Lamc3 (laminin subunit gamma 3) - Rat Genome Database

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Gene: Lamc3 (laminin subunit gamma 3) Rattus norvegicus
Analyze
Symbol: Lamc3
Name: laminin subunit gamma 3
RGD ID: 1309399
Description: Predicted to act upstream of or within several processes, including astrocyte development; retina development in camera-type eye; and visual perception. Predicted to be located in basement membrane. Orthologous to human LAMC3 (laminin subunit gamma 3); PARTICIPATES IN cell-extracellular matrix signaling pathway; Entamoebiasis pathway; small cell lung carcinoma pathway; INTERACTS WITH 1,3-dinitrobenzene; 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: laminin gamma 3; laminin subunit gamma-3; laminin subunit gamma-3-like; LOC102554659; LOC311862
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2315,165,220 - 15,226,697 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl315,165,220 - 15,226,697 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx318,238,584 - 18,299,655 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0326,823,588 - 26,884,640 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0325,070,910 - 25,131,824 (+)NCBIRnor_WKY
Rnor_6.039,265,407 - 9,327,107 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl39,267,122 - 9,326,993 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0314,625,724 - 14,686,842 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4310,989,308 - 11,050,417 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1310,885,526 - 10,945,074 (+)NCBI
Celera39,912,895 - 9,973,971 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16608848   PMID:18757743   PMID:19907020  


Genomics

Comparative Map Data
Lamc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2315,165,220 - 15,226,697 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl315,165,220 - 15,226,697 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx318,238,584 - 18,299,655 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0326,823,588 - 26,884,640 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0325,070,910 - 25,131,824 (+)NCBIRnor_WKY
Rnor_6.039,265,407 - 9,327,107 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl39,267,122 - 9,326,993 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0314,625,724 - 14,686,842 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4310,989,308 - 11,050,417 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1310,885,526 - 10,945,074 (+)NCBI
Celera39,912,895 - 9,973,971 (+)NCBICelera
Cytogenetic Map3p12NCBI
LAMC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389131,009,174 - 131,094,473 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl9131,009,174 - 131,094,473 (+)EnsemblGRCh38hg38GRCh38
GRCh379133,884,561 - 133,969,860 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369132,874,325 - 132,958,267 (+)NCBINCBI36Build 36hg18NCBI36
Build 349130,914,057 - 130,997,000NCBI
Celera9104,423,595 - 104,507,538 (+)NCBICelera
Cytogenetic Map9q34.12NCBI
HuRef9103,375,168 - 103,459,104 (+)NCBIHuRef
CHM1_19134,033,642 - 134,117,628 (+)NCBICHM1_1
T2T-CHM13v2.09143,217,399 - 143,302,700 (+)NCBIT2T-CHM13v2.0
Lamc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39231,777,293 - 31,839,095 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl231,777,303 - 31,836,551 (+)EnsemblGRCm39 Ensembl
GRCm38231,887,281 - 31,949,083 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl231,887,291 - 31,946,539 (+)EnsemblGRCm38mm10GRCm38
MGSCv37231,742,801 - 31,802,055 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36231,709,290 - 31,768,544 (+)NCBIMGSCv36mm8
Celera231,589,981 - 31,649,498 (+)NCBICelera
Cytogenetic Map2BNCBI
Lamc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955513881,092 - 934,458 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955513872,301 - 934,234 (+)NCBIChiLan1.0ChiLan1.0
LAMC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19130,777,182 - 130,861,292 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9130,777,182 - 130,861,292 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09102,131,594 - 102,213,829 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LAMC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1952,970,313 - 53,028,817 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl952,970,306 - 53,028,821 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha952,170,894 - 52,229,552 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0953,871,275 - 53,929,956 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl953,871,276 - 53,930,688 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1952,648,766 - 52,707,409 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0952,969,239 - 53,027,948 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0953,062,336 - 53,121,064 (-)NCBIUU_Cfam_GSD_1.0
Lamc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947198,142,146 - 198,190,116 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493648717,910,673 - 17,958,641 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LAMC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1271,004,433 - 271,071,223 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11271,004,423 - 271,071,223 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21305,075,031 - 305,098,322 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LAMC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1127,048,396 - 7,134,405 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660798,364,706 - 8,454,343 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lamc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247604,760,351 - 4,807,720 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247604,759,680 - 4,807,720 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lamc3
442 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:60
Count of miRNA genes:47
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000013172
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat

Markers in Region
RH132596  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2315,212,239 - 15,212,420 (-)MAPPERmRatBN7.2
Rnor_6.039,279,813 - 9,279,993NCBIRnor6.0
Rnor_5.0314,640,130 - 14,640,310UniSTSRnor5.0
RGSC_v3.4311,035,962 - 11,036,142UniSTSRGSC3.4
Celera39,959,536 - 9,959,716UniSTS
RH 3.4 Map359.8UniSTS
Cytogenetic Map3p12-p11UniSTS
RH133133  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2315,225,164 - 15,226,030 (-)MAPPERmRatBN7.2
Rnor_6.039,266,074 - 9,266,939NCBIRnor6.0
Rnor_5.0314,626,391 - 14,627,256UniSTSRnor5.0
RGSC_v3.4311,048,885 - 11,049,750UniSTSRGSC3.4
Celera39,972,439 - 9,973,304UniSTS
RH 3.4 Map360.0UniSTS
Cytogenetic Map3p12-p11UniSTS
RH144007  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2315,227,005 - 15,227,123 (-)MAPPERmRatBN7.2
Rnor_6.039,264,981 - 9,265,098NCBIRnor6.0
Rnor_5.0314,625,298 - 14,625,415UniSTSRnor5.0
RGSC_v3.4311,050,726 - 11,050,843UniSTSRGSC3.4
Celera39,974,280 - 9,974,397UniSTS
Cytogenetic Map3p12-p11UniSTS


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 appendage
High
Medium 2 15 16 3
Low 20 10 2 6 8 72 20 25 8 6
Below cutoff 3 23 21 15 16 15 2 3 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078431
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl39,937,945 - 9,959,655 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090137   ⟹   ENSRNOP00000071272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl315,165,220 - 15,226,697 (+)Ensembl
Rnor_6.0 Ensembl39,267,122 - 9,326,993 (-)Ensembl
RefSeq Acc Id: NM_001107830   ⟹   NP_001101300
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2315,165,220 - 15,226,697 (+)NCBI
Rnor_6.039,265,407 - 9,327,047 (-)NCBI
Rnor_5.0314,625,724 - 14,686,842 (-)NCBI
RGSC_v3.4310,989,308 - 11,050,417 (+)RGD
Celera39,912,895 - 9,973,971 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101300 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93262 (Get FASTA)   NCBI Sequence Viewer  
  EDL93263 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101300   ⟸   NM_001107830
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000071272   ⟸   ENSRNOT00000090137
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K023-F1-model_v2 AlphaFold A0A0G2K023 1-1582 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:1309399 AgrOrtholog
BioCyc Gene G2FUF-50167 BioCyc
Ensembl Genes ENSRNOG00000056129 Ensembl
  ENSRNOG00000059507 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071272 ENTREZGENE
  ENSRNOP00000071272.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000090137 ENTREZGENE
  ENSRNOT00000090137.2 UniProtKB/TrEMBL
InterPro EGF-like_dom UniProtKB/TrEMBL
  EGF_laminin UniProtKB/TrEMBL
  Laminin_B_type_IV UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
NCBI Gene 311862 ENTREZGENE
Pfam Laminin_B UniProtKB/TrEMBL
  Laminin_EGF UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
PhenoGen Lamc3 PhenoGen
PROSITE EGF_LAM_1 UniProtKB/TrEMBL
  EGF_LAM_2 UniProtKB/TrEMBL
  LAMININ_IVA UniProtKB/TrEMBL
  LAMININ_NTER UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_Lam UniProtKB/TrEMBL
  LamB UniProtKB/TrEMBL
  LamNT UniProtKB/TrEMBL
UniProt A0A0G2K023_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Lamc3  laminin subunit gamma 3  LOC102554659  laminin subunit gamma-3-like  Data Merged 737654 PROVISIONAL
2015-12-02 Lamc3  laminin subunit gamma 3  Lamc3  laminin gamma 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-17 LOC102554659  laminin subunit gamma-3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Lamc3  laminin gamma 3   Lamc3_predicted  laminin gamma 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lamc3_predicted  laminin gamma 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED