Calhm4 (calcium homeostasis modulator family member 4) - Rat Genome Database

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Gene: Calhm4 (calcium homeostasis modulator family member 4) Rattus norvegicus
Analyze
Symbol: Calhm4
Name: calcium homeostasis modulator family member 4
RGD ID: 1595701
Description: Predicted to enable monoatomic cation channel activity. Predicted to be involved in monoatomic cation transmembrane transport. Predicted to be located in membrane. Predicted to be active in plasma membrane. Orthologous to human CALHM4 (calcium homeostasis modulator family member 4); INTERACTS WITH alpha-Zearalanol; bisphenol A; endosulfan.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: calcium homeostasis modulator protein 4; Fam26d; family with sequence similarity 26, member D; LOC499445; similar to Protein C6orf78 homolog
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
GRCr82026,533,296 - 26,536,305 (-)NCBIGRCr8
mRatBN7.22025,990,164 - 25,993,173 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2025,990,462 - 25,993,173 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.02027,573,809 - 27,578,269 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2027,575,533 - 27,578,244 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02029,402,812 - 29,405,574 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42037,780,887 - 37,783,598 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2027,443,217 - 27,447,677 (-)NCBICelera
Cytogenetic Map20q11NCBI
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

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. 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

Genomics

Comparative Map Data
Calhm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82026,533,296 - 26,536,305 (-)NCBIGRCr8
mRatBN7.22025,990,164 - 25,993,173 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2025,990,462 - 25,993,173 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.02027,573,809 - 27,578,269 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2027,575,533 - 27,578,244 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02029,402,812 - 29,405,574 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42037,780,887 - 37,783,598 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2027,443,217 - 27,447,677 (-)NCBICelera
Cytogenetic Map20q11NCBI
CALHM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386116,529,043 - 116,561,127 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6116,529,013 - 116,561,127 (+)EnsemblGRCh38hg38GRCh38
GRCh376116,850,206 - 116,882,290 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366116,956,888 - 116,986,724 (+)NCBINCBI36Build 36hg18NCBI36
Build 346116,956,935 - 116,988,979NCBI
Celera6117,593,268 - 117,623,104 (+)NCBICelera
Cytogenetic Map6q22.1NCBI
HuRef6114,429,758 - 114,459,612 (+)NCBIHuRef
CHM1_16117,113,805 - 117,143,648 (+)NCBICHM1_1
T2T-CHM13v2.06117,712,775 - 117,744,838 (+)NCBIT2T-CHM13v2.0
Calhm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391033,914,780 - 33,920,309 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1033,914,780 - 33,920,306 (-)EnsemblGRCm39 Ensembl
GRCm381034,038,784 - 34,044,313 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1034,038,784 - 34,044,310 (-)EnsemblGRCm38mm10GRCm38
MGSCv371033,758,590 - 33,764,119 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361033,728,200 - 33,733,729 (-)NCBIMGSCv36mm8
Celera1034,948,920 - 34,954,449 (-)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1018.85NCBI
Calhm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955526132,040 - 136,106 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955526126,100 - 137,551 (-)NCBIChiLan1.0ChiLan1.0
CALHM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25136,557,734 - 136,574,983 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16134,450,753 - 134,468,016 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06114,337,385 - 114,369,423 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16118,482,269 - 118,514,298 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6118,482,269 - 118,512,046 (+)Ensemblpanpan1.1panPan2
CALHM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1156,923,115 - 56,978,067 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl156,973,036 - 56,978,049 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha157,718,241 - 57,773,787 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0157,104,936 - 57,160,491 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl157,154,863 - 57,159,877 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1156,999,389 - 57,054,932 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0156,847,582 - 56,903,077 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0157,476,529 - 57,531,581 (+)NCBIUU_Cfam_GSD_1.0
Calhm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946107,373,807 - 107,378,639 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049368241,098,792 - 1,103,797 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049368241,098,792 - 1,103,607 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALHM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl182,149,968 - 82,154,057 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1182,109,535 - 82,154,349 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2192,343,679 - 92,378,009 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CALHM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11357,252,414 - 57,257,474 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1357,252,676 - 57,257,116 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604029,584,062 - 29,598,729 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Calhm4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248561,845,809 - 1,849,885 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248561,845,710 - 1,849,885 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Calhm4
5 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:18
Count of miRNA genes:15
Interacting mature miRNAs:18
Transcripts:ENSRNOT00000000708
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
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat


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
Low 2 1 11 16 1 1 11 9 5 9 1
Below cutoff 1 10 9 4 3 4 4 6 2 7 2 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000708   ⟹   ENSRNOP00000000708
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2025,990,462 - 25,993,173 (-)Ensembl
Rnor_6.0 Ensembl2027,575,533 - 27,578,244 (-)Ensembl
RefSeq Acc Id: XM_574768   ⟹   XP_574768
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,533,296 - 26,536,305 (-)NCBI
mRatBN7.22025,990,164 - 25,993,173 (-)NCBI
Rnor_6.02027,573,809 - 27,578,269 (-)NCBI
Rnor_5.02029,402,812 - 29,405,574 (-)NCBI
RGSC_v3.42037,780,887 - 37,783,598 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_574768 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000708
  ENSRNOP00000000708.3
Reference Protein Sequences
RefSeq Acc Id: XP_574768   ⟸   XM_574768
- UniProtKB: D3ZDN4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000708   ⟸   ENSRNOT00000000708

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZDN4-F1-model_v2 AlphaFold D3ZDN4 1-315 view protein structure

Transcriptome

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

Promoters
RGD ID:13701582
Promoter ID:EPDNEW_R12098
Type:single initiation site
Name:Calhm4_1
Description:calcium homeostasis modulator family member 4
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_6.02027,578,285 - 27,578,345EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595701 AgrOrtholog
BioCyc Gene G2FUF-3795 BioCyc
Ensembl Genes ENSRNOG00000000580 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000708 ENTREZGENE
  ENSRNOT00000000708.4 UniProtKB/TrEMBL
InterPro FAM26 UniProtKB/TrEMBL
KEGG Report rno:499445 UniProtKB/TrEMBL
NCBI Gene 499445 ENTREZGENE
PANTHER PTHR32261 UniProtKB/TrEMBL
  PTHR32261:SF5 UniProtKB/TrEMBL
Pfam Ca_hom_mod UniProtKB/TrEMBL
PhenoGen Calhm4 PhenoGen
RatGTEx ENSRNOG00000000580 RatGTEx
UniProt D3ZDN4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-07-31 Calhm4  calcium homeostasis modulator family member 4  Fam26d  family with sequence similarity 26, member D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Fam26d  family with sequence similarity 26, member D  LOC499445  similar to Protein C6orf78 homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC499445  similar to Protein C6orf78 homolog      Symbol and Name status set to provisional 70820 PROVISIONAL