Sm domain-containing protein

Overview
NameSm domain-containing protein
Smed IDSMED30007036
Length (bp)469
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 Sm domain-containing protein (SMED30007036) t-SNE clustered cells

Violin plots show distribution of expression levels for Sm domain-containing protein (SMED30007036) 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 Sm domain-containing protein (SMED30007036) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Sm domain-containing protein (SMED30007036) 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



SMED30007036

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30007036SMESG000078103.1 SmedASXL_006105SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30007036SMESG000078103.1 dd_Smed_v4_7745_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007036SMESG000078103.1 dd_Smed_v4_7745_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30007036SMESG000078103.1 dd_Smed_v4_7745_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
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BLAST of Sm domain-containing protein vs. TrEMBL
Match: A0A5K3EPI8 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 2.016e-8
Identity = 27/77 (35.06%), Postives = 45/77 (58.44%), Query Frame = 2 
Query:   17 KFNGLLNFWNV---------KCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKV 220
            KF  +++FWN              GP   +   M+  S + ++TR +  +R+I+IG+LVAFD++WNLV+ +  EYK+
Sbjct:   34 KFRTIIDFWNTLERNLDGGGSGTLGPMERLMRAMREASTLYVVTRGMREIRAILIGRLVAFDRYWNLVLANVTEYKI 110
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BLAST of Sm domain-containing protein vs. TrEMBL
Match: A0A183RY55 (Sm domain-containing protein OS=Schistosoma rodhaini OX=6188 PE=4 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 8.021e-8
Identity = 23/48 (47.92%), Postives = 38/48 (79.17%), Query Frame = 2 
Query:   77 MYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKV 220
            +++ MQNQS+I+++TR L   R+ +IG LVAFD++WNL++++  EY V
Sbjct:    4 LWKAMQNQSQIMVMTRGLKEPRASIIGNLVAFDRYWNLILKNVTEYSV 51
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BLAST of Sm domain-containing protein vs. TrEMBL
Match: G4VK62 (Sm domain-containing protein OS=Schistosoma mansoni OX=6183 GN=Smp_160100 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 2.619e-7
Identity = 24/53 (45.28%), Postives = 40/53 (75.47%), Query Frame = 2 
Query:   62 GPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKV 220
             P + +++ MQNQS+I+++TR L   R+ +IG LVAFD++WNL++++  EY V
Sbjct:  190 SPMASLWKAMQNQSQIMVMTRGLKEPRASIIGNLVAFDRYWNLILKNVTEYSV 242
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BLAST of Sm domain-containing protein vs. TrEMBL
Match: A0A094ZP74 (Sm domain-containing protein (Fragment) OS=Schistosoma haematobium OX=6185 GN=MS3_04809 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 4.111e-7
Identity = 23/53 (43.40%), Postives = 40/53 (75.47%), Query Frame = 2 
Query:   62 GPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKV 220
             P + +++ MQNQS+I+++TR L   R+ +IG L+AFD++WNL++++  EY V
Sbjct:   62 SPMASLWKAMQNQSQIMVMTRGLKEPRASIIGNLIAFDRYWNLILKNVTEYSV 114
[Close]
BLAST of Sm domain-containing protein vs. TrEMBL
Match: A0A068WSG8 (Like Sm ribonucleoprotein core OS=Echinococcus granulosus OX=6210 GN=EgrG_001126300 PE=4 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 1.155e-6
Identity = 22/80 (27.50%), Postives = 45/80 (56.25%), Query Frame = 2 
Query:   14 KKFNGLLNFWN-----------VKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKV 220
            +KF  +L++W            ++   GP   + + M + + + ++TR +  +R+I+ G++VAFD++WNL++    EYK 
Sbjct:   31 QKFGSILDYWGRLERKLDHSMTLEGVLGPMERLMQAMHDSAAVYVVTRGMREIRAILTGRMVAFDRYWNLILADVTEYKT 110
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BLAST of Sm domain-containing protein vs. Ensembl Sea Lamprey
Match: lsm11 (LSM11, U7 small nuclear RNA associated [Source:ZFIN;Acc:ZDB-GENE-050309-124])

HSP 1 Score: 43.8986 bits (102), Expect = 3.888e-6
Identity = 18/52 (34.62%), Postives = 27/52 (51.92%), Query Frame = 2 
Query:   41 WNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVI 196
            W  K   GP   +Y  ++N+  I +  R    LR +  G L+AFDK WN+ +
Sbjct:  127 WMSKLEHGPLGGLYRCVKNRLPISVHVRTFRGLRGVCKGYLLAFDKFWNMAL 178
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BLAST of Sm domain-containing protein vs. Planmine SMEST
Match: SMESG000078103.1 (SMESG000078103.1)

HSP 1 Score: 210.305 bits (534), Expect = 4.176e-71
Identity = 122/122 (100.00%), Postives = 122/122 (100.00%), Query Frame = 2 
Query:    2 MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKVKNXXXXXXXXXXXXXXXXXLEELKSVFSDQLLLRGDSIIAVHLAQLPKI 367
            MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKVKNSTKKSGSKFSMSSFTESLEELKSVFSDQLLLRGDSIIAVHLAQLPKI
Sbjct:    1 MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKVKNSTKKSGSKFSMSSFTESLEELKSVFSDQLLLRGDSIIAVHLAQLPKI 122
[Close]
BLAST of Sm domain-containing protein vs. Planmine SMEST
Match: SMESG000078103.1 (SMESG000078103.1)

HSP 1 Score: 210.69 bits (535), Expect = 1.204e-70
Identity = 122/122 (100.00%), Postives = 122/122 (100.00%), Query Frame = 2 
Query:    2 MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKVKNXXXXXXXXXXXXXXXXXLEELKSVFSDQLLLRGDSIIAVHLAQLPKI 367
            MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKVKNSTKKSGSKFSMSSFTESLEELKSVFSDQLLLRGDSIIAVHLAQLPKI
Sbjct:    1 MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKVKNSTKKSGSKFSMSSFTESLEELKSVFSDQLLLRGDSIIAVHLAQLPKI 122
[Close]
BLAST of Sm domain-containing protein vs. Planmine SMEST
Match: SMESG000078103.1 (SMESG000078103.1)

HSP 1 Score: 209.92 bits (533), Expect = 2.856e-70
Identity = 122/122 (100.00%), Postives = 122/122 (100.00%), Query Frame = 2 
Query:    2 MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKVKNXXXXXXXXXXXXXXXXXLEELKSVFSDQLLLRGDSIIAVHLAQLPKI 367
            MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKVKNSTKKSGSKFSMSSFTESLEELKSVFSDQLLLRGDSIIAVHLAQLPKI
Sbjct:    1 MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIVIGKLVAFDKHWNLVIQSSREYKVKNSTKKSGSKFSMSSFTESLEELKSVFSDQLLLRGDSIIAVHLAQLPKI 122
The following BLAST results are available for this feature:
BLAST of Sm domain-containing 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 Sm domain-containing 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 Sm domain-containing 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 Sm domain-containing 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 Sm domain-containing 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 Sm domain-containing 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 Sm domain-containing 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 Sm domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A5K3EPI82.016e-835.06Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A183RY558.021e-847.92Sm domain-containing protein OS=Schistosoma rodhai... [more]
G4VK622.619e-745.28Sm domain-containing protein OS=Schistosoma manson... [more]
A0A094ZP744.111e-743.40Sm domain-containing protein (Fragment) OS=Schisto... [more]
A0A068WSG81.155e-627.50Like Sm ribonucleoprotein core OS=Echinococcus gra... [more]
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BLAST of Sm domain-containing 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 Sm domain-containing protein vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
lsm113.888e-634.62LSM11, U7 small nuclear RNA associated [Source:ZFI... [more]
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BLAST of Sm domain-containing 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 Sm domain-containing 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 Sm domain-containing 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 Sm domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000078103.14.176e-71100.00SMESG000078103.1[more]
SMESG000078103.11.204e-70100.00SMESG000078103.1[more]
SMESG000078103.12.856e-70100.00SMESG000078103.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007036 ID=SMED30007036|Name=Sm domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=469bp
CATGAGTAATACAAAGAAATTTAACGGATTACTTAACTTTTGGAATGTTA
AATGTAATTCTGGTCCATTTTCGTTAATGTATGAGTGGATGCAAAATCAA
TCTGAAATTGTTATTTTAACAAGAAATTTAAATTCTCTACGCAGCATTGT
TATAGGTAAATTGGTTGCATTTGATAAACATTGGAATTTAGTAATTCAAA
GCAGCAGAGAATATAAAGTTAAAAATTCCACTAAAAAATCAGGGTCAAAA
TTTTCAATGTCTTCTTTTACCGAATCTTTAGAAGAATTAAAAAGCGTATT
TTCAGATCAATTATTATTACGTGGAGATAGCATCATTGCTGTGCATTTAG
CTCAACTGCCTAAAATATAGTTTTATATTTGAATTATTGATTCTACTTTG
TCCTAAAGTTTTAATATTGAGGTCTTGGAATCAAACAATGCAATTATTTT
GCGTTGCTTTTAATGCAAA
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protein sequence of SMED30007036-orf-1

>SMED30007036-orf-1 ID=SMED30007036-orf-1|Name=SMED30007036-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MSNTKKFNGLLNFWNVKCNSGPFSLMYEWMQNQSEIVILTRNLNSLRSIV
IGKLVAFDKHWNLVIQSSREYKVKNSTKKSGSKFSMSSFTESLEELKSVF
SDQLLLRGDSIIAVHLAQLPKI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0071209U7 snRNA binding
GO:0003674molecular_function
GO:0003723RNA binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR039267Lsm11
IPR001163LSM_dom_euk/arc
IPR010920LSM_dom_sf
Vocabulary: biological process
TermDefinition
GO:0000398mRNA splicing, via spliceosome
GO:0006397mRNA processing
GO:0008380RNA splicing
GO:0033962cytoplasmic mRNA processing body assembly
Vocabulary: cellular component
TermDefinition
GO:0000932P-body
GO:0005634nucleus
GO:0005688U6 snRNP
GO:0030529intracellular ribonucleoprotein complex
GO:0030532small nuclear ribonucleoprotein complex
GO:0046540U4/U6 x U5 tri-snRNP complex
GO:0071011precatalytic spliceosome
GO:0071013catalytic step 2 spliceosome
GO:1990726Lsm1-7-Pat1 complex
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001163LSM domain, eukaryotic/archaea-typeSMARTSM00651Sm3coord: 27..116
e-value: 5.2E-4
score: 29.3
IPR001163LSM domain, eukaryotic/archaea-typePFAMPF01423LSMcoord: 48..115
e-value: 3.6E-9
score: 36.2
NoneNo IPR availableGENE3DG3DSA:2.30.30.100coord: 3..117
e-value: 5.7E-19
score: 69.9
IPR039267U7 snRNA-associated Sm-like protein Lsm11PANTHERPTHR21415U7 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM11coord: 18..81
IPR010920LSM domain superfamilySUPERFAMILYSSF50182Sm-like ribonucleoproteinscoord: 21..117