Malrd1 (MAM and LDL receptor class A domain containing 1) - Rat Genome Database

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Gene: Malrd1 (MAM and LDL receptor class A domain containing 1) Rattus norvegicus
Analyze
Symbol: Malrd1
Name: MAM and LDL receptor class A domain containing 1
RGD ID: 2320868
Description: Predicted to act upstream of or within cholesterol homeostasis and negative regulation of bile acid biosynthetic process. Predicted to be located in Golgi apparatus. Orthologous to human MALRD1 (MAM and LDL receptor class A domain containing 1); INTERACTS WITH bisphenol A; glyphosate; lidocaine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Diet1; hypothetical protein LOC100361092; LOC100361092; LOC100912561; LOC291332; LOC502147; MAM and LDL-receptor class A domain-containing protein 1; MAM and LDL-receptor class A domain-containing protein C10orf112-like; RGD1559888; RGD1563652; similar to apical early endosomal glycoprotein; similar to novel MAM domain containing protein; uncharacterized protein LOC100361092
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81783,327,372 - 84,039,558 (+)NCBIGRCr8
mRatBN7.21778,418,819 - 79,131,015 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1778,418,819 - 79,131,016 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1781,870,320 - 82,594,821 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01785,705,782 - 86,430,283 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01779,750,382 - 80,457,370 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01782,430,836 - 83,156,696 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1782,430,836 - 82,953,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01784,168,046 - 84,892,095 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41789,607,379 - 89,780,519 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1777,741,837 - 78,442,699 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO)
Golgi apparatus  (IBA,ISO)
membrane  (IEA)

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:10744778   PMID:23747249  


Genomics

Comparative Map Data
Malrd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81783,327,372 - 84,039,558 (+)NCBIGRCr8
mRatBN7.21778,418,819 - 79,131,015 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1778,418,819 - 79,131,016 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1781,870,320 - 82,594,821 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01785,705,782 - 86,430,283 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01779,750,382 - 80,457,370 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01782,430,836 - 83,156,696 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1782,430,836 - 82,953,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01784,168,046 - 84,892,095 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41789,607,379 - 89,780,519 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1777,741,837 - 78,442,699 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
MALRD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381019,046,927 - 19,734,478 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1019,048,801 - 19,790,401 (+)EnsemblGRCh38hg38GRCh38
GRCh371019,337,730 - 20,023,407 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361019,585,919 - 19,820,636 (+)NCBINCBI36Build 36hg18NCBI36
Celera1019,077,832 - 19,709,527 (+)NCBICelera
Cytogenetic Map10p12.31NCBI
HuRef1018,999,191 - 19,687,579 (+)NCBIHuRef
CHM1_11019,337,662 - 20,023,348 (+)NCBICHM1_1
T2T-CHM13v2.01019,065,969 - 19,752,737 (+)NCBIT2T-CHM13v2.0
Malrd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39215,531,290 - 16,260,368 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl215,531,290 - 16,260,366 (+)EnsemblGRCm39 Ensembl
GRCm38215,526,479 - 16,255,557 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl215,526,479 - 16,255,555 (+)EnsemblGRCm38mm10GRCm38
Celera215,429,298 - 16,159,403 (+)NCBICelera
Cytogenetic Map2A2NCBI
cM Map25.8NCBI
Malrd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554298,634,944 - 9,235,688 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554298,634,713 - 9,235,666 (-)NCBIChiLan1.0ChiLan1.0
MALRD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2831,765,645 - 32,407,891 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11031,770,966 - 32,413,213 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01019,461,865 - 19,886,155 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11019,573,166 - 20,185,006 (+)NCBIpanpan1.1PanPan1.1panPan2
LOC608668
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1213,151,316 - 13,904,122 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2519,960,641 - 20,225,118 (-)NCBIDog10K_Boxer_Tasha
Malrd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934419,434,202 - 20,034,532 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365207,926,280 - 8,526,149 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365207,926,273 - 8,504,777 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MALRD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1054,785,314 - 55,380,957 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11054,782,806 - 55,381,043 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21060,986,398 - 61,270,301 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MALRD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1918,964,693 - 19,640,356 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605124,657,503 - 25,353,844 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Malrd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247968,384,081 - 9,074,878 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247968,383,901 - 9,074,860 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Malrd1
6566 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
1358295Aocep1Aortic cell protein QTL 16.17e-07thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)177177462182479847Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176570358081153923Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175349882882479847Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176261951686533673Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175090909986022412Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)174992015486533673Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)177100332581153923Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)176078142686533673Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)175724684382046127Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175004027186533673Rat


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 nervous system renal system reproductive system respiratory system
High
Medium 15
Low 6 6 3
Below cutoff 8 21 10 3 10 178 55 75 9

Sequence


Ensembl Acc Id: ENSRNOT00000083164   ⟹   ENSRNOP00000074998
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1778,418,819 - 79,131,016 (+)Ensembl
Rnor_6.0 Ensembl1782,430,836 - 82,953,864 (+)Ensembl
RefSeq Acc Id: NM_001287618   ⟹   NP_001274547
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81783,327,372 - 84,039,558 (+)NCBI
mRatBN7.21778,418,819 - 79,131,015 (+)NCBI
Rnor_6.01782,430,836 - 83,156,696 (+)NCBI
Celera1777,741,837 - 78,442,699 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001274547 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AGN95662 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000074998.2
RefSeq Acc Id: NP_001274547   ⟸   NM_001287618
- Peptide Label: precursor
- UniProtKB: A0A0G2K9H4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000074998   ⟸   ENSRNOT00000083164
Protein Domains
EGF-like   MAM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K9H4-F1-model_v2 AlphaFold A0A0G2K9H4 1-1679 view protein structure

Transcriptome

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

Promoters
RGD ID:13700602
Promoter ID:EPDNEW_R11126
Type:initiation region
Name:Malrd1_1
Description:MAM and LDL receptor class A domain containing 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01782,430,852 - 82,430,912EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2320868 AgrOrtholog
BioCyc Gene G2FUF-8588 BioCyc
Ensembl Genes ENSRNOG00000052916 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000083164.2 UniProtKB/TrEMBL
Gene3D-CATH 2.40.128.620 UniProtKB/TrEMBL
  2.60.120.200 UniProtKB/TrEMBL
  4.10.400.10 UniProtKB/TrEMBL
  Laminin UniProtKB/TrEMBL
InterPro ConA-like_dom UniProtKB/TrEMBL
  EG-like_dom UniProtKB/TrEMBL
  LDL_receptor-like_sf UniProtKB/TrEMBL
  LDLR_class-A_CS UniProtKB/TrEMBL
  LDrepeatLR_classA_rpt UniProtKB/TrEMBL
  MAM_dom UniProtKB/TrEMBL
  MAM_domain-containing UniProtKB/TrEMBL
KEGG Report rno:100361092 UniProtKB/TrEMBL
NCBI Gene 100361092 ENTREZGENE
PANTHER APICAL ENDOSOMAL GLYCOPROTEIN PRECURSOR UniProtKB/TrEMBL
  ENDOSOMAL GLYCOPROTEIN PRECURSOR, PUTATIVE-RELATED UniProtKB/TrEMBL
Pfam Ldl_recept_a UniProtKB/TrEMBL
  MAM UniProtKB/TrEMBL
PhenoGen Malrd1 PhenoGen
PRINTS LDLRECEPTOR UniProtKB/TrEMBL
PROSITE EGF_1 UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  LDLRA_1 UniProtKB/TrEMBL
  LDLRA_2 UniProtKB/TrEMBL
  MAM_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000052916 RatGTEx
SMART EGF UniProtKB/TrEMBL
  LDLa UniProtKB/TrEMBL
  MAM UniProtKB/TrEMBL
Superfamily-SCOP EGF/Laminin UniProtKB/TrEMBL
  SSF49899 UniProtKB/TrEMBL
  SSF57424 UniProtKB/TrEMBL
UniProt A0A0G2K9H4 ENTREZGENE, UniProtKB/TrEMBL
  R9W7X6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Malrd1  MAM and LDL receptor class A domain containing 1  LOC100912561  MAM and LDL-receptor class A domain-containing protein C10orf112-like  Data merged from RGD:6486240 737654 PROVISIONAL
2015-07-29 Malrd1  MAM and LDL receptor class A domain containing 1  RGD1559888  similar to apical early endosomal glycoprotein  Data merged from RGD:1559888 737654 PROVISIONAL
2015-07-29 Malrd1  MAM and LDL receptor class A domain containing 1  RGD1563652  similar to novel MAM domain containing protein  Data merged from RGD:1563652 737654 PROVISIONAL
2015-07-23 Malrd1  MAM and LDL receptor class A domain containing 1  LOC100361092  hypothetical protein LOC100361092  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100912561  MAM and LDL-receptor class A domain-containing protein C10orf112-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-05 LOC100361092  hypothetical protein LOC100361092      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 RGD1563652  similar to novel MAM domain containing protein   RGD1563652_predicted  similar to novel MAM domain containing protein (predicted)  'predicted' is removed 2292626 APPROVED
2008-04-30 RGD1559888  similar to apical early endosomal glycoprotein   RGD1559888_predicted  similar to apical early endosomal glycoprotein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563652_predicted  similar to novel MAM domain containing protein (predicted)  LOC291332  similar to novel MAM domain containing protein  Symbol and Name status set to approved 1299863 APPROVED
2006-03-07 RGD1559888_predicted  similar to apical early endosomal glycoprotein (predicted)  LOC502147  similar to apical early endosomal glycoprotein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC291332  similar to novel MAM domain containing protein      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-02-09 LOC502147  similar to apical early endosomal glycoprotein      Symbol and Name status set to provisional 70820 PROVISIONAL