAT
ATATTTTTAATTTAATAAATTTTATATTTGATTTCATTTTGAAATTGTTT
GACATAATTGTTTTATTGGCG
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protein sequence of SMED30022790-orf-1

>SMED30022790-orf-1 ID=SMED30022790-orf-1|Name=SMED30022790-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=161bp
MISKLVLILLVFFSNKFLNAANPEERKFLPLLNISCYVCETSQKTKNMNP
IEWKVKNDECTTKPEIFKKICDPAMRPRGCGKIFTRTVDQLPFAKKRVVE
LISRFCSSADETENGCNEMESHGGIQTYCLCSGDFCNYSSKIYLNKYFLF
FMASIFYVLL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0002075pigment cell
PLANA:0003116parenchymal cell
PLANA:0007528glial cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.754