Slc48a1 (solute carrier family 48 member 1) - Rat Genome Database

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Gene: Slc48a1 (solute carrier family 48 member 1) Rattus norvegicus
Analyze
Symbol: Slc48a1
Name: solute carrier family 48 member 1
RGD ID: 1562880
Description: Predicted to enable heme binding activity and heme transmembrane transporter activity. Predicted to be involved in heme transport. Predicted to be located in endosome membrane. Predicted to be active in lysosomal membrane and plasma membrane. Orthologous to human SLC48A1 (solute carrier family 48 member 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: heme transporter HRG1; Heme-responsive gene 1 protein homolog; HRG-1; Hrg1; LOC300191; MGC125237; similar to RIKEN cDNA 4930570C03; solute carrier family 48 (heme transporter), member 1
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
mRatBN7.27128,915,136 - 128,923,929 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7128,915,195 - 128,923,024 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7130,712,333 - 130,720,120 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07132,937,868 - 132,945,655 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07132,850,334 - 132,858,120 (+)NCBIRnor_WKY
Rnor_6.07139,271,698 - 139,279,499 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7139,271,698 - 139,279,499 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,463,280 - 139,471,081 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,492,421 - 136,500,222 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7125,406,532 - 125,414,333 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process
heme transport  (IBA,IEA,ISO)

Cellular Component
endosome membrane  (IEA,ISO)
lysosomal membrane  (IBA,IEA,ISO)
plasma membrane  (IBA,ISO)

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
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334   PMID:18418376   PMID:19875448   PMID:23395172  


Genomics

Comparative Map Data
Slc48a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27128,915,136 - 128,923,929 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7128,915,195 - 128,923,024 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7130,712,333 - 130,720,120 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07132,937,868 - 132,945,655 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07132,850,334 - 132,858,120 (+)NCBIRnor_WKY
Rnor_6.07139,271,698 - 139,279,499 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7139,271,698 - 139,279,499 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,463,280 - 139,471,081 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,492,421 - 136,500,222 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7125,406,532 - 125,414,333 (+)NCBICelera
Cytogenetic Map7q36NCBI
SLC48A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381247,753,934 - 47,782,751 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1247,753,916 - 47,782,751 (+)EnsemblGRCh38hg38GRCh38
GRCh371248,167,021 - 48,176,534 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361246,453,258 - 46,461,720 (+)NCBINCBI36Build 36hg18NCBI36
Celera1246,964,517 - 46,974,086 (+)NCBICelera
Cytogenetic Map12q13.11NCBI
HuRef1245,198,127 - 45,207,696 (+)NCBIHuRef
CHM1_11248,132,870 - 48,142,439 (+)NCBICHM1_1
T2T-CHM13v2.01247,734,631 - 47,744,144 (+)NCBIT2T-CHM13v2.0
Slc48a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391597,682,246 - 97,690,573 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1597,676,401 - 97,690,573 (+)EnsemblGRCm39 Ensembl
GRCm381597,784,365 - 97,792,692 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1597,778,520 - 97,792,692 (+)EnsemblGRCm38mm10GRCm38
MGSCv371597,614,796 - 97,623,123 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361597,612,399 - 97,620,722 (+)NCBIMGSCv36mm8
Celera1599,911,999 - 99,920,320 (+)NCBICelera
Cytogenetic Map15F1NCBI
Slc48a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555006,679,908 - 6,691,942 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555006,675,631 - 6,691,942 (+)NCBIChiLan1.0ChiLan1.0
SLC48A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11241,825,080 - 41,852,173 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01240,950,511 - 40,977,994 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SLC48A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1276,970,510 - 6,978,837 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl276,971,402 - 6,978,942 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2739,328,772 - 39,337,048 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0277,037,538 - 7,045,841 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl277,037,538 - 7,045,938 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1276,974,515 - 6,982,758 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0277,009,903 - 7,018,204 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02739,617,239 - 39,625,518 (+)NCBIUU_Cfam_GSD_1.0
Slc48a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494567,484,328 - 67,505,445 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365125,672,952 - 5,684,113 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365125,672,952 - 5,680,502 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC48A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl578,141,236 - 78,150,583 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1578,141,220 - 78,150,584 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SLC48A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11143,979,255 - 44,001,567 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1143,993,272 - 44,000,177 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037202,379,991 - 202,407,693 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc48a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248164,476,491 - 4,485,030 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248164,476,502 - 4,496,641 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc48a1
41 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:160
Count of miRNA genes:117
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000010957
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
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
RH141101  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27128,922,803 - 128,922,992 (+)MAPPERmRatBN7.2
Rnor_6.07139,279,279 - 139,279,467NCBIRnor6.0
Rnor_5.07139,470,861 - 139,471,049UniSTSRnor5.0
RGSC_v3.47136,500,002 - 136,500,190UniSTSRGSC3.4
Celera7125,414,113 - 125,414,301UniSTS
RH 3.4 Map71096.2UniSTS
Cytogenetic Map7q36UniSTS


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079388   ⟹   ENSRNOP00000071123
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7128,915,241 - 128,923,018 (+)Ensembl
Rnor_6.0 Ensembl7139,271,698 - 139,279,499 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105518   ⟹   ENSRNOP00000077408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7128,915,195 - 128,923,024 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110329   ⟹   ENSRNOP00000093159
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7128,915,196 - 128,923,000 (+)Ensembl
RefSeq Acc Id: NM_001127456   ⟹   NP_001120928
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27128,915,223 - 128,923,024 (+)NCBI
Rnor_6.07139,271,698 - 139,279,499 (+)NCBI
Rnor_5.07139,463,280 - 139,471,081 (+)NCBI
RGSC_v3.47136,492,421 - 136,500,222 (+)RGD
Celera7125,406,532 - 125,414,333 (+)RGD
Sequence:
RefSeq Acc Id: XM_039078912   ⟹   XP_038934840
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27128,915,136 - 128,923,929 (+)NCBI
RefSeq Acc Id: XM_039078913   ⟹   XP_038934841
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27128,921,000 - 128,923,929 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001120928   ⟸   NM_001127456
- UniProtKB: Q3KR77 (UniProtKB/Swiss-Prot),   B0BNL4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071123   ⟸   ENSRNOT00000079388
RefSeq Acc Id: XP_038934840   ⟸   XM_039078912
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934841   ⟸   XM_039078913
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000077408   ⟸   ENSRNOT00000105518
RefSeq Acc Id: ENSRNOP00000093159   ⟸   ENSRNOT00000110329

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B0BNL4-F1-model_v2 AlphaFold B0BNL4 1-146 view protein structure

Transcriptome

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

Promoters
RGD ID:13695616
Promoter ID:EPDNEW_R6141
Type:initiation region
Name:Slc48a1_1
Description:solute carrier family 48 member 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_6.07139,271,689 - 139,271,749EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562880 AgrOrtholog
BioCyc Gene G2FUF-32176 BioCyc
Ensembl Genes ENSRNOG00000053196 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071123.2 UniProtKB/TrEMBL
  ENSRNOP00000077408 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000093159 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000079388.2 UniProtKB/TrEMBL
  ENSRNOT00000105518 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000110329 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7930286 IMAGE-MGC_LOAD
InterPro HRG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:300191 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188505 IMAGE-MGC_LOAD
NCBI Gene 300191 ENTREZGENE
PANTHER PTHR31525 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HRG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc48a1 PhenoGen
PRINTS TRNSPORTRHRG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2R3J2_RAT UniProtKB/TrEMBL
  B0BNL4 ENTREZGENE, UniProtKB/Swiss-Prot
  Q3KR77 ENTREZGENE
UniProt Secondary Q3KR77 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Slc48a1  solute carrier family 48 member 1  Slc48a1  solute carrier family 48 (heme transporter), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-01-21 Slc48a1  solute carrier family 48 (heme transporter), member 1  LOC300191  similar to RIKEN cDNA 4930570C03  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC300191  similar to RIKEN cDNA 4930570C03      Symbol and Name status set to provisional 70820 PROVISIONAL