Expressed conserved protein

Overview
NameExpressed conserved protein
Smed IDSMED30003846
Length (bp)645
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 Expressed conserved protein (SMED30003846) t-SNE clustered cells

Violin plots show distribution of expression levels for Expressed conserved protein (SMED30003846) 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 Expressed conserved protein (SMED30003846) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Expressed conserved protein (SMED30003846) 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



SMED30003846

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
nervous systemSMED30003846SMESG000068288.1 dd_Smed_v4_3595_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30003846SMESG000068288.1 dd_Smed_v4_3595_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30003846SMESG000068288.1 dd_Smed_v4_3595_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30003846SMESG000068288.1 OX_Smed_1.0.08824ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30003846SMESG000068288.1 dd_Smed_v4_3595_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30003846SMESG000068288.1 dd_Smed_v4_3595_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism 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: A0A0R3UGE9 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS6297 PE=4 SV=1)

HSP 1 Score: 95.9005 bits (237), Expect = 1.715e-21
Identity = 43/119 (36.13%), Postives = 70/119 (58.82%), Query Frame = 1 
Query:  154 LQCYQCNIIQRQNEQTLRSCDPLKNEITTFTNCSACAKITTVMAYDYRKPRFLQDYFLTTDLSRFCLRNFAPAWPNQCVNYYGSNTIQTRCFCDTNLCNSKISLVISGRLIFTSILLII 510
            L CY+C  I  Q + +L  CD       T TNC+AC K T V   D+RKPR+ Q+  +    +R+C+  F P +P+QC+ YYGS+++  +CFC ++ CN+  +L +   L+  S+ ++ 
Sbjct:   16 LTCYECEYINWQYDNSLWPCDQSAGPWKTLTNCTACIKQTEVQKSDFRKPRWGQEETVLKTTTRYCVVRFPPNFPDQCIYYYGSSSVMEQCFCSSDFCNTTKNLKLHSSLLLYSMFILF 134
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BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A183MZ51 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS21326 PE=4 SV=1)

HSP 1 Score: 92.4337 bits (228), Expect = 4.692e-20
Identity = 47/125 (37.60%), Postives = 69/125 (55.20%), Query Frame = 1 
Query:  154 LQCYQCNIIQRQNEQTLRSCDPLKNEITTFTNCSACAKITTVMAYDYRKPRFLQDYFLTTDLSRFCLRNFAPAWPNQCVNYYGSNTIQTRCFCDTNLCN-SKISLVISGRLIFT--SILLIIWYV 519
            L CY+C I+ R+ + +L  CD           C AC KI  V   D+RKPR+ Q Y     +SR CLR F P++ + C   YGS++ Q RC+C T+ CN    +L +S + +F   S+ ++I YV
Sbjct:   26 LSCYECEIVDRERKMSLWPCDESSGPWQKLDGCKACIKIEEVQRIDFRKPRWGQQYHEIKTVSRLCLRKFEPSFSDTCFQTYGSSSTQKRCYCSTDYCNYDPKTLSVSYKSLFAICSLSVLILYV 150
[Close]
BLAST of Expressed conserved protein vs. TrEMBL
Match: Q5DFI4 (SJCHGC04727 protein OS=Schistosoma japonicum OX=6182 PE=2 SV=1)

HSP 1 Score: 89.7373 bits (221), Expect = 4.193e-19
Identity = 47/137 (34.31%), Postives = 71/137 (51.82%), Query Frame = 1 
Query:  118 YAFGDENLNKPGLQCYQCNIIQRQNEQTLRSCDPLKNEITTFTNCSACAKITTVMAYDYRKPRFLQDYFLTTDLSRFCLRNFAPAWPNQCVNYYGSNTIQTRCFCDTNLCN-SKISLVISGRLIFT--SILLIIWYV 519
            Y +     +   L CY+C I+ R+ + TL  CD           C AC KI  V   D+RKPR+ Q Y     +SR CLR + P++ + C   YGS++ Q RC+C T+ CN +  +  +S +++F+  S  L I Y 
Sbjct:   14 YFYIPGRFSSANLTCYECEIVDRERKMTLWPCDESNGPWQKLDGCKACIKIEEVQRIDFRKPRWGQQYHEIKTVSRLCLRKYEPSFTDTCYQTYGSSSTQKRCYCATDYCNFNSKAFSVSFKVLFSICSFSLFILYA 150
[Close]
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A5J4NJD0 (Uncharacterized protein OS=Paragonimus westermani OX=34504 GN=DEA37_0002586 PE=4 SV=1)

HSP 1 Score: 87.4261 bits (215), Expect = 3.471e-18
Identity = 42/117 (35.90%), Postives = 59/117 (50.43%), Query Frame = 1 
Query:  154 LQCYQCNIIQRQNEQTLRSCDPLKNEITTFTNCSACAKITTVMAYDYRKPRFLQDYFLTTDLSRFCLRNFAPAWPNQCVNYYGSNTIQTRCFCDTNLCNSKISLVISGRLIFTSILL 504
            + CY+C I+ R+ + +L  CD           C AC KI      D+RKPR+ Q+YF     SR CLR F P   + C   YGS + Q +C+C T  CN K S V   + +  S+ +
Sbjct:   28 ISCYECEIVDRERQHSLWPCDGSMGPWEEVQGCRACVKIEETQRIDFRKPRWGQEYFEVVTESRLCLRKFVPLHMDTCTQTYGSASAQKKCYCSTPFCN-KSSSVYHFKWLLLSVFV 143
[Close]
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A0R3T0G5 (Uncharacterized protein OS=Rodentolepis nana OX=102285 GN=HNAJ_LOCUS305 PE=4 SV=1)

HSP 1 Score: 84.3445 bits (207), Expect = 5.020e-17
Identity = 38/102 (37.25%), Postives = 59/102 (57.84%), Query Frame = 1 
Query:  145 KPGLQCYQCNIIQRQNEQTLRSCDPLKNEITTFTNCSACAKITTVMAYDYRKPRFLQDYFLTTDLSRFCLRNFAPAWPNQCVNYYGSNTIQTRCFCDTNLCN 450
            +  + CY C  I  + E  L  CD         +NC++C K T V   D+ KPR+ Q+  +    SR+C+ +FAP +PNQC+ +YGS+++  +CFC T+ CN
Sbjct:   13 EASVSCYGCEYINWRYESALWPCDQSAGPWKILSNCTSCIKQTEVQESDFMKPRWGQEATVLKTTSRYCVVDFAPRYPNQCIFFYGSSSVIEQCFCSTDFCN 114
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
A0A0R3UGE91.715e-2136.13Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A183MZ514.692e-2037.60Uncharacterized protein OS=Schistosoma margrebowie... [more]
Q5DFI44.193e-1934.31SJCHGC04727 protein OS=Schistosoma japonicum OX=61... [more]
A0A5J4NJD03.471e-1835.90Uncharacterized protein OS=Paragonimus westermani ... [more]
A0A0R3T0G55.020e-1737.25Uncharacterized protein OS=Rodentolepis nana OX=10... [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: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003846 ID=SMED30003846|Name=Expressed conserved protein|organism=Schmidtea mediterranea sexual|type=transcript|length=645bp
CCACATTCAAAACATTATCTTGTTGAAAAGGATTTAAACGTATAAATTTA
AAATTATTTCAGGAAATTAATTTAATTTTAAATGATATTATTTTTCCTGT
TAATAACTTTTAATTATTATGCATTTGGGGATGAAAATTTGAACAAGCCA
GGATTACAATGTTACCAATGCAACATTATTCAGCGTCAAAACGAACAAAC
TCTTCGTTCTTGTGATCCATTGAAAAATGAAATTACTACATTTACAAATT
GTAGTGCTTGTGCTAAAATCACTACGGTTATGGCATATGATTATCGAAAA
CCTCGCTTTCTTCAAGATTATTTTCTTACTACTGATTTAAGTAGGTTTTG
CTTAAGAAATTTTGCACCTGCTTGGCCTAATCAATGCGTCAATTACTACG
GATCTAACACCATACAAACTCGATGTTTTTGTGATACAAATTTATGTAAT
TCCAAAATTTCTCTTGTCATATCAGGCCGTTTAATTTTCACTTCGATATT
ATTGATCATATGGTATGTCTAACTTTAAAATAATGTACCATATCTATATC
ATTGTGGCTGTGCTTTTTTGTAAAAATTGATATCCATTTATTTGATTTTA
AATGTATATTTCTTTAGTAAACTATGTTTTGTATTATTAAAACAA
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protein sequence of SMED30003846-orf-1

>SMED30003846-orf-1 ID=SMED30003846-orf-1|Name=SMED30003846-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=147bp
MILFFLLITFNYYAFGDENLNKPGLQCYQCNIIQRQNEQTLRSCDPLKNE
ITTFTNCSACAKITTVMAYDYRKPRFLQDYFLTTDLSRFCLRNFAPAWPN
QCVNYYGSNTIQTRCFCDTNLCNSKISLVISGRLIFTSILLIIWYV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000034epidermis
PLANA:0000418head
PLANA:0002032epidermal 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..16
score: 0.815