Slc35a1 (solute carrier family 35 member A1) - Rat Genome Database

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Gene: Slc35a1 (solute carrier family 35 member A1) Rattus norvegicus
Analyze
Symbol: Slc35a1
Name: solute carrier family 35 member A1
RGD ID: 1311359
Description: Predicted to enable CMP-N-acetylneuraminate transmembrane transporter activity and antiporter activity. Predicted to be involved in CMP-N-acetylneuraminate transmembrane transport. Predicted to be located in Golgi membrane. Human ortholog(s) of this gene implicated in congenital disorder of glycosylation type IIf. Orthologous to human SLC35A1 (solute carrier family 35 member A1); INTERACTS WITH 3-chloropropane-1,2-diol; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CMP-sialic acid transporter; LOC313139; solute carrier family 35 (CMP-sialic acid transporter), member 1; solute carrier family 35 (CMP-sialic acid transporter), member A1
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
mRatBN7.2549,225,599 - 49,248,382 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl549,225,602 - 49,248,335 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx551,418,902 - 51,441,636 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0553,019,125 - 53,041,862 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0552,930,774 - 52,953,552 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0550,119,880 - 50,142,689 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl550,119,881 - 50,142,724 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0554,688,834 - 54,711,626 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4551,271,752 - 51,290,346 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1551,272,681 - 51,301,972 (-)NCBI
Celera547,976,033 - 47,994,630 (-)NCBICelera
Cytogenetic Map5q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
Golgi membrane  (ISO)
membrane  (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. 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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:30985278  


Genomics

Comparative Map Data
Slc35a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2549,225,599 - 49,248,382 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl549,225,602 - 49,248,335 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx551,418,902 - 51,441,636 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0553,019,125 - 53,041,862 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0552,930,774 - 52,953,552 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0550,119,880 - 50,142,689 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl550,119,881 - 50,142,724 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0554,688,834 - 54,711,626 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4551,271,752 - 51,290,346 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1551,272,681 - 51,301,972 (-)NCBI
Celera547,976,033 - 47,994,630 (-)NCBICelera
Cytogenetic Map5q21NCBI
SLC35A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38687,472,974 - 87,512,336 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl687,470,623 - 87,512,336 (+)EnsemblGRCh38hg38GRCh38
GRCh37688,182,692 - 88,222,054 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36688,239,414 - 88,278,766 (+)NCBINCBI36Build 36hg18NCBI36
Build 34688,239,413 - 88,278,766NCBI
Celera688,601,449 - 88,640,875 (+)NCBICelera
Cytogenetic Map6q15NCBI
HuRef685,398,693 - 85,438,291 (+)NCBIHuRef
CHM1_1688,280,066 - 88,319,504 (+)NCBICHM1_1
T2T-CHM13v2.0688,681,733 - 88,721,067 (+)NCBIT2T-CHM13v2.0
Slc35a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39434,663,257 - 34,688,113 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl434,663,257 - 34,687,438 (-)EnsemblGRCm39 Ensembl
GRCm38434,663,257 - 34,688,113 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl434,663,257 - 34,687,438 (-)EnsemblGRCm38mm10GRCm38
MGSCv37434,610,506 - 34,634,687 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36434,852,144 - 34,876,240 (-)NCBIMGSCv36mm8
Celera434,392,843 - 34,405,208 (-)NCBICelera
Cytogenetic Map4A5NCBI
cM Map416.86NCBI
Slc35a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541114,443,839 - 14,468,246 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541114,443,957 - 14,469,590 (+)NCBIChiLan1.0ChiLan1.0
SLC35A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan16105,448,009 - 105,487,823 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0685,349,674 - 85,389,462 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1688,624,423 - 88,663,940 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl688,624,423 - 88,663,940 (+)Ensemblpanpan1.1panPan2
SLC35A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11246,968,664 - 46,992,620 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1246,968,521 - 46,991,872 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1246,776,734 - 46,799,860 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01247,774,701 - 47,798,640 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1247,774,558 - 47,798,640 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11247,066,605 - 47,089,701 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01246,994,022 - 47,017,198 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01247,183,318 - 47,206,486 (+)NCBIUU_Cfam_GSD_1.0
Slc35a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494682,094,861 - 82,126,278 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365104,341,758 - 4,376,109 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365104,344,765 - 4,376,009 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC35A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl155,859,614 - 55,895,784 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1155,859,619 - 55,895,785 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2162,552,706 - 62,588,752 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC35A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11311,957,786 - 11,993,746 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1311,958,122 - 11,996,471 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040188,212,181 - 188,248,088 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc35a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247996,805,364 - 6,829,406 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247996,805,364 - 6,829,288 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc35a1
133 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:349
Count of miRNA genes:210
Interacting mature miRNAs:266
Transcripts:ENSRNOT00000011969
Prediction methods:Microtar, Miranda, 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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53518915368564008Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat

Markers in Region
RH143460  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map5267.5UniSTS
Cytogenetic Map5q21UniSTS


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 30 57 41 19 41 1 3 72 35 34 11 1
Low 13 7 8 2 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011969   ⟹   ENSRNOP00000011969
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl549,225,602 - 49,244,855 (-)Ensembl
Rnor_6.0 Ensembl550,119,881 - 50,138,475 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081150   ⟹   ENSRNOP00000071048
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl549,225,602 - 49,248,335 (-)Ensembl
Rnor_6.0 Ensembl550,120,590 - 50,142,724 (-)Ensembl
RefSeq Acc Id: NM_001107924   ⟹   NP_001101394
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2549,225,599 - 49,248,382 (-)NCBI
Rnor_6.0550,119,881 - 50,138,475 (-)NCBI
Rnor_5.0554,688,834 - 54,711,626 (-)NCBI
RGSC_v3.4551,271,752 - 51,290,346 (-)RGD
Celera547,976,033 - 47,994,630 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101394 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL98597 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001101394   ⟸   NM_001107924
- UniProtKB: A0A0G2JZH4 (UniProtKB/TrEMBL),   D3ZZ48 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011969   ⟸   ENSRNOT00000011969
RefSeq Acc Id: ENSRNOP00000071048   ⟸   ENSRNOT00000081150

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JZH4-F1-model_v2 AlphaFold A0A0G2JZH4 1-336 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:1311359 AgrOrtholog
BioCyc Gene G2FUF-41654 BioCyc
Ensembl Genes ENSRNOG00000008908 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011969.5 UniProtKB/TrEMBL
  ENSRNOP00000071048 ENTREZGENE
  ENSRNOP00000071048.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011969.7 UniProtKB/TrEMBL
  ENSRNOT00000081150 ENTREZGENE
  ENSRNOT00000081150.2 UniProtKB/TrEMBL
InterPro Nuc_sug_transpt UniProtKB/TrEMBL
KEGG Report rno:313139 UniProtKB/TrEMBL
NCBI Gene 313139 ENTREZGENE
PANTHER CMP-SIALIC ACID TRANSPORTER UniProtKB/TrEMBL
  Nuc_sug_transpt UniProtKB/TrEMBL
Pfam Nuc_sug_transp UniProtKB/TrEMBL
PhenoGen Slc35a1 PhenoGen
PIRSF UDP-gal_transpt UniProtKB/TrEMBL
Superfamily-SCOP Multidrug resistance efflux transporter EmrE UniProtKB/TrEMBL
UniProt A0A0G2JZH4 ENTREZGENE, UniProtKB/TrEMBL
  A6IIM7_RAT UniProtKB/TrEMBL
  D3ZZ48 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc35a1  solute carrier family 35 member A1  Slc35a1  solute carrier family 35 (CMP-sialic acid transporter), member A1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-20 Slc35a1  solute carrier family 35 (CMP-sialic acid transporter), member A1  Slc35a1  solute carrier family 35 (CMP-sialic acid transporter), member 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Slc35a1  solute carrier family 35 (CMP-sialic acid transporter), member 1   Slc35a1_predicted  solute carrier family 35 (CMP-sialic acid transporter), member 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slc35a1_predicted  solute carrier family 35 (CMP-sialic acid transporter), member 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED