MS4A4E (membrane spanning 4-domains A4E) - Rat Genome Database

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Gene: MS4A4E (membrane spanning 4-domains A4E) Homo sapiens
Analyze
Symbol: MS4A4E
Name: membrane spanning 4-domains A4E
RGD ID: 1348228
HGNC Page HGNC:14284
Description: Predicted to be located in Golgi apparatus and plasma membrane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: membrane-spanning 4-domains subfamily A member 4E; membrane-spanning 4-domains, subfamily A, member 4E; putative membrane-spanning 4-domains subfamily A member 4E
RGD Orthologs
Bonobo
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381160,200,270 - 60,243,137 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1160,200,270 - 60,243,137 (-)EnsemblGRCh38hg38GRCh38
GRCh371159,967,743 - 60,010,610 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361159,737,138 - 59,754,099 (-)NCBINCBI36Build 36hg18NCBI36
Celera1157,333,103 - 57,374,946 (-)NCBICelera
Cytogenetic Map11q12.2NCBI
HuRef1156,315,550 - 56,357,414 (-)NCBIHuRef
CHM1_11159,834,703 - 59,876,613 (-)NCBICHM1_1
T2T-CHM13v2.01160,151,543 - 60,194,426 (-)NCBIT2T-CHM13v2.0
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

Cellular Component
membrane  (IEA)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11486273   PMID:20379614   PMID:21460840   PMID:21873635   PMID:23118302   PMID:23954108   PMID:26449541   PMID:27781389  


Genomics

Comparative Map Data
MS4A4E
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381160,200,270 - 60,243,137 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1160,200,270 - 60,243,137 (-)EnsemblGRCh38hg38GRCh38
GRCh371159,967,743 - 60,010,610 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361159,737,138 - 59,754,099 (-)NCBINCBI36Build 36hg18NCBI36
Celera1157,333,103 - 57,374,946 (-)NCBICelera
Cytogenetic Map11q12.2NCBI
HuRef1156,315,550 - 56,357,414 (-)NCBIHuRef
CHM1_11159,834,703 - 59,876,613 (-)NCBICHM1_1
T2T-CHM13v2.01160,151,543 - 60,194,426 (-)NCBIT2T-CHM13v2.0
MS4A4E
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2961,340,888 - 61,380,612 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11162,385,008 - 62,408,597 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01155,434,950 - 55,474,784 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11158,881,192 - 58,920,219 (-)NCBIpanpan1.1PanPan1.1panPan2

Variants

.
Variants in MS4A4E
6 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NC_000011.10:g.60229930C>T single nucleotide variant Malignant melanoma [RCV000069539] Chr11:60229930 [GRCh38]
Chr11:59997403 [GRCh37]
Chr11:59753979 [NCBI36]
Chr11:11q12.2		 not provided
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3		 pathogenic
GRCh38/hg38 11q12.1-12.2(chr11:59851273-60699280)x1 copy number loss See cases [RCV000143668] Chr11:59851273..60699280 [GRCh38]
Chr11:59618746..60466753 [GRCh37]
Chr11:59375322..60223329 [NCBI36]
Chr11:11q12.1-12.2		 likely benign|uncertain significance
GRCh37/hg19 11p13-q25(chr11:32799481-134938470)x3 copy number gain MISSED ABORTION [RCV002282973] Chr11:32799481..134938470 [GRCh37]
Chr11:11p13-q25		 pathogenic
GRCh37/hg19 11q12.1-12.2(chr11:59679631-60167878)x3 copy number gain See cases [RCV000449175] Chr11:59679631..60167878 [GRCh37]
Chr11:11q12.1-12.2		 uncertain significance
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11q12.1-12.3(chr11:58935215-62177656)x3 copy number gain not provided [RCV000683362] Chr11:58935215..62177656 [GRCh37]
Chr11:11q12.1-12.3		 likely pathogenic
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
NC_000011.9:g.(?_59596957)_(68707199_?)dup duplication Familial temporal lobe epilepsy 8 [RCV001372442] Chr11:59596957..68707199 [GRCh37]
Chr11:11q12.1-13.3		 uncertain significance
NC_000011.9:g.(?_58916346)_(64972349_?)dup duplication Leukocyte adhesion deficiency 3 [RCV003113394]|not provided [RCV003113393] Chr11:58916346..64972349 [GRCh37]
Chr11:11q12.1-13.1		 uncertain significance|no classifications from unflagged records
NC_000011.9:g.(?_59939307)_(60235941_?)dup duplication not provided [RCV003113750] Chr11:59939307..60235941 [GRCh37]
Chr11:11q12.2		 uncertain significance
GRCh37/hg19 11p11.2-q12.2(chr11:51581311-54891247)x3 copy number gain See cases [RCV002286338] Chr11:51581311..54891247 [GRCh37]
Chr11:11p11.2-q12.2		 pathogenic
GRCh37/hg19 11q12.2-13.5(chr11:59923608-76272324)x3 copy number gain not provided [RCV003484842] Chr11:59923608..76272324 [GRCh37]
Chr11:11q12.2-13.5		 pathogenic
GRCh37/hg19 11p11.12-q13.1(chr11:50398499-63924462)x3 copy number gain not specified [RCV003986918] Chr11:50398499..63924462 [GRCh37]
Chr11:11p11.12-q13.1		 likely pathogenic
GRCh37/hg19 11q12.1-13.3(chr11:56895955-69295402)x3 copy number gain not specified [RCV003986944] Chr11:56895955..69295402 [GRCh37]
Chr11:11q12.1-13.3		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1221
Count of miRNA genes:477
Interacting mature miRNAs:519
Transcripts:ENST00000398984, ENST00000398986, ENST00000425663, ENST00000427611, ENST00000526086, ENST00000526153, ENST00000528394, ENST00000532442
Prediction methods:Microtar, Miranda, Rnahybrid
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.

Markers in Region
D11S4191  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371159,999,717 - 59,999,829UniSTSGRCh37
Build 361159,756,293 - 59,756,405RGDNCBI36
Celera1157,364,103 - 57,364,218RGD
Cytogenetic Map11q12.2UniSTS
HuRef1156,346,541 - 56,346,671UniSTS
Marshfield Genetic Map1160.09RGD
Marshfield Genetic Map1160.09UniSTS
Genethon Genetic Map1163.4UniSTS
TNG Radiation Hybrid Map1126344.0UniSTS
deCODE Assembly Map1164.96UniSTS
Whitehead-YAC Contig Map11 UniSTS


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 pharyngeal arch
High
Medium 87 35 13 7 178 5 167 47 66 7 16 39 6 118 73
Low 2206 2291 1457 556 1257 405 3354 1482 1041 241 1162 1376 158 1058 1998 4 1
Below cutoff 131 649 247 58 219 53 820 651 2067 156 257 187 7 27 705 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001351235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001393391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011545416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011545418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011545419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017018641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054369644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054369645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_007062493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_008488423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_008488424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_950143 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_950144 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB231725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB231726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB231727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB231728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB231729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB231730 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB231731 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF354936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK300102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AP003970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000398984   ⟹   ENSP00000381954
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1160,213,089 - 60,230,055 (-)Ensembl
RefSeq Acc Id: ENST00000398986   ⟹   ENSP00000381956
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1160,206,673 - 60,230,071 (-)Ensembl
RefSeq Acc Id: ENST00000425663
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1160,213,089 - 60,230,055 (-)Ensembl
RefSeq Acc Id: ENST00000526086
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1160,213,095 - 60,230,055 (-)Ensembl
RefSeq Acc Id: ENST00000526153   ⟹   ENSP00000436124
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1160,213,089 - 60,230,044 (-)Ensembl
RefSeq Acc Id: ENST00000528394
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1160,213,095 - 60,230,055 (-)Ensembl
RefSeq Acc Id: ENST00000532442   ⟹   ENSP00000435345
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1160,201,253 - 60,243,088 (-)Ensembl
RefSeq Acc Id: ENST00000638529   ⟹   ENSP00000492712
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1160,213,089 - 60,230,050 (-)Ensembl
RefSeq Acc Id: ENST00000651255   ⟹   ENSP00000499123
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1160,200,270 - 60,243,137 (-)Ensembl
RefSeq Acc Id: NM_001351235   ⟹   NP_001338164
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,201,253 - 60,243,137 (-)NCBI
T2T-CHM13v2.01160,152,527 - 60,194,426 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001393391   ⟹   NP_001380320
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,200,270 - 60,243,137 (-)NCBI
T2T-CHM13v2.01160,151,543 - 60,194,426 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011545416   ⟹   XP_011543718
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,204,188 - 60,243,137 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017018641   ⟹   XP_016874130
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,207,599 - 60,243,137 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054369644   ⟹   XP_054225619
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01160,155,006 - 60,194,426 (-)NCBI
RefSeq Acc Id: XM_054369645   ⟹   XP_054225620
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01160,157,075 - 60,194,426 (-)NCBI
RefSeq Acc Id: XR_007062493
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,207,599 - 60,243,137 (-)NCBI
RefSeq Acc Id: XR_008488423
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01160,153,103 - 60,194,426 (-)NCBI
RefSeq Acc Id: XR_008488424
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01160,157,075 - 60,194,426 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_011543718   ⟸   XM_011545416
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_016874130   ⟸   XM_017018641
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: NP_001338164   ⟸   NM_001351235
- Peptide Label: isoform 1
- UniProtKB: B4DT89 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000381954   ⟸   ENST00000398984
RefSeq Acc Id: ENSP00000381956   ⟸   ENST00000398986
RefSeq Acc Id: ENSP00000492712   ⟸   ENST00000638529
RefSeq Acc Id: ENSP00000435345   ⟸   ENST00000532442
RefSeq Acc Id: ENSP00000499123   ⟸   ENST00000651255
RefSeq Acc Id: ENSP00000436124   ⟸   ENST00000526153
RefSeq Acc Id: NP_001380320   ⟸   NM_001393391
- Peptide Label: isoform 2
- UniProtKB: A0A494C1L8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_054225619   ⟸   XM_054369644
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054225620   ⟸   XM_054369645
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q96PG1-F1-model_v2 AlphaFold Q96PG1 1-132 view protein structure

Promoters
RGD ID:7220463
Promoter ID:EPDNEW_H15977
Type:initiation region
Name:MS4A4E_1
Description:membrane spanning 4-domains A4E
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,243,088 - 60,243,148EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:14284 AgrOrtholog
COSMIC MS4A4E COSMIC
Ensembl Genes ENSG00000214787 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000398984.6 UniProtKB/Swiss-Prot
  ENST00000526153.5 UniProtKB/TrEMBL
  ENST00000532442.5 UniProtKB/TrEMBL
  ENST00000638529.1 UniProtKB/TrEMBL
  ENST00000651255 ENTREZGENE
  ENST00000651255.1 UniProtKB/TrEMBL
GTEx ENSG00000214787 GTEx
HGNC ID HGNC:14284 ENTREZGENE
Human Proteome Map MS4A4E Human Proteome Map
InterPro CD20-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MS4A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 643680 ENTREZGENE
OMIM 608401 OMIM
PANTHER MEMBRANE-SPANNING 4-DOMAINS SUBFAMILY A MEMBER 4A UniProtKB/TrEMBL
  MEMBRANE-SPANNING 4-DOMAINS SUBFAMILY A MS4A -RELATED UniProtKB/Swiss-Prot
  MEMBRANE-SPANNING 4-DOMAINS, SUBFAMILY A, MEMBER 4A UniProtKB/Swiss-Prot
  PTHR23320 UniProtKB/TrEMBL
Pfam CD20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA31117 PharmGKB
UniProt A0A1W2PRK6_HUMAN UniProtKB/TrEMBL
  A0A494C1L8 ENTREZGENE, UniProtKB/TrEMBL
  B4DT89 ENTREZGENE, UniProtKB/TrEMBL
  E9PKS5_HUMAN UniProtKB/TrEMBL
  H0YEM0_HUMAN UniProtKB/TrEMBL
  M4A4E_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q3C1W1 UniProtKB/Swiss-Prot
  Q3C1W3 UniProtKB/Swiss-Prot
  Q3C1W4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-26 MS4A4E  membrane spanning 4-domains A4E  MS4A4E  membrane-spanning 4-domains subfamily A member 4E  Symbol and/or name change 5135510 APPROVED
2016-01-19 MS4A4E  membrane-spanning 4-domains subfamily A member 4E  MS4A4E  membrane-spanning 4-domains, subfamily A, member 4E  Symbol and/or name change 5135510 APPROVED