U6 snRNA-associated Sm-like protein LSm3

Overview
NameU6 snRNA-associated Sm-like protein LSm3
Smed IDSMED30020216
Length (bp)433
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 U6 snRNA-associated Sm-like protein LSm3 (SMED30020216) t-SNE clustered cells

Violin plots show distribution of expression levels for U6 snRNA-associated Sm-like protein LSm3 (SMED30020216) 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 U6 snRNA-associated Sm-like protein LSm3 (SMED30020216) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for U6 snRNA-associated Sm-like protein LSm3 (SMED30020216) 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



SMED30020216

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30020216 SmedASXL_018984SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30020216 dd_Smed_v4_1641_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020216 dd_Smed_v4_1641_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020216 dd_Smed_v4_1641_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020216 dd_Smed_v4_1641_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 U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Human
Match: LSM3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated [Source:HGNC Symbol;Acc:HGNC:17874])

HSP 1 Score: 117.087 bits (292), Expect = 1.913e-34
Identity = 67/90 (74.44%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Celegans
Match: lsm-3 (U6 snRNA-associated Sm-like protein LSm3 [Source:UniProtKB/TrEMBL;Acc:Q9U1W8])

HSP 1 Score: 114.775 bits (286), Expect = 5.810e-34
Identity = 64/91 (70.33%), Postives = 81/91 (89.01%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLKG 385
            ++ ++EPLDL+RLSL+ER+YVKM+NDRELRG+L AFD HLNM LS+VEETITT E+D++T EEI+K TKR +PMLFVRGD VILVSPP++ 
Sbjct:   11 SATVEEPLDLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITTREVDEDTFEEIYKQTKRVVPMLFVRGDSVILVSPPIRA 101
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Celegans
Match: lsm-5 (U6 snRNA-associated Sm-like protein LSm5 [Source:UniProtKB/TrEMBL;Acc:O18694])

HSP 1 Score: 47.7506 bits (112), Expect = 5.977e-8
Identity = 20/41 (48.78%), Postives = 28/41 (68.29%), Query Frame = 2 
Query:  131 PLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDV 253
            PL+LI   +  +I+V MKND+E+ G L  FD ++NM L DV
Sbjct:   14 PLELIDKCIGSKIWVIMKNDKEIVGTLTGFDDYVNMVLEDV 54
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Celegans
Match: lsm-5 (U6 snRNA-associated Sm-like protein LSm5 [Source:UniProtKB/TrEMBL;Acc:O18694])

HSP 1 Score: 47.7506 bits (112), Expect = 5.977e-8
Identity = 20/41 (48.78%), Postives = 28/41 (68.29%), Query Frame = 2 
Query:  131 PLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDV 253
            PL+LI   +  +I+V MKND+E+ G L  FD ++NM L DV
Sbjct:   14 PLELIDKCIGSKIWVIMKNDKEIVGTLTGFDDYVNMVLEDV 54
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Fly
Match: LSm3 (gene:FBgn0051184 transcript:FBtr0084505)

HSP 1 Score: 113.235 bits (282), Expect = 3.777e-33
Identity = 64/87 (73.56%), Postives = 80/87 (91.95%), Query Frame = 2 
Query:  122 IDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
            + EPLDLIRLSL+E++YVKM+N+RELRG+L+AFD HLNM L D EET+TT+EID+ET EE++KT KR+IPMLFVRGDGVILVSPP++
Sbjct:   15 VKEPLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEVYKTAKRTIPMLFVRGDGVILVSPPMR 101
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Fly
Match: LSm3 (gene:FBgn0051184 transcript:FBtr0300648)

HSP 1 Score: 113.235 bits (282), Expect = 3.777e-33
Identity = 64/87 (73.56%), Postives = 80/87 (91.95%), Query Frame = 2 
Query:  122 IDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
            + EPLDLIRLSL+E++YVKM+N+RELRG+L+AFD HLNM L D EET+TT+EID+ET EE++KT KR+IPMLFVRGDGVILVSPP++
Sbjct:   15 VKEPLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEVYKTAKRTIPMLFVRGDGVILVSPPMR 101
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Fly
Match: CG6610 (gene:FBgn0035675 transcript:FBtr0332059)

