LSM3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LSM3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated) Homo sapiens
Analyze
Symbol: LSM3
Name: LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated
RGD ID: 1314318
HGNC Page HGNC:17874
Description: Enables U6 snRNA 3'-end binding activity. Acts upstream of or within mRNA splicing, via spliceosome. Located in nucleus. Part of Lsm2-8 complex; U4/U6 x U5 tri-snRNP complex; and spliceosomal complex.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LSM3 homolog, U6 small nuclear RNA associated; LSM3 U6 small nuclear RNA and mRNA degradation associated; SMX4; U6 snRNA-associated Sm-like protein LSm3; USS2; YLR438C
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC100303749   LSM3P1   LSM3P2   LSM3P3   LSM3P4   LSM3P5  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38314,178,817 - 14,201,122 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl314,178,817 - 14,201,122 (+)EnsemblGRCh38hg38GRCh38
GRCh37314,220,317 - 14,242,622 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36314,195,341 - 14,214,842 (+)NCBINCBI36Build 36hg18NCBI36
Build 34314,195,340 - 14,214,840NCBI
Celera314,158,457 - 14,178,097 (+)NCBICelera
Cytogenetic Map3p25.1NCBI
HuRef314,155,207 - 14,174,845 (+)NCBIHuRef
CHM1_1314,170,613 - 14,190,252 (+)NCBICHM1_1
T2T-CHM13v2.0314,180,681 - 14,202,982 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
mRNA processing  (IEA,TAS)
mRNA splicing, via spliceosome  (IBA,IC,IDA,IEA,NAS)
P-body assembly  (IBA,IEA)
RNA splicing  (IEA)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. Chen YI, etal., Nucleic Acids Res. 2007;35(12):3928-44. Epub 2007 May 30.
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, etal., Cell. 2009 Feb 20;136(4):701-18. doi: 10.1016/j.cell.2009.02.009.
Additional References at PubMed
PMID:10369684   PMID:10523320   PMID:10851237   PMID:11920408   PMID:11991638   PMID:12477932   PMID:12515382   PMID:14667819   PMID:15231747   PMID:15489334   PMID:16169070   PMID:16189514  
PMID:16344560   PMID:17643375   PMID:18187620   PMID:19060904   PMID:19628699   PMID:21516116   PMID:21873635   PMID:21988832   PMID:22365833   PMID:22623428   PMID:22658674   PMID:22681889  
PMID:22939629   PMID:23443559   PMID:23463506   PMID:23667531   PMID:23986595   PMID:25277244   PMID:25416956   PMID:25544563   PMID:26264872   PMID:26344197   PMID:26496610   PMID:26725010  
PMID:26777405   PMID:26871637   PMID:26912367   PMID:27107012   PMID:27247266   PMID:28276505   PMID:28302793   PMID:28514442   PMID:28781166   PMID:28878014   PMID:29229926   PMID:29298432  
PMID:29395067   PMID:29509190   PMID:29510985   PMID:29656893   PMID:29845934   PMID:29997244   PMID:30209976   PMID:30217970   PMID:30804502   PMID:30975767   PMID:31467278   PMID:31527615  
PMID:32296183   PMID:32393512   PMID:32807901   PMID:32814053   PMID:33060197   PMID:33306668   PMID:33729478   PMID:33961781   PMID:34315543   PMID:34373451   PMID:34578187   PMID:35271311  
PMID:35780119   PMID:35906200   PMID:35944360  


Genomics

Comparative Map Data
LSM3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38314,178,817 - 14,201,122 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl314,178,817 - 14,201,122 (+)EnsemblGRCh38hg38GRCh38
GRCh37314,220,317 - 14,242,622 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36314,195,341 - 14,214,842 (+)NCBINCBI36Build 36hg18NCBI36
Build 34314,195,340 - 14,214,840NCBI
Celera314,158,457 - 14,178,097 (+)NCBICelera
Cytogenetic Map3p25.1NCBI
HuRef314,155,207 - 14,174,845 (+)NCBIHuRef
CHM1_1314,170,613 - 14,190,252 (+)NCBICHM1_1
T2T-CHM13v2.0314,180,681 - 14,202,982 (+)NCBIT2T-CHM13v2.0
Lsm3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39691,493,017 - 91,499,602 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl691,492,910 - 91,499,607 (+)EnsemblGRCm39 Ensembl
GRCm38691,516,035 - 91,522,620 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl691,515,928 - 91,522,625 (+)EnsemblGRCm38mm10GRCm38
MGSCv37691,466,029 - 91,472,614 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36691,481,539 - 91,488,124 (+)NCBIMGSCv36mm8
Celera693,409,326 - 93,415,908 (+)NCBICelera
Cytogenetic Map6D1NCBI
cM Map640.58NCBI
Lsm3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84125,578,185 - 125,584,429 (+)NCBIGRCr8
mRatBN7.24124,021,023 - 124,027,269 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4124,021,023 - 124,027,269 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4129,486,995 - 129,493,234 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04125,261,423 - 125,267,662 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04123,885,977 - 123,892,216 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04123,162,086 - 123,168,330 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4123,162,086 - 123,168,330 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04187,377,370 - 187,383,614 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44125,700,026 - 125,706,270 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14125,945,303 - 125,950,751 (+)NCBI
Celera4112,940,482 - 112,946,726 (+)NCBICelera
Cytogenetic Map4q34NCBI
Lsm3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542916,968,490 - 16,977,517 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542916,968,490 - 16,977,517 (+)NCBIChiLan1.0ChiLan1.0
LSM3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2214,156,329 - 14,225,193 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1314,161,091 - 14,229,955 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0314,097,035 - 14,165,942 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1314,437,497 - 14,456,727 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl314,437,497 - 14,456,726 (+)Ensemblpanpan1.1panPan2
LSM3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1204,328,930 - 4,342,731 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl204,329,038 - 4,342,859 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha204,366,825 - 4,380,622 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0204,350,284 - 4,364,092 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl204,350,392 - 4,364,220 (+)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl1411,266,194 - 11,266,502 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1204,069,769 - 4,083,561 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0204,392,051 - 4,405,847 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0204,356,498 - 4,370,300 (+)NCBIUU_Cfam_GSD_1.0
Lsm3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494218,762,653 - 18,769,706 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936602140,004 - 147,035 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936602140,014 - 147,000 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1370,336,907 - 70,348,651 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11370,339,685 - 70,349,802 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21377,737,428 - 77,746,329 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSM3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12250,121,674 - 50,141,071 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041116,354,553 - 116,374,034 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsm3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248721,428,073 - 1,438,563 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248721,428,885 - 1,438,633 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LSM3
7 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:52066-20280127)x3 copy number gain See cases [RCV000051690] Chr3:52066..20280127 [GRCh38]
Chr3:93749..20321619 [GRCh37]
Chr3:68749..20296623 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:52266-29248782)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|See cases [RCV000051718] Chr3:52266..29248782 [GRCh38]
Chr3:93949..29290273 [GRCh37]
Chr3:68949..29265277 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3 copy number gain See cases [RCV000051719] Chr3:63843..19510600 [GRCh38]
Chr3:105526..19552092 [GRCh37]
Chr3:80526..19527096 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p25.3-22.2(chr3:11463328-38919543)x3 copy number gain See cases [RCV000051720] Chr3:11463328..38919543 [GRCh38]
Chr3:11504802..38961034 [GRCh37]
Chr3:11479802..38936038 [NCBI36]
Chr3:3p25.3-22.2		 pathogenic
GRCh38/hg38 3p25.1(chr3:14053769-15011686)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053925]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053925]|See cases [RCV000053925] Chr3:14053769..15011686 [GRCh38]
Chr3:14095269..15053193 [GRCh37]
Chr3:14070270..15028197 [NCBI36]
Chr3:3p25.1		 uncertain significance
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3 copy number gain See cases [RCV000137941] Chr3:32241..20334387 [GRCh38]
Chr3:73914..20375879 [GRCh37]
Chr3:48914..20350883 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1		 pathogenic
GRCh38/hg38 3p26.1-25.1(chr3:7356110-14360442)x3 copy number gain See cases [RCV000143766] Chr3:7356110..14360442 [GRCh38]
Chr3:7397797..14401942 [GRCh37]
Chr3:7372797..14376946 [NCBI36]
Chr3:3p26.1-25.1		 pathogenic
GRCh37/hg19 3p26.3-24.2(chr3:61891-24432821)x3 copy number gain See cases [RCV000447247] Chr3:61891..24432821 [GRCh37]
Chr3:3p26.3-24.2		 pathogenic
GRCh37/hg19 3p26.3-22.2(chr3:61891-36710181)x3 copy number gain See cases [RCV000448528] Chr3:61891..36710181 [GRCh37]
Chr3:3p26.3-22.2		 pathogenic
GRCh37/hg19 3p26.3-22.3(chr3:61891-33958201)x3 copy number gain See cases [RCV000510429] Chr3:61891..33958201 [GRCh37]
Chr3:3p26.3-22.3		 pathogenic
GRCh37/hg19 3p26.3-22.2(chr3:61891-37459464)x3 copy number gain See cases [RCV000511463] Chr3:61891..37459464 [GRCh37]
Chr3:3p26.3-22.2		 pathogenic
GRCh37/hg19 3p25.1-24.3(chr3:13720222-17808236)x1 copy number loss See cases [RCV000511037] Chr3:13720222..17808236 [GRCh37]
Chr3:3p25.1-24.3		 likely pathogenic
NM_014463.3(LSM3):c.20A>T (p.Gln7Leu) single nucleotide variant Inborn genetic diseases [RCV003247927] Chr3:14178880 [GRCh38]
Chr3:14220380 [GRCh37]
Chr3:3p25.1		 uncertain significance
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-24.3(chr3:1897972-19519085)x3 copy number gain not provided [RCV000682215] Chr3:1897972..19519085 [GRCh37]
Chr3:3p26.3-24.3		 pathogenic
GRCh37/hg19 3p26.1-24.3(chr3:5173870-16760262)x3 copy number gain not provided [RCV000682233] Chr3:5173870..16760262 [GRCh37]
Chr3:3p26.1-24.3		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p25.2-24.2(chr3:13276005-24295240)x3 copy number gain not provided [RCV000742260] Chr3:13276005..24295240 [GRCh37]
Chr3:3p25.2-24.2		 pathogenic
Single allele deletion 3p- syndrome [RCV002280352] Chr3:13371737..20095506 [GRCh38]
Chr3:3p25.1-24.3		 pathogenic
NM_014463.3(LSM3):c.36C>T (p.Asn12=) single nucleotide variant not provided [RCV000955311] Chr3:14181574 [GRCh38]
Chr3:14223074 [GRCh37]
Chr3:3p25.1		 benign
NM_014463.3(LSM3):c.21+136C>G single nucleotide variant not provided [RCV001698796] Chr3:14179017 [GRCh38]
Chr3:14220517 [GRCh37]
Chr3:3p25.1		 benign
NC_000003.12:g.(?_14170428)_(14178939_?)del deletion not provided [RCV001032357] Chr3:14211928..14220439 [GRCh37]
Chr3:3p25.1		 pathogenic
NM_014463.3(LSM3):c.21+58C>T single nucleotide variant not provided [RCV001516007] Chr3:14178939 [GRCh38]
Chr3:14220439 [GRCh37]
Chr3:3p25.1		 benign|likely benign
NC_000003.11:g.(?_14166684)_(14220439_?)del deletion not provided [RCV001384233] Chr3:14166684..14220439 [GRCh37]
Chr3:3p25.1		 pathogenic
NC_000003.11:g.(?_14206303)_(14220439_?)del deletion not provided [RCV001949510] Chr3:14206303..14220439 [GRCh37]
Chr3:3p25.1		 pathogenic
GRCh37/hg19 3p26.3-24.2(chr3:61891-24432821) copy number gain not specified [RCV002053299] Chr3:61891..24432821 [GRCh37]
Chr3:3p26.3-24.2		 pathogenic
GRCh37/hg19 3p26.3-22.2(chr3:61891-36710181) copy number gain not specified [RCV002053300] Chr3:61891..36710181 [GRCh37]
Chr3:3p26.3-22.2		 pathogenic
NC_000003.11:g.(?_14214357)_(14220439_?)del deletion not provided [RCV003113557] Chr3:14214357..14220439 [GRCh37]
Chr3:3p25.1		 pathogenic
GRCh37/hg19 3p25.1-24.2(chr3:13836340-25357427)x3 copy number gain See cases [RCV002287839] Chr3:13836340..25357427 [GRCh37]
Chr3:3p25.1-24.2		 pathogenic
NM_014463.3(LSM3):c.302T>C (p.Val101Ala) single nucleotide variant Inborn genetic diseases [RCV002897724] Chr3:14198109 [GRCh38]
Chr3:14239609 [GRCh37]
Chr3:3p25.1		 uncertain significance
NM_014463.3(LSM3):c.259G>C (p.Val87Leu) single nucleotide variant Inborn genetic diseases [RCV003342907] Chr3:14198066 [GRCh38]
Chr3:14239566 [GRCh37]
Chr3:3p25.1		 uncertain significance
GRCh37/hg19 3p26.3-24.1(chr3:310747-28297447)x3 copy number gain not provided [RCV003484107] Chr3:310747..28297447 [GRCh37]
Chr3:3p26.3-24.1		 pathogenic
GRCh37/hg19 3p26.3-22.3(chr3:61891-33946644)x3 copy number gain not specified [RCV003986437] Chr3:61891..33946644 [GRCh37]
Chr3:3p26.3-22.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1686
Count of miRNA genes:796
Interacting mature miRNAs:918
Transcripts:ENST00000306024
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 2319 2002 1535 442 1183 304 4315 1983 2975 393 1439 1580 150 1191 2761 4
Low 113 960 188 180 743 160 40 210 733 25 9 28 20 13 27
Below cutoff 22 22

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000306024   ⟹   ENSP00000302160
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl314,178,817 - 14,201,122 (+)Ensembl
RefSeq Acc Id: NM_014463   ⟹   NP_055278
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38314,178,817 - 14,201,122 (+)NCBI
GRCh37314,220,228 - 14,239,869 (+)RGD
Build 36314,195,341 - 14,214,842 (+)NCBI Archive
Celera314,158,457 - 14,178,097 (+)RGD
HuRef314,155,207 - 14,174,845 (+)ENTREZGENE
CHM1_1314,170,613 - 14,190,252 (+)NCBI
T2T-CHM13v2.0314,180,681 - 14,202,982 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_055278   ⟸   NM_014463
- UniProtKB: Q6IAH0 (UniProtKB/Swiss-Prot),   Q9Y4Z1 (UniProtKB/Swiss-Prot),   P62310 (UniProtKB/Swiss-Prot),   B2R5H5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000302160   ⟸   ENST00000306024
Protein Domains
Sm

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P62310-F1-model_v2 AlphaFold P62310 1-102 view protein structure

Promoters
RGD ID:6863700
Promoter ID:EPDNEW_H4997
Type:initiation region
Name:LSM3_1
Description:LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38314,178,856 - 14,178,916EPDNEW
RGD ID:6801268
Promoter ID:HG_KWN:43865
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   Lymphoblastoid
Transcripts:OTTHUMT00000252078
Position:
Human AssemblyChrPosition (strand)Source
Build 36314,194,116 - 14,195,347 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:17874 AgrOrtholog
COSMIC LSM3 COSMIC
Ensembl Genes ENSG00000170860 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000306024 ENTREZGENE
  ENST00000306024.4 UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.30.100 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000170860 GTEx
HGNC ID HGNC:17874 ENTREZGENE
Human Proteome Map LSM3 Human Proteome Map
InterPro IPR047575 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lsm3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LSM_dom_euk/arc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LSM_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sm-like_LSM3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:27258 UniProtKB/Swiss-Prot
NCBI Gene 27258 ENTREZGENE
OMIM 607283 OMIM
PANTHER PTHR13110 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LSM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134881991 PharmGKB
PROSITE PS52002 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00651 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50182 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B2R5H5 ENTREZGENE, UniProtKB/TrEMBL
  LSM3_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q6IAH0 ENTREZGENE
  Q9Y4Z1 ENTREZGENE
UniProt Secondary Q6IAH0 UniProtKB/Swiss-Prot
  Q9Y4Z1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-07 LSM3  LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated  LSM3  LSM3 U6 small nuclear RNA and mRNA degradation associated  Symbol and/or name change 5135510 APPROVED
2015-06-30 LSM3  LSM3 U6 small nuclear RNA and mRNA degradation associated  LSM3  LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED