Icam4 (intercellular adhesion molecule 4, Landsteiner-Wiener blood group) - Rat Genome Database

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Gene: Icam4 (intercellular adhesion molecule 4, Landsteiner-Wiener blood group) Rattus norvegicus
Analyze
Symbol: Icam4
Name: intercellular adhesion molecule 4, Landsteiner-Wiener blood group
RGD ID: 1308971
Description: Predicted to enable integrin binding activity. Predicted to be involved in cell adhesion. Predicted to be located in cytoplasm; extracellular space; and plasma membrane. Orthologous to human ICAM4 (intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: intercellular adhesion molecule 4; LOC100360240; LOC298702; rCG31766-like
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
GRCr8827,842,255 - 27,843,351 (+)NCBIGRCr8
mRatBN7.2819,566,075 - 19,567,171 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,566,075 - 19,567,171 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx823,585,495 - 23,586,591 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,883,354 - 21,884,450 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,795,742 - 19,796,838 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,047,697 - 22,048,793 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,047,697 - 22,048,793 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,104,565 - 22,105,661 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4820,052,606 - 20,053,227 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera820,960,500 - 20,961,596 (+)NCBICelera
Cytogenetic Map8q13NCBI
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

Cellular Component
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. 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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12406883  


Genomics

Comparative Map Data
Icam4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8827,842,255 - 27,843,351 (+)NCBIGRCr8
mRatBN7.2819,566,075 - 19,567,171 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,566,075 - 19,567,171 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx823,585,495 - 23,586,591 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,883,354 - 21,884,450 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,795,742 - 19,796,838 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,047,697 - 22,048,793 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,047,697 - 22,048,793 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,104,565 - 22,105,661 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4820,052,606 - 20,053,227 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera820,960,500 - 20,961,596 (+)NCBICelera
Cytogenetic Map8q13NCBI
ICAM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381910,286,955 - 10,288,520 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1910,286,955 - 10,288,522 (+)EnsemblGRCh38hg38GRCh38
GRCh371910,397,631 - 10,399,196 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,258,650 - 10,260,198 (+)NCBINCBI36Build 36hg18NCBI36
Build 341910,258,679 - 10,260,198NCBI
Celera1910,293,046 - 10,294,594 (+)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef199,977,622 - 9,979,239 (+)NCBIHuRef
CHM1_11910,397,908 - 10,399,525 (+)NCBICHM1_1
T2T-CHM13v2.01910,413,067 - 10,414,632 (+)NCBIT2T-CHM13v2.0
Icam4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39920,940,728 - 20,941,892 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl920,940,669 - 20,941,891 (+)EnsemblGRCm39 Ensembl
GRCm38921,029,432 - 21,030,596 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,029,373 - 21,030,595 (+)EnsemblGRCm38mm10GRCm38
MGSCv37920,833,817 - 20,834,975 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36920,779,856 - 20,780,896 (+)NCBIMGSCv36mm8
Celera918,297,959 - 18,299,117 (+)NCBICelera
Cytogenetic Map9A3NCBI
cM Map97.69NCBI
Icam4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554951,574,341 - 1,575,442 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554951,573,444 - 1,575,595 (+)NCBIChiLan1.0ChiLan1.0
ICAM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22015,203,802 - 15,205,573 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11914,202,337 - 14,204,192 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0199,837,157 - 9,838,862 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11910,501,005 - 10,502,114 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1910,501,005 - 10,502,176 (+)Ensemblpanpan1.1panPan2
ICAM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12050,817,199 - 50,818,551 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2050,817,411 - 50,818,498 (-)EnsemblCanFam3.1canFam3CanFam3.1
Icam4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,726,039 - 209,727,208 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936659627,560 - 628,644 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936659627,560 - 628,644 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ICAM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl269,108,690 - 69,110,962 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1269,108,610 - 69,110,053 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2269,442,993 - 69,444,403 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ICAM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.169,338,478 - 9,340,029 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl69,338,588 - 9,340,185 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607410,701,018 - 10,702,586 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Icam4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248282,452,151 - 2,454,863 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248282,451,978 - 2,454,863 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:23
Count of miRNA genes:22
Interacting mature miRNAs:23
Transcripts:ENSRNOT00000067741
Prediction methods: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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat

Markers in Region
RH94539  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2819,565,254 - 19,565,417 (+)MAPPERmRatBN7.2
Rnor_6.0822,046,877 - 22,047,039NCBIRnor6.0
Rnor_5.0822,103,745 - 22,103,907UniSTSRnor5.0
RGSC_v3.4820,051,767 - 20,051,929UniSTSRGSC3.4
Celera820,959,680 - 20,959,842UniSTS
RH 3.4 Map8206.11UniSTS
Cytogenetic Map8q13UniSTS
UniSTS:492613  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2819,566,012 - 19,567,171 (+)MAPPERmRatBN7.2
Rnor_6.0822,047,635 - 22,048,793NCBIRnor6.0
Rnor_5.0822,104,503 - 22,105,661UniSTSRnor5.0
RGSC_v3.4820,052,525 - 20,053,683UniSTSRGSC3.4
Celera820,960,438 - 20,961,596UniSTS
Cytogenetic Map8q13UniSTS


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 6 18 18 4 18
Low 12 15 15 7 15 20 2 15 11
Below cutoff 2 14 18 8 6 8 1 2 16 20 19 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067741   ⟹   ENSRNOP00000060742
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl819,566,075 - 19,567,171 (+)Ensembl
Rnor_6.0 Ensembl822,047,697 - 22,048,793 (+)Ensembl
RefSeq Acc Id: NM_001172077   ⟹   NP_001165548
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,842,255 - 27,843,351 (+)NCBI
mRatBN7.2819,566,075 - 19,567,171 (+)NCBI
Rnor_6.0822,047,697 - 22,048,793 (+)NCBI
Rnor_5.0822,104,565 - 22,105,661 (+)NCBI
Celera820,960,500 - 20,961,596 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001165548 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL78333 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000060742
  ENSRNOP00000060742.2
Reference Protein Sequences
RefSeq Acc Id: NP_001165548   ⟸   NM_001172077
- Peptide Label: precursor
- UniProtKB: D3ZP29 (UniProtKB/TrEMBL),   A6JNN3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000060742   ⟸   ENSRNOT00000067741
Protein Domains
Intercellular adhesion molecule N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZP29-F1-model_v2 AlphaFold D3ZP29 1-264 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:1308971 AgrOrtholog
BioCyc Gene G2FUF-31443 BioCyc
Ensembl Genes ENSRNOG00000042078 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067741 ENTREZGENE
  ENSRNOT00000067741.3 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro ICAM_N UniProtKB/TrEMBL
  ICAM_VCAM UniProtKB/TrEMBL
  ICAM_VCAM_N UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
KEGG Report rno:298702 UniProtKB/TrEMBL
NCBI Gene Icam4 ENTREZGENE
PANTHER INTERCELLULAR ADHESION MOLECULE UniProtKB/TrEMBL
  INTERCELLULAR ADHESION MOLECULE 4 UniProtKB/TrEMBL
Pfam ICAM_N UniProtKB/TrEMBL
PhenoGen Icam4 PhenoGen
PRINTS ICAMVCAM1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000042078 RatGTEx
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A6JNN3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZP29 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-06 Icam4  intercellular adhesion molecule 4, Landsteiner-Wiener blood group  LOC100360240  rCG31766-like  Data merged from RGD:2322510 737654 APPROVED
2012-07-05 Icam4  intercellular adhesion molecule 4, Landsteiner-Wiener blood group  Icam4  intercellular adhesion molecule 4, Landsteiner-Wiener blood group  Gene reactivated at release of RGSC5.0 assembly 2298974 REACTIVATED
2010-05-06 LOC100360240  rCG31766-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Icam4  intercellular adhesion molecule 4, Landsteiner-Wiener blood group   Icam4_predicted  intercellular adhesion molecule 4, Landsteiner-Wiener blood group (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Icam4_predicted  intercellular adhesion molecule 4, Landsteiner-Wiener blood group (predicted)      Symbol and Name status set to approved 70820 APPROVED