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Slc4a4 solute carrier family 4 (anion exchanger), member 4 [ Mus musculus (house mouse) ]

Gene ID: 54403, updated on 8-Jan-2023

Summary

Official Symbol
Slc4a4provided by MGI
Official Full Name
solute carrier family 4 (anion exchanger), member 4provided by MGI
Primary source
MGI:MGI:1927555
See related
Ensembl:ENSMUSG00000060961 AllianceGenome:MGI:1927555
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
NBC; NBC1
Summary
Predicted to enable identical protein binding activity and sodium:bicarbonate symporter activity. Involved in regulation of intracellular pH. Acts upstream of or within bicarbonate transport and sodium ion transport. Predicted to be located in cell surface and membrane. Predicted to be active in basolateral plasma membrane. Is expressed in several structures, including brain; metanephros; spinal cord floor plate; and thyroid primordium. Used to study renal tubular acidosis. Human ortholog(s) of this gene implicated in renal tubular acidosis. Orthologous to human SLC4A4 (solute carrier family 4 member 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in kidney adult (RPKM 60.8), cerebellum adult (RPKM 27.2) and 9 other tissues See more
Orthologs
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Genomic context

See Slc4a4 in Genome Data Viewer
Location:
5; 5 E1
Exon count:
30
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (88941717..89387515)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (88793858..89239656)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene predicted gene 15682 Neighboring gene MOB kinase activator 1B Neighboring gene deoxycytidine kinase Neighboring gene makorin, ring finger protein 1, pseudogene 1 Neighboring gene predicted gene, 35855 Neighboring gene vitamin D binding protein Neighboring gene predicted gene 6366

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC171146

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables monoatomic anion transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sodium:bicarbonate symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables sodium:bicarbonate symporter activity IDA
Inferred from Direct Assay
more info
PubMed 
enables sodium:bicarbonate symporter activity ISO
Inferred from Sequence Orthology
more info
 
enables sodium:bicarbonate symporter activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
enables solute:inorganic anion antiporter activity IEA
Inferred from Electronic Annotation
more info
 
enables symporter activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in bicarbonate transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within bicarbonate transport IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in bicarbonate transport ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within bicarbonate transport ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
acts_upstream_of_or_within establishment of localization in cell IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in monoatomic anion transport IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within monoatomic ion transport IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of positive regulation of glycolytic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of positive regulation of glycolytic process ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of intracellular pH IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of regulation of intracellular pH IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of intracellular pH IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of regulation of intracellular pH ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of regulation of membrane potential IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of regulation of membrane potential ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of pH TAS
Traceable Author Statement
more info
PubMed 
involved_in sodium ion export across plasma membrane ISO
Inferred from Sequence Orthology
more info
 
involved_in sodium ion transmembrane transport ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within sodium ion transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in sodium ion transport ISO
Inferred from Sequence Orthology
more info
 
involved_in transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in transmembrane transport ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
is_active_in basolateral plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in basolateral plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in basolateral plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in cell surface ISO
Inferred from Sequence Orthology
more info
 
is_active_in membrane ISO
Inferred from Sequence Orthology
more info
 
located_in membrane ISO
Inferred from Sequence Orthology
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
electrogenic sodium bicarbonate cotransporter 1
Names
Na(+)/HCO3(-) cotransporter
pancreas sodium bicarbonate cotransporter
sodium bicarbonate cotransporter
solute carrier family 4 member 4
solute carrier family 4, sodium bicarbonate cotransporter, member 4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001136260.1NP_001129732.1  electrogenic sodium bicarbonate cotransporter 1 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon and another exon in the 3' end compared to variant 4, that causes a frameshift. The resulting isoform (b) lacks an alternate internal segment and has a shorter and distinct C-terminus compared to isoform d.
    Source sequence(s)
    AC165240, AF020195, AF141934, BC129864, BF460877
    Consensus CDS
    CCDS51541.1
    UniProtKB/Swiss-Prot
    O88343
    UniProtKB/TrEMBL
    A0A8C6MXW7, A2VDF7, E9Q8N8
    Related
    ENSMUSP00000121744.2, ENSMUST00000156238.8
    Conserved Domains (1) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
  2. NM_001197147.1NP_001184076.1  electrogenic sodium bicarbonate cotransporter 1 isoform c

    See identical proteins and their annotated locations for NP_001184076.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate in-frame splice junction compared to variant 4, that causes a frameshift. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform d.
    Source sequence(s)
    AC165240, AK163619, BF460877, CD364018, HQ204220
    Consensus CDS
    CCDS57352.1
    UniProtKB/TrEMBL
    A7E1Z5
    Related
    ENSMUSP00000108844.4, ENSMUST00000113218.10
    Conserved Domains (3) summary
    TIGR00834
    Location:109994
    ae; anion exchange protein
    pfam00955
    Location:427946
    HCO3_cotransp; HCO3- transporter family
    pfam07565
    Location:137379
    Band_3_cyto; Band 3 cytoplasmic domain
  3. NM_001359211.1NP_001346140.1  electrogenic sodium bicarbonate cotransporter 1 isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (d).
    Source sequence(s)
    AC140492, AC162690, AC165240
    UniProtKB/TrEMBL
    A0A668KM61
    Related
    ENSMUSP00000159229.2, ENSMUST00000239214.2
    Conserved Domains (1) summary
    cl26877
    Location:1091035
    Band_3_cyto; Band 3 cytoplasmic domain
  4. NM_001359212.1NP_001346141.1  electrogenic sodium bicarbonate cotransporter 1 isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (e) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform d.
    Source sequence(s)
    AC140492, AC165240, HQ018820
    Consensus CDS
    CCDS89936.1
    UniProtKB/TrEMBL
    E1AWU4
    Related
    ENSMUSP00000118413.2, ENSMUST00000130041.8
    Conserved Domains (1) summary
    TIGR00834
    Location:65959
    ae; anion exchange protein
  5. NM_001359213.1NP_001346142.1  electrogenic sodium bicarbonate cotransporter 1 isoform f

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence, lacks an alternate in-frame exon, and uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (f) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform d.
    Source sequence(s)
    AC140492, AC165240, HQ285250
    UniProtKB/TrEMBL
    E3VWA1
    Conserved Domains (1) summary
    cl26877
    Location:65950
    Band_3_cyto; Band 3 cytoplasmic domain
  6. NM_018760.2NP_061230.2  electrogenic sodium bicarbonate cotransporter 1 isoform a

    See identical proteins and their annotated locations for NP_061230.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 4. The resulting isoform (a) has the same N- and C-termini but is shorter compared to isoform d.
    Source sequence(s)
    AC165240, AF141934, AW124701, BC129863, BF460877, CB524421, CF744823
    Consensus CDS
    CCDS19406.1
    UniProtKB/Swiss-Prot
    O88343, Q9R1C4
    UniProtKB/TrEMBL
    A0A8C6HFB5
    Related
    ENSMUSP00000119325.2, ENSMUST00000148750.8
    Conserved Domains (3) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
    pfam00955
    Location:436955
    HCO3_cotransp; HCO3- transporter family
    pfam07565
    Location:137388
    Band_3_cyto; Band 3 cytoplasmic domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    88941717..89387515
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030254704.1XP_030110564.1  electrogenic sodium bicarbonate cotransporter 1 isoform X4

    Conserved Domains (1) summary
    TIGR00834
    Location:1141008
    ae; anion exchange protein
  2. XM_017320995.2XP_017176484.1  electrogenic sodium bicarbonate cotransporter 1 isoform X2

    Conserved Domains (1) summary
    cl26877
    Location:1141040
    Band_3_cyto; Band 3 cytoplasmic domain
  3. XM_006535136.5XP_006535199.1  electrogenic sodium bicarbonate cotransporter 1 isoform X3

    Conserved Domains (1) summary
    cl26877
    Location:1091035
    Band_3_cyto; Band 3 cytoplasmic domain
  4. XM_030254705.2XP_030110565.1  electrogenic sodium bicarbonate cotransporter 1 isoform X6

    Conserved Domains (1) summary
    TIGR00834
    Location:109994
    ae; anion exchange protein
  5. XM_036165313.1XP_036021206.1  electrogenic sodium bicarbonate cotransporter 1 isoform X5

    UniProtKB/TrEMBL
    A0A8C6MXW7, E9Q8N8
    Conserved Domains (1) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
  6. XM_011249542.1XP_011247844.1  electrogenic sodium bicarbonate cotransporter 1 isoform X1

    Conserved Domains (1) summary
    cl26877
    Location:1091026
    Band_3_cyto; Band 3 cytoplasmic domain