Expressed conserved protein

Overview
NameExpressed conserved protein
Smed IDSMED30002517
Length (bp)846
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 (SMED30002517) t-SNE clustered cells

Violin plots show distribution of expression levels for Expressed conserved protein (SMED30002517) 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 (SMED30002517) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Expressed conserved protein (SMED30002517) 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




SMED30002517

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
headSMED30002517SMESG000004480.1 dd_Smed_v4_8607_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30002517SMESG000004480.1 dd_Smed_v4_8607_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30002517SMESG000004480.1 dd_Smed_v4_8607_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A0X3Q0M0 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=TR154398 PE=4 SV=1)

HSP 1 Score: 100.908 bits (250), Expect = 1.420e-21
Identity = 63/164 (38.41%), Postives = 94/164 (57.32%), Query Frame = 3
Query:  243 NFYSPNDYRYSGTMFPYKPEIIN-MPTMQSAPSQPFLIPMPRNRQ---TVPKSM----------PP--FDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYXXXXXXXXXXFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKLFNKQI 686
            N   P +Y +  T +P  P   N + +MQ+    P LI    N Q   T+P SM          PP  +D+CP I SL ++  CPITC CS PA V+S+C+Y D+R  D+  +R  SD A+RL+I+ACI+GL+L + W+I  ++Y + ML LL + I+   + +
Sbjct:   96 NHVIPGEYMHVTTGYPGGPNSGNHVVSMQN----PALISAAINSQAYQTLPPSMSQMQSNSAQTPPQSYDRCPAICSLFAIFCCPITCWCSFPALVYSVCAYSDYRASDMYEYRSKSDVARRLVIIACIIGLILCICWAILTFLYYEPMLALLGDIIRTVQRHL 255          
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A5K3FMN5 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 100.908 bits (250), Expect = 1.784e-21
Identity = 47/97 (48.45%), Postives = 67/97 (69.07%), Query Frame = 3
Query:  396 PFDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYXXXXXXXXXXFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKLFNKQI 686
            P+D+CP I SL ++  CPITC CSLPA  +SLC+Y D+R  D+  +R  SD A+R +I+ACI+GL+L +IW+I  ++Y   ML LL + IK   + I
Sbjct:  158 PYDRCPAICSLFAIFCCPITCWCSLPALAYSLCAYTDYRANDMHSYRSKSDVARRCVIIACIVGLILCIIWAILTFLYYGEMLLLLGDVIKAVQRHI 254          
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A5K3FKN1 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 100.908 bits (250), Expect = 1.939e-21
Identity = 47/97 (48.45%), Postives = 67/97 (69.07%), Query Frame = 3
Query:  396 PFDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYXXXXXXXXXXFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKLFNKQI 686
            P+D+CP I SL ++  CPITC CSLPA  +SLC+Y D+R  D+  +R  SD A+R +I+ACI+GL+L +IW+I  ++Y   ML LL + IK   + I
Sbjct:  167 PYDRCPAICSLFAIFCCPITCWCSLPALAYSLCAYTDYRANDMHSYRSKSDVARRCVIIACIVGLILCIIWAILTFLYYGEMLLLLGDVIKAVQRHI 263          
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A183S7D9 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS137 PE=4 SV=1)

HSP 1 Score: 100.523 bits (249), Expect = 2.128e-21
Identity = 63/164 (38.41%), Postives = 94/164 (57.32%), Query Frame = 3
Query:  243 NFYSPNDYRYSGTMFPYKPEIIN-MPTMQSAPSQPFLIPMPRNRQ---TVPKSM----------PP--FDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYXXXXXXXXXXFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKLFNKQI 686
            N   P +Y +  T +P  P   N + +MQ+    P LI    N Q   T+P SM          PP  +D+CP I SL ++  CPITC CS PA V+S+C+Y D+R  D+  +R  SD A+RL+I+ACI+GL+L + W+I  ++Y + ML LL + I+   + +
Sbjct:   95 NHVIPGEYMHVTTGYPGGPNSGNHVVSMQN----PALISAAINSQAYQTLPPSMSQMQSNSAQTPPQSYDRCPAICSLFAIFCCPITCWCSFPALVYSVCAYSDYRASDMYEYRNKSDVARRLVIIACIIGLILCICWAILTFLYYEPMLALLGDIIRTVQRHL 254          
BLAST of Expressed conserved protein vs. TrEMBL
Match: G4VIW4 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 GN=Smp_145460 PE=4 SV=1)

HSP 1 Score: 100.908 bits (250), Expect = 3.698e-21
Identity = 54/152 (35.53%), Postives = 93/152 (61.18%), Query Frame = 3
Query:  246 FYSPNDYRYSGTMFPYKPEIINMPTMQSAPSQPFLIPMPRNRQTVPKSMPP-----FDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYXXXXXXXXXXFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKLFNKQI 686
            +  P++++ +  +  Y+P+      ++SA     +I + +N    P    P     FDKCPI+ SL ++  CPIT  CSLPA V+SLC+Y D+R  D++++R  SD A+ L+I ACI+GLLL + W+I  + Y + ML + ++ I++ +++I
Sbjct:  163 YQQPHNHQQTHYVHQYQPQAAKTLLVRSASG---IIGIDQNNHNNPDVFRPLSNETFDKCPIVCSLFAILCCPITIWCSLPALVYSLCAYSDYRASDINQYRRKSDIARHLVITACIVGLLLCITWAILTFFYYELMLSVFNDIIRVISQRI 311          
BLAST of Expressed conserved protein vs. Planmine SMEST
Match: SMESG000004480.1 (SMESG000004480.1)

HSP 1 Score: 382.874 bits (982), Expect = 3.188e-136
Identity = 197/197 (100.00%), Postives = 197/197 (100.00%), Query Frame = 3
Query:  102 MNQSRRNSIDKGSETSTNGGINDTGSEIQADNESITMTQHPGYFYSPNFYSPNDYRYSGTMFPYKPEIINMPTMQSAPSQPFLIPMPRNRQTVPKSMPPFDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYXXXXXXXXXXFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKLFNKQISG 692
            MNQSRRNSIDKGSETSTNGGINDTGSEIQADNESITMTQHPGYFYSPNFYSPNDYRYSGTMFPYKPEIINMPTMQSAPSQPFLIPMPRNRQTVPKSMPPFDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYVDHRVRDVDRFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKLFNKQISG
Sbjct:    1 MNQSRRNSIDKGSETSTNGGINDTGSEIQADNESITMTQHPGYFYSPNFYSPNDYRYSGTMFPYKPEIINMPTMQSAPSQPFLIPMPRNRQTVPKSMPPFDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYVDHRVRDVDRFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKLFNKQISG 197          
BLAST of Expressed conserved protein vs. Planmine SMEST
Match: SMESG000026093.1 (SMESG000026093.1)

HSP 1 Score: 105.916 bits (263), Expect = 6.537e-28
Identity = 64/130 (49.23%), Postives = 83/130 (63.85%), Query Frame = 3
Query:  312 MPTMQSAPSQPFLIPMPR----NRQTV------PKSMPPFDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYXXXXXXXXXXFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKL 671
            MPT   + +    IP PR    N+Q V      P    PFDKCPII SL +L  CPIT CCSLPA + S+CSY D+RV D+ RFR  SD A+RLII ACI+GL++V  WS+  Y+Y+ H+L+ L   I++
Sbjct:   33 MPTGTMSGAGYVTIPAPRHPSLNQQMVMRDFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQI 162          
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
A0A0X3Q0M01.420e-2138.41Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A5K3FMN51.784e-2148.45Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A5K3FKN11.939e-2148.45Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A183S7D92.128e-2138.41Uncharacterized protein OS=Schistocephalus solidus... [more]
G4VIW43.698e-2135.53Uncharacterized protein OS=Schistosoma mansoni 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: 2
Match NameE-valueIdentityDescription
SMESG000004480.13.188e-136100.00SMESG000004480.1[more]
SMESG000026093.16.537e-2849.23SMESG000026093.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002517 ID=SMED30002517|Name=Expressed conserved protein|organism=Schmidtea mediterranea sexual|type=transcript|length=846bp
CGACAAATAACATATGGTTACTATACTGTATATGGATCGATTTAGGCATA
TCAATATAGTAATGTCAATCTCATTCACTTAATGATTCTTTTAAAAGACA
AATGAATCAATCTCGCAGGAATAGTATCGATAAGGGTTCTGAAACCAGCA
CAAACGGAGGAATTAACGATACAGGAAGTGAAATCCAGGCCGACAATGAG
TCTATTACAATGACTCAACATCCTGGATATTTCTATTCGCCAAACTTTTA
TTCACCGAATGATTACCGATACTCCGGCACGATGTTTCCGTACAAACCGG
AAATTATCAATATGCCAACTATGCAATCAGCACCATCTCAACCATTTTTA
ATTCCAATGCCTAGAAATAGACAAACAGTTCCAAAGTCAATGCCCCCATT
CGATAAATGTCCAATTATATTCAGTCTATTATCTCTCTGCCTGTGTCCGA
TTACGTGTTGTTGTTCGTTGCCAGCATTTGTGTTTTCTCTCTGCAGTTAT
GTCGATCATAGAGTTCGTGACGTCGATCGTTTTCGGATCAATTCAGACTA
CGCTAAACGGTTAATCATTGTCGCTTGTATTCTTGGTTTGTTACTTGTGG
TTATCTGGTCAATTTTTGTATACATCTACAAGGATCACATGTTGCGCCTT
CTTTCAGAACATATAAAATTATTCAATAAACAAATTTCAGGTTGATTTAA
GCTTCGTTGTTTGATCGATTTTCAATTACAACCAAATGTGACGAAAAAAA
GGTCGCCTTTGTCCAAAAAATATATCTAAACATTATTTTATATATACACA
GATATGTTTATGGTTAAAATTTTCATTGTGATAATTATCGATCGTG
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protein sequence of SMED30002517-orf-1

>SMED30002517-orf-1 ID=SMED30002517-orf-1|Name=SMED30002517-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=198bp
MNQSRRNSIDKGSETSTNGGINDTGSEIQADNESITMTQHPGYFYSPNFY
SPNDYRYSGTMFPYKPEIINMPTMQSAPSQPFLIPMPRNRQTVPKSMPPF
DKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYVDHRVRDVDRFRINSDY
AKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKLFNKQISG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000101muscle cell
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR007593CD225/Dispanin_fam
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
GO:0016020membrane
Vocabulary: biological process
TermDefinition
GO:0009607response to biotic stimulus
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007593CD225/Dispanin familyPFAMPF04505CD225coord: 108..169
e-value: 1.6E-6
score: 28.2
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..25
NoneNo IPR availableTMHMMTMhelixcoord: 154..176
NoneNo IPR availableTMHMMTMhelixcoord: 105..127