HSP 1 Score: 42.743 bits (99), Expect = 7.186e-6
Identity = 19/41 (46.34%), Postives = 27/41 (65.85%), Query Frame = 2 
Query:  131 PLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDV 253
            PL+L+   +  RI++ MKND+E+ G L  FD  +NM L DV
Sbjct:   15 PLELVDKCIGSRIHIIMKNDKEMVGTLLGFDDFVNMLLDDV 55
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Fly
Match: CG6610 (gene:FBgn0035675 transcript:FBtr0332060)

HSP 1 Score: 42.743 bits (99), Expect = 7.186e-6
Identity = 19/41 (46.34%), Postives = 27/41 (65.85%), Query Frame = 2 
Query:  131 PLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDV 253
            PL+L+   +  RI++ MKND+E+ G L  FD  +NM L DV
Sbjct:   15 PLELVDKCIGSRIHIIMKNDKEMVGTLLGFDDFVNMLLDDV 55
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Fly
Match: CG6610 (gene:FBgn0035675 transcript:FBtr0077048)

HSP 1 Score: 42.743 bits (99), Expect = 7.186e-6
Identity = 19/41 (46.34%), Postives = 27/41 (65.85%), Query Frame = 2 
Query:  131 PLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDV 253
            PL+L+   +  RI++ MKND+E+ G L  FD  +NM L DV
Sbjct:   15 PLELVDKCIGSRIHIIMKNDKEMVGTLLGFDDFVNMLLDDV 55
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Zebrafish
Match: lsm3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated [Source:ZFIN;Acc:ZDB-GENE-161207-2])

HSP 1 Score: 117.472 bits (293), Expect = 9.060e-35
Identity = 67/90 (74.44%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTVEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Zebrafish
Match: lsm5 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated [Source:ZFIN;Acc:ZDB-GENE-070822-23])

HSP 1 Score: 44.2838 bits (103), Expect = 2.480e-6
Identity = 19/41 (46.34%), Postives = 27/41 (65.85%), Query Frame = 2 
Query:  131 PLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDV 253
            PL+L+   +  RI++ MKND+E+ G L  FD  +NM L DV
Sbjct:   14 PLELVDKCIGSRIHIVMKNDKEIVGTLLGFDDFVNMVLEDV 54
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Xenopus
Match: ube2w (ubiquitin conjugating enzyme E2W (putative) [Source:Xenbase;Acc:XB-GENE-954746])

HSP 1 Score: 117.087 bits (292), Expect = 1.678e-34
Identity = 67/94 (71.28%), Postives = 84/94 (89.36%), Query Frame = 2 
Query:  101 LHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
                 + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:    7 FQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Xenopus
Match: ube2w (ubiquitin conjugating enzyme E2W (putative) [Source:Xenbase;Acc:XB-GENE-954746])

HSP 1 Score: 117.087 bits (292), Expect = 1.753e-34
Identity = 67/90 (74.44%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Mouse
Match: Lsm3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated [Source:MGI Symbol;Acc:MGI:1914928])

HSP 1 Score: 117.087 bits (292), Expect = 1.313e-34
Identity = 67/90 (74.44%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Mouse
Match: Lsm3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated [Source:MGI Symbol;Acc:MGI:1914928])

HSP 1 Score: 117.087 bits (292), Expect = 1.313e-34
Identity = 67/90 (74.44%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. UniProt/SwissProt
Match: sp|P62311|LSM3_MOUSE (U6 snRNA-associated Sm-like protein LSm3 OS=Mus musculus OX=10090 GN=Lsm3 PE=1 SV=2)

HSP 1 Score: 117.087 bits (292), Expect = 9.184e-34
Identity = 67/90 (74.44%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. UniProt/SwissProt
Match: sp|P62310|LSM3_HUMAN (U6 snRNA-associated Sm-like protein LSm3 OS=Homo sapiens OX=9606 GN=LSM3 PE=1 SV=2)

HSP 1 Score: 117.087 bits (292), Expect = 9.184e-34
Identity = 67/90 (74.44%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. UniProt/SwissProt
Match: sp|Q32PE9|LSM3_BOVIN (U6 snRNA-associated Sm-like protein LSm3 OS=Bos taurus OX=9913 GN=LSM3 PE=3 SV=3)

HSP 1 Score: 117.087 bits (292), Expect = 9.184e-34
Identity = 67/90 (74.44%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. UniProt/SwissProt
Match: sp|Q9LMN4|LSM3A_ARATH (Sm-like protein LSM3A OS=Arabidopsis thaliana OX=3702 GN=LSM3A PE=1 SV=1)

HSP 1 Score: 111.309 bits (277), Expect = 1.670e-31
Identity = 70/95 (73.68%), Postives = 83/95 (87.37%), Query Frame = 2 
Query:   98 NLHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
            ++  DA+V  EPLDLIRLS+ ERIYVK+++DRELRGKL+AFD HLNM L DVEE ITT+EIDDET EEI +TTKR++P LFVRGDGVILVSPPL+
Sbjct:    2 SVEEDATV-REPLDLIRLSIEERIYVKLRSDRELRGKLHAFDQHLNMILGDVEEVITTIEIDDETYEEIVRTTKRTVPFLFVRGDGVILVSPPLR 95
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. UniProt/SwissProt
Match: sp|Q9C6K5|LSM3B_ARATH (Sm-like protein LSM3B OS=Arabidopsis thaliana OX=3702 GN=LSM3B PE=1 SV=1)

HSP 1 Score: 110.153 bits (274), Expect = 4.395e-31
Identity = 69/91 (75.82%), Postives = 81/91 (89.01%), Query Frame = 2 
Query:  110 DASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
            + + + EPLDLIRLSL+ERIYVK+++DRELRGKL+AFD HLNM L DVEETITT+EIDDET EEI +TTKR+I  LFVRGDGVILVSPPL+
Sbjct:    5 EEATVREPLDLIRLSLDERIYVKLRSDRELRGKLHAFDQHLNMILGDVEETITTVEIDDETYEEIVRTTKRTIEFLFVRGDGVILVSPPLR 95
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. TrEMBL
Match: A0A087U5A3 (U6 snRNA-associated Sm-like protein LSm3 (Fragment) OS=Stegodyphus mimosarum OX=407821 GN=LSM3 PE=3 SV=1)

HSP 1 Score: 129.413 bits (324), Expect = 7.130e-36
Identity = 74/108 (68.52%), Postives = 94/108 (87.04%), Query Frame = 2 
Query:   62 IFYKKMDSSAGDNLHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLKG 385
            IF K M   A DN  + A+ ++EPLDLIRLSL+ERIYVKM+N+RELRG+L+A+D HLNM L DVEET+TT+EID+ET EE+++TTKR++PMLFVRGDGVILVSPP++G
Sbjct:   10 IFEKNM---ADDNEQSAANAVEEPLDLIRLSLDERIYVKMRNERELRGRLHAYDQHLNMVLGDVEETVTTVEIDEETYEEVYRTTKRTVPMLFVRGDGVILVSPPIRG 114
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. TrEMBL
Match: A0A4Y2JVI3 (U6 snRNA-associated Sm-like protein LSm3 OS=Araneus ventricosus OX=182803 GN=Lsm3_1 PE=3 SV=1)

HSP 1 Score: 126.331 bits (316), Expect = 6.896e-35
Identity = 70/99 (70.71%), Postives = 90/99 (90.91%), Query Frame = 2 
Query:   89 AGDNLHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLKG 385
            A DN  + A+ ++EPLDLIRLSL+ERIYVKM+N+RELRG+L+A+D HLNM L DVEET+TT+EID+ET EE+++TTKR++PMLFVRGDGVILVSPP++G
Sbjct:    2 ADDNEQSAANAVEEPLDLIRLSLDERIYVKMRNERELRGRLHAYDQHLNMVLGDVEETVTTIEIDEETYEEVYRTTKRTVPMLFVRGDGVILVSPPIRG 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. TrEMBL
Match: C3YAV8 (U6 snRNA-associated Sm-like protein LSm3 (Fragment) OS=Branchiostoma floridae OX=7739 GN=LSM3 PE=3 SV=1)

HSP 1 Score: 123.25 bits (308), Expect = 1.038e-33
Identity = 71/91 (78.02%), Postives = 86/91 (94.51%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLKG 385
             +V++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+KTTKR+IPMLFVRGDGVILV+PPL+G
Sbjct:    5 TAVVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTVEIDEETYEEIYKTTKRNIPMLFVRGDGVILVAPPLRG 95
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. TrEMBL
Match: A0A2L2YH15 (U6 snRNA-associated Sm-like protein LSm3 OS=Parasteatoda tepidariorum OX=114398 GN=LSM3 PE=2 SV=1)

HSP 1 Score: 122.865 bits (307), Expect = 1.622e-33
Identity = 68/97 (70.10%), Postives = 88/97 (90.72%), Query Frame = 2 
Query:   95 DNLHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLKG 385
            D   + A+ ++EPLDLIRLSL+ERIYVKM+N+RELRG+L+A+D HLNM L DVEET+TT+EID+ET EE+++TTKR++PMLFVRGDGVILVSPP++G
Sbjct:    4 DTEQSAANAVEEPLDLIRLSLDERIYVKMRNERELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEVYRTTKRTVPMLFVRGDGVILVSPPIRG 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. TrEMBL
Match: B7PD40 (U6 snRNA-associated Sm-like protein LSm3 OS=Ixodes scapularis OX=6945 GN=8028134 PE=3 SV=1)

HSP 1 Score: 122.479 bits (306), Expect = 2.203e-33
Identity = 68/99 (68.69%), Postives = 88/99 (88.89%), Query Frame = 2 
Query:   89 AGDNLHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLKG 385
            A D   A  + ++EPLDL+RLSL+E+IYVKM+N+RELRG+L+A+D HLNM L DVEET+T++EID+ET EE++K+TKRSIPMLFVRGDGVILVSPP++G
Sbjct:    2 ADDGEQAPTTAVEEPLDLVRLSLDEKIYVKMRNERELRGRLHAYDQHLNMILGDVEETVTSVEIDEETYEEVYKSTKRSIPMLFVRGDGVILVSPPVRG 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Cavefish
Match: lsm3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated [Source:NCBI gene;Acc:103043938])

HSP 1 Score: 117.472 bits (293), Expect = 7.595e-35
Identity = 67/90 (74.44%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EEI+K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTVEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Yeast
Match: LSM3 (Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA; protein increases in abundance and relocalizes from nucleus to cytoplasmic foci upon DNA replication stress [Source:SGD;Acc:S000006434])

HSP 1 Score: 67.3958 bits (163), Expect = 3.565e-16
Identity = 37/85 (43.53%), Postives = 55/85 (64.71%), Query Frame = 2 
Query:  122 IDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPP 376
            ++ PLDL++L+L+ER+Y+K++  R L G L AFDSH N+ LSD  ETI  L  ++         ++R   M+F+RGD V L+S P
Sbjct:    1 METPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEEL------SESERRCEMVFIRGDTVTLISTP 79
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Nematostella
Match: EDO46880 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RNM2])

HSP 1 Score: 114.775 bits (286), Expect = 3.199e-34
Identity = 66/89 (74.16%), Postives = 83/89 (93.26%), Query Frame = 2 
Query:  116 SVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
            + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM LSDVEETITT+EID+ET EE+ +T KR++PM+F+RGDGVILVSPPL+
Sbjct:   11 NTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILSDVEETITTVEIDEETFEELFRTNKRTVPMMFIRGDGVILVSPPLR 99
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Nematostella
Match: EDO33263 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SSP8])

HSP 1 Score: 42.3578 bits (98), Expect = 6.794e-6
Identity = 28/82 (34.15%), Postives = 46/82 (56.10%), Query Frame = 2 
Query:  131 PLDLIRLSL--NERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTK-RSIPMLFVRGDGVILV 367
            PL ++  S+  N ++ +  +N+R+L  ++ AFD H NM L +V+E  T      +  ++     K R I  +F+RGD VILV
Sbjct:   29 PLSVLTQSVKNNTQVLINCRNNRKLLARVKAFDRHCNMVLENVKEMWTETPKSGKGKKKAKPVNKDRYIAKMFLRGDSVILV 110
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Medaka
Match: LSM3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated [Source:NCBI gene;Acc:101175071])

HSP 1 Score: 116.701 bits (291), Expect = 1.317e-34
Identity = 66/90 (73.33%), Postives = 84/90 (93.33%), Query Frame = 2 
Query:  113 ASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLK 382
             + ++EPLDLIRLSL+ERIYVKM+NDRELRG+L+A+D HLNM L DVEET+TT+EID+ET EE++K+TKR+IPMLFVRGDGV+LV+PPL+
Sbjct:   11 TNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTVEIDEETYEELYKSTKRNIPMLFVRGDGVVLVAPPLR 100
[Close]
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Planmine SMEST
Match: SMESG000072617.1 (SMESG000072617.1)

HSP 1 Score: 176.792 bits (447), Expect = 2.776e-58
Identity = 106/106 (100.00%), Postives = 106/106 (100.00%), Query Frame = 2 
Query:   77 MDSSAGDNLHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVXXXXXXXXXXXXXXXXXHKTTKRSIPMLFVRGDGVILVSPPLKGQPN 394
            MDSSAGDNLHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVEETITTLEIDDETLEEIHKTTKRSIPMLFVRGDGVILVSPPLKGQPN
Sbjct:    1 MDSSAGDNLHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDSHLNMALSDVEETITTLEIDDETLEEIHKTTKRSIPMLFVRGDGVILVSPPLKGQPN 106
The following BLAST results are available for this feature:
BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 1
Match NameE-valueIdentityDescription
LSM31.913e-3474.44LSM3 homolog, U6 small nuclear RNA and mRNA degrad... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 3
Match NameE-valueIdentityDescription
lsm-35.810e-3470.33U6 snRNA-associated Sm-like protein LSm3 [Source:... [more]
lsm-55.977e-848.78U6 snRNA-associated Sm-like protein LSm5 [Source:... [more]
lsm-55.977e-848.78U6 snRNA-associated Sm-like protein LSm5 [Source:... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 5
Match NameE-valueIdentityDescription
LSm33.777e-3373.56gene:FBgn0051184 transcript:FBtr0084505[more]
LSm33.777e-3373.56gene:FBgn0051184 transcript:FBtr0300648[more]
CG66107.186e-646.34gene:FBgn0035675 transcript:FBtr0332059[more]
CG66107.186e-646.34gene:FBgn0035675 transcript:FBtr0332060[more]
CG66107.186e-646.34gene:FBgn0035675 transcript:FBtr0077048[more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
lsm39.060e-3574.44LSM3 homolog, U6 small nuclear RNA and mRNA degrad... [more]
lsm52.480e-646.34LSM5 homolog, U6 small nuclear RNA and mRNA degrad... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 2
Match NameE-valueIdentityDescription
ube2w1.678e-3471.28ubiquitin conjugating enzyme E2W (putative) [Sourc... [more]
ube2w1.753e-3474.44ubiquitin conjugating enzyme E2W (putative) [Sourc... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Lsm31.313e-3474.44LSM3 homolog, U6 small nuclear RNA and mRNA degrad... [more]
Lsm31.313e-3474.44LSM3 homolog, U6 small nuclear RNA and mRNA degrad... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 5
Match NameE-valueIdentityDescription
sp|P62311|LSM3_MOUSE9.184e-3474.44U6 snRNA-associated Sm-like protein LSm3 OS=Mus mu... [more]
sp|P62310|LSM3_HUMAN9.184e-3474.44U6 snRNA-associated Sm-like protein LSm3 OS=Homo s... [more]
sp|Q32PE9|LSM3_BOVIN9.184e-3474.44U6 snRNA-associated Sm-like protein LSm3 OS=Bos ta... [more]
sp|Q9LMN4|LSM3A_ARATH1.670e-3173.68Sm-like protein LSM3A OS=Arabidopsis thaliana OX=3... [more]
sp|Q9C6K5|LSM3B_ARATH4.395e-3175.82Sm-like protein LSM3B OS=Arabidopsis thaliana OX=3... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A087U5A37.130e-3668.52U6 snRNA-associated Sm-like protein LSm3 (Fragment... [more]
A0A4Y2JVI36.896e-3570.71U6 snRNA-associated Sm-like protein LSm3 OS=Araneu... [more]
C3YAV81.038e-3378.02U6 snRNA-associated Sm-like protein LSm3 (Fragment... [more]
A0A2L2YH151.622e-3370.10U6 snRNA-associated Sm-like protein LSm3 OS=Parast... [more]
B7PD402.203e-3368.69U6 snRNA-associated Sm-like protein LSm3 OS=Ixodes... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
lsm37.595e-3574.44LSM3 homolog, U6 small nuclear RNA and mRNA degrad... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 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 U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
LSM33.565e-1643.53Lsm (Like Sm) protein; part of heteroheptameric co... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 2
Match NameE-valueIdentityDescription
EDO468803.199e-3474.16Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO332636.794e-634.15Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
LSM31.317e-3473.33LSM3 homolog, U6 small nuclear RNA and mRNA degrad... [more]
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BLAST of U6 snRNA-associated Sm-like protein LSm3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000072617.12.776e-58100.00SMESG000072617.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020216 ID=SMED30020216|Name=U6 snRNA-associated Sm-like protein LSm3|organism=Schmidtea mediterranea sexual|type=transcript|length=433bp
CTCAATTATAAATTTGATTCTAATATTTTTATTTTTGGTTTTGGTTTTGT
TTAAATAATATATATTTTATAAAAAAATGGATTCTTCTGCTGGGGATAAT
TTACATGCCGATGCTTCTGTAATCGACGAACCTCTAGATCTAATCAGACT
CAGCTTAAATGAAAGAATTTATGTAAAAATGAAAAATGACAGAGAGTTAA
GAGGCAAATTGAATGCTTTTGACTCTCATTTAAACATGGCTCTCAGTGAT
GTTGAAGAAACTATAACTACTTTGGAAATTGACGATGAAACTCTCGAGGA
AATTCACAAAACAACAAAAAGATCTATTCCTATGCTATTCGTTCGTGGTG
ATGGCGTCATTCTTGTTAGTCCGCCTTTGAAAGGGCAACCTAACTAATTT
TGAAAATAAAAATGGCTTTTTATCTTTTCTAAA
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protein sequence of SMED30020216-orf-1

