Lsm14b (LSM family member 14B) - Rat Genome Database

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Gene: Lsm14b (LSM family member 14B) Rattus norvegicus
Analyze
Symbol: Lsm14b
Name: LSM family member 14B
RGD ID: 1563798
Description: Predicted to enable mRNA binding activity. Predicted to be involved in several processes, including maternal mRNA clearance; meiotic cell cycle process involved in oocyte maturation; and ovarian follicle development. Predicted to be located in cytoplasmic ribonucleoprotein granule. Predicted to be part of ribonucleoprotein complex. Orthologous to human LSM14B (LSM family member 14B); INTERACTS WITH amphetamine; Brodifacoum; poly(I:C).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC499950; LSM14 homolog B; LSM14B, SCD6 homolog B; LSM14B, SCD6 homolog B (S. cerevisiae); RGD1563798; similar to BC040823 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83187,503,251 - 187,514,041 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3187,503,045 - 187,512,473 (+)EnsemblGRCr8
mRatBN7.23167,125,633 - 167,136,417 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3167,125,628 - 167,136,432 (+)EnsemblmRatBN7.2
Rnor_6.03175,408,433 - 175,419,180 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3175,408,629 - 175,417,610 (+)Ensemblrn6Rnor6.0
Rnor_5.03181,699,503 - 181,710,240 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera3165,443,306 - 165,453,870 (-)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:22681889  


Genomics

Comparative Map Data
Lsm14b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83187,503,251 - 187,514,041 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3187,503,045 - 187,512,473 (+)EnsemblGRCr8
mRatBN7.23167,125,633 - 167,136,417 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3167,125,628 - 167,136,432 (+)EnsemblmRatBN7.2
Rnor_6.03175,408,433 - 175,419,180 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3175,408,629 - 175,417,610 (+)Ensemblrn6Rnor6.0
Rnor_5.03181,699,503 - 181,710,240 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera3165,443,306 - 165,453,870 (-)NCBICelera
Cytogenetic Map3q43NCBI
LSM14B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382062,122,475 - 62,135,374 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2062,122,444 - 62,136,728 (+)Ensemblhg38GRCh38
GRCh372060,697,531 - 60,710,430 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362060,130,912 - 60,143,829 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342060,131,587 - 60,142,908NCBI
Celera2057,432,693 - 57,445,609 (+)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2057,474,993 - 57,487,913 (+)NCBIHuRef
CHM1_12060,598,581 - 60,611,498 (+)NCBICHM1_1
T2T-CHM13v2.02063,913,343 - 63,926,242 (+)NCBIT2T-CHM13v2.0
Lsm14b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392179,666,770 - 179,677,254 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2179,666,780 - 179,677,258 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm382180,024,900 - 180,035,466 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2180,024,987 - 180,035,465 (+)Ensemblmm10GRCm38
MGSCv372179,759,692 - 179,770,166 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362179,955,806 - 179,964,064 (+)NCBIMGSCv36mm8
Celera2184,109,492 - 184,120,048 (+)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2102.54NCBI
Lsm14b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555281,888,946 - 1,898,833 (-)Ensembl
ChiLan1.0NW_0049555281,889,016 - 1,901,051 (-)NCBIChiLan1.0ChiLan1.0
LSM14B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22167,903,806 - 67,916,769 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12067,896,936 - 67,909,889 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02058,488,140 - 58,501,094 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12059,808,993 - 59,821,192 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2059,806,927 - 59,819,284 (+)EnsemblpanPan2panpan1.1
LSM14B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12446,170,214 - 46,180,430 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2446,169,790 - 46,179,532 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2445,406,314 - 45,417,690 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02447,025,777 - 47,037,158 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2447,024,979 - 47,036,260 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12446,127,386 - 46,138,751 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02446,250,333 - 46,261,685 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02447,004,515 - 47,015,933 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Lsm14b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640194,345,322 - 194,354,281 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365149,798,912 - 9,807,909 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365149,798,966 - 9,807,924 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM14B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1761,553,971 - 61,564,431 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11761,553,953 - 61,566,504 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21769,084,357 - 69,090,568 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSM14B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.122,102,416 - 2,115,298 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl22,104,281 - 2,115,142 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605050,052,308 - 50,065,206 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsm14b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474127,998,581 - 28,010,543 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474127,998,800 - 28,010,548 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Lsm14b
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v15157,112,186 - 157,122,929 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:170
Count of miRNA genes:56
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000011856, ENSRNOT00000051922, ENSRNOT00000055058
Prediction methods:Miranda, Rnahybrid, Targetscan
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3152055202189428310Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3142898802187898802Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)3145335553189428310Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3151075912189428310Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161492708189428310Rat
1582256Insul9Insulin level QTL 94.40.0016blood insulin amount (VT:0001560)absolute change in serum insulin level (CMO:0002038)3155759447189428310Rat
1582248Insul7Insulin level QTL 73.90.0041blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3151075912189428310Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3181611379189428310Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3166376089189428310Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3151075912189428310Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3144575244189428310Rat
1582213Insul6Insulin level QTL 63.70.0009blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3166376089189428310Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000081344   ⟹   ENSRNOP00000071227
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3187,503,045 - 187,512,473 (+)Ensembl
mRatBN7.2 Ensembl3167,125,628 - 167,136,432 (+)Ensembl
Rnor_6.0 Ensembl3175,408,629 - 175,417,610 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000108127   ⟹   ENSRNOP00000076798
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3187,503,116 - 187,512,473 (+)Ensembl
mRatBN7.2 Ensembl3167,125,628 - 167,136,432 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000117745   ⟹   ENSRNOP00000086105
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3187,503,128 - 187,512,473 (+)Ensembl
mRatBN7.2 Ensembl3167,125,628 - 167,136,432 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000119096   ⟹   ENSRNOP00000079430
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3187,503,078 - 187,512,473 (+)Ensembl
mRatBN7.2 Ensembl3167,125,628 - 167,136,432 (+)Ensembl
RefSeq Acc Id: XM_002729258   ⟹   XP_002729304
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83187,503,251 - 187,514,041 (+)NCBI
mRatBN7.23167,125,635 - 167,136,417 (+)NCBI
Rnor_6.03175,408,437 - 175,419,180 (+)NCBI
Rnor_5.03181,699,503 - 181,710,240 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235827   ⟹   XP_006235889
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83187,503,263 - 187,514,041 (+)NCBI
mRatBN7.23167,125,635 - 167,136,417 (+)NCBI
Rnor_6.03175,408,437 - 175,419,180 (+)NCBI
Rnor_5.03181,699,503 - 181,710,240 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235828   ⟹   XP_006235890
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83187,503,261 - 187,514,041 (+)NCBI
mRatBN7.23167,125,633 - 167,136,417 (+)NCBI
Rnor_6.03175,408,433 - 175,419,180 (+)NCBI
Rnor_5.03181,699,503 - 181,710,240 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039106756   ⟹   XP_038962684
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83187,503,264 - 187,514,041 (+)NCBI
mRatBN7.23167,125,635 - 167,136,417 (+)NCBI
RefSeq Acc Id: XM_039106757   ⟹   XP_038962685
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83187,505,055 - 187,514,041 (+)NCBI
mRatBN7.23167,127,411 - 167,136,417 (+)NCBI
RefSeq Acc Id: XM_063285136   ⟹   XP_063141206
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83187,503,251 - 187,514,041 (+)NCBI
RefSeq Acc Id: XP_002729304   ⟸   XM_002729258
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006235890   ⟸   XM_006235828
- Peptide Label: isoform X2
- UniProtKB: A0A0G2JZY0 (UniProtKB/TrEMBL),   A0A8I5Y947 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235889   ⟸   XM_006235827
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000071227   ⟸   ENSRNOT00000081344
RefSeq Acc Id: XP_038962684   ⟸   XM_039106756
- Peptide Label: isoform X5
- UniProtKB: A0A8I6A557 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038962685   ⟸   XM_039106757
- Peptide Label: isoform X6
- UniProtKB: A6KMD0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000086105   ⟸   ENSRNOT00000117745
Ensembl Acc Id: ENSRNOP00000079430   ⟸   ENSRNOT00000119096
Ensembl Acc Id: ENSRNOP00000076798   ⟸   ENSRNOT00000108127
RefSeq Acc Id: XP_063141206   ⟸   XM_063285136
- Peptide Label: isoform X4
- UniProtKB: A0A8I5ZN03 (UniProtKB/TrEMBL)
Protein Domains
DFDF   FFD box profile   Sm   TFG box profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JZY0-F1-model_v2 AlphaFold A0A0G2JZY0 1-424 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563798 AgrOrtholog
BioCyc Gene G2FUF-46374 BioCyc
Ensembl Genes ENSRNOG00000054557 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000081344 ENTREZGENE
  ENSRNOT00000081344.3 UniProtKB/TrEMBL
  ENSRNOT00000108127 ENTREZGENE
  ENSRNOT00000108127.2 UniProtKB/TrEMBL
  ENSRNOT00000117745 ENTREZGENE
  ENSRNOT00000117745.2 UniProtKB/TrEMBL
  ENSRNOT00000119096 ENTREZGENE
  ENSRNOT00000119096.2 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro DFDF UniProtKB/TrEMBL
  DFDF_motif UniProtKB/TrEMBL
  FFD_box UniProtKB/TrEMBL
  IPR047575 UniProtKB/TrEMBL
  Lsm14_N UniProtKB/TrEMBL
  LSM_dom UniProtKB/TrEMBL
  TFG_box UniProtKB/TrEMBL
KEGG Report rno:100362102 UniProtKB/TrEMBL
NCBI Gene Lsm14b ENTREZGENE
PANTHER PROTEIN LSM14 HOMOLOG B UniProtKB/TrEMBL
  SCD6 PROTEIN-RELATED UniProtKB/TrEMBL
Pfam DFDF UniProtKB/TrEMBL
  LSM14 UniProtKB/TrEMBL
PhenoGen Lsm14b PhenoGen
PROSITE DFDF UniProtKB/TrEMBL
  FFD UniProtKB/TrEMBL
  PS52002 UniProtKB/TrEMBL
  TFG UniProtKB/TrEMBL
RatGTEx ENSRNOG00000054557 RatGTEx
SMART FDF UniProtKB/TrEMBL
  LSM14 UniProtKB/TrEMBL
Superfamily-SCOP Sm_like_riboprot UniProtKB/TrEMBL
UniProt A0A0G2JZY0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5Y947 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZN03 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A557 ENTREZGENE, UniProtKB/TrEMBL
  A6KMC8 ENTREZGENE, UniProtKB/TrEMBL
  A6KMC9 ENTREZGENE, UniProtKB/TrEMBL
  A6KMD0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-01 Lsm14b  LSM family member 14B  Lsm14b  LSM14B, SCD6 homolog B (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-12 Lsm14b  LSM14B, SCD6 homolog B (S. cerevisiae)  RGD1563798  similar to BC040823 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-02 RGD1563798  similar to BC040823 protein  LOC100362102  LSM14 homolog B  Data merged from RGD:2318780 1643240 APPROVED
2010-05-05 LOC100362102  LSM14 homolog B      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 RGD1563798  similar to BC040823 protein   RGD1563798_predicted  similar to BC040823 protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563798_predicted  similar to BC040823 protein (predicted)  LOC499950  similar to BC040823 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499950  similar to BC040823 protein      Symbol and Name status set to provisional 70820 PROVISIONAL