Slc4a10 solute carrier family 4, sodium bicarbonate cotransporter-like, member 10 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Slc4a10provided by MGI
Official Full Name: solute carrier family 4, sodium bicarbonate cotransporter-like, member 10provided by MGI
Primary source: MGI:MGI:2150150
See related: Ensembl:ENSMUSG00000026904 AllianceGenome:MGI:2150150
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: NCBE; mKIAA4136
Summary: Enables anion:anion antiporter activity and sodium:bicarbonate symporter activity. Involved in regulation of short-term neuronal synaptic plasticity and visual perception. Acts upstream of or within several processes, including brain development; locomotory exploration behavior; and regulation of cellular pH. Located in several cellular components, including basolateral plasma membrane; dendrite; and neuronal cell body. Is expressed in several structures, including gut; nervous system; sensory organ; and testis. Orthologous to human SLC4A10 (solute carrier family 4 member 10). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in frontal lobe adult (RPKM 22.9), cortex adult (RPKM 20.5) and 4 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 C1.3; 2 35.79 cM

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (61876815..62157087)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (62046472..62326743)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Biallelic variants in SLC4A10 encoding a sodium-dependent bicarbonate transporter lead to a neurodevelopmental disorder.
Title: Biallelic variants in SLC4A10 encoding a sodium-dependent bicarbonate transporter lead to a neurodevelopmental disorder.
In vitro investigation of the effect of proinflammatory cytokines on mouse choroid plexus membrane transporters Ncbe and NKCC1.
Title: In vitro investigation of the effect of proinflammatory cytokines on mouse choroid plexus membrane transporters Ncbe and NKCC1.
SLC4A10 mutation causes a neurological disorder associated with impaired GABAergic transmission.
Title: SLC4A10 mutation causes a neurological disorder associated with impaired GABAergic transmission.
Genetic disruption of slc4a10 alters the capacity for cellular metabolism and vectorial ion transport in the choroid plexus epithelium.
Title: Genetic disruption of slc4a10 alters the capacity for cellular metabolism and vectorial ion transport in the choroid plexus epithelium.
Disruption of Slc4a10 results in loss of Slc4a7 expression specifically in inner ear fibrocytes but not in other tissues. At the ultrastructural level, mitochondria of spiral ligament knockout fibrocytes show severe alterations.
Title: Early Hearing Loss upon Disruption of Slc4a10 in C57BL/6 Mice.
finding show that somatodendritic expression of Slc4a10 undergoes neuron type- and input pathway-dependent regulation in adult brains
Title: Neuron type- and input pathway-dependent expression of Slc4a10 in adult mouse brains.
We conclude that alternative transcription and splicing of Slc4a10 products are regulated in a tissue-specific manner. Our findings provide critical insights that will greatly influence the study of the physiology of NBCn2.
Title: Cloning and functional characterization of novel variants and tissue-specific expression of alternative amino and carboxyl termini of products of slc4a10.
Data indicate that sodium-driven chloride bicarbonate exchanger NCBE (Slc4a10) is strongly expressed in the mouse retina.
Title: Lack of the sodium-driven chloride bicarbonate exchanger NCBE impairs visual function in the mouse retina.
Slc4a10 knockout is more deleterious to choroid plexus epithelium than aquaporin 1 (AQP1) knockout.
Title: Genetic ablation of Slc4a10 alters the expression pattern of transporters involved in solute movement in the mouse choroid plexus.
Cloning of the NBCn2-A transcript demonstrates that it is dominant in the subcortex and medulla of mouse brain.
Title: Expression and distribution of NBCn2 (Slc4a10) splice variants in mouse brain: cloning of novel variant NBCn2-D.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (3) 1 citation
Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Slc4a10 (e-PCR), detects polymorphism
- UniSTS:547348

D1S3690 (e-PCR)
- UniSTS:474268

NoName (e-PCR)
- UniSTS:234409

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables antiporter activity	IEA Inferred from Electronic Annotation more info
enables monoatomic anion transmembrane transporter activity	IEA Inferred from Electronic Annotation more info
enables sodium,bicarbonate:chloride antiporter activity	IDA Inferred from Direct Assay more info	PubMed
enables sodium,bicarbonate:chloride antiporter activity	ISO Inferred from Sequence Orthology more info
enables sodium:bicarbonate symporter activity	IBA Inferred from Biological aspect of Ancestor more info
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 solute:inorganic anion antiporter activity	IEA Inferred from Electronic Annotation more info
enables symporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in bicarbonate transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within brain morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within locomotory exploration behavior	IMP Inferred from Mutant Phenotype 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_or_within multicellular organism growth	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within post-embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein glycosylation	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within proton transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pyramidal neuron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of cellular pH	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of intracellular pH	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of pH	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of short-term neuronal synaptic plasticity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to light stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sodium ion transport	IEA Inferred from Electronic Annotation more info
involved_in transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in visual perception	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in CA3 pyramidal cell dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in apical dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in apical plasma membrane	ISO Inferred from Sequence Orthology more info
located_in axon terminus	IDA Inferred from Direct Assay more info	PubMed
located_in basal dendrite	IDA Inferred from Direct Assay more info	PubMed
is_active_in basolateral plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
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 projection	IEA Inferred from Electronic Annotation more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISA Inferred from Sequence Alignment more info	PubMed
located_in somatodendritic compartment	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sodium-driven chloride bicarbonate exchanger

Names: sodium bicarbonate cotransporter NBCn2-E; sodium bicarbonate cotransporter member 10 variant NBCn2-E'

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)

NM_001242378.2 → NP_001229307.1 sodium-driven chloride bicarbonate exchanger isoform 1

See identical proteins and their annotated locations for NP_001229307.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

Q8C943

Conserved Domains (3) summary

TIGR00834
Location:118 → 1061

ae; anion exchange protein

pfam00955
Location:476 → 989

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 435

Band_3_cyto; Band 3 cytoplasmic domain
NM_001242379.2 → NP_001229308.1 sodium-driven chloride bicarbonate exchanger isoform 3

See identical proteins and their annotated locations for NP_001229308.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) lacks an alternate internal segment compared to isoform 1.

Source sequence(s)

AL772323, AL928613, AL928804

Consensus CDS

CCDS57173.1

UniProtKB/TrEMBL

B1AWV9, Q8C943

Related

ENSMUSP00000061411.9, ENSMUST00000054484.15

Conserved Domains (3) summary

TIGR00834
Location:118 → 1031

ae; anion exchange protein

pfam00955
Location:446 → 959

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 405

Band_3_cyto; Band 3 cytoplasmic domain
NM_001242380.2 → NP_001229309.1 sodium-driven chloride bicarbonate exchanger isoform 4

See identical proteins and their annotated locations for NP_001229309.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AL772323, AL928613, AL928804

Consensus CDS

CCDS57172.1

UniProtKB/Swiss-Prot

E9NX85, F1DFN1, G3F8Y7, G3F8Y8, G3F8Y9, G3F8Z0, I6VS12, J7K287, Q5DTL9, Q8CFS3, Q9EST0

UniProtKB/TrEMBL

Q8C943

Related

ENSMUSP00000108099.3, ENSMUST00000112480.3

Conserved Domains (3) summary

TIGR00834
Location:118 → 1061

ae; anion exchange protein

pfam00955
Location:476 → 989

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 435

Band_3_cyto; Band 3 cytoplasmic domain
NM_001242381.2 → NP_001229310.1 sodium-driven chloride bicarbonate exchanger isoform 5

See identical proteins and their annotated locations for NP_001229310.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) uses an alternate in-frame splice junction at the 