>SMED30020216-orf-1 ID=SMED30020216-orf-1|Name=SMED30020216-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp
MDSSAGDNLHADASVIDEPLDLIRLSLNERIYVKMKNDRELRGKLNAFDS
HLNMALSDVEETITTLEIDDETLEEIHKTTKRSIPMLFVRGDGVILVSPP
LKGQPN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003723RNA binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005681spliceosomal complex
GO:0005688U6 snRNP
GO:0046540U4/U6 x U5 tri-snRNP complex
Vocabulary: biological process
TermDefinition
GO:0006397mRNA processing
GO:0008380RNA splicing
GO:0000398mRNA splicing, via spliceosome
GO:0000956nuclear-transcribed mRNA catabolic process
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0003001lateral region of the whole animal
Vocabulary: INTERPRO
TermDefinition
IPR040002Sm-like_LSM3
IPR034105Lsm3
IPR001163LSM_dom_euk/arc
IPR010920LSM_dom_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001163LSM domain, eukaryotic/archaea-typeSMARTSM00651Sm3coord: 21..99
e-value: 3.6E-20
score: 83.0
IPR001163LSM domain, eukaryotic/archaea-typePFAMPF01423LSMcoord: 23..99
e-value: 4.2E-20
score: 71.2
NoneNo IPR availableGENE3DG3DSA:2.30.30.100coord: 11..101
e-value: 2.4E-28
score: 99.8
NoneNo IPR availablePANTHERPTHR13110:SF8U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3coord: 13..102
IPR040002U6 snRNA-associated Sm-like protein Lsm3PANTHERPTHR13110U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3coord: 13..102
IPR034105Sm-like protein Lsm3CDDcd01730LSm3coord: 18..99
e-value: 1.83069E-52
score: 157.387
IPR010920LSM domain superfamilySUPERFAMILYSSF50182Sm-like ribonucleoproteinscoord: 18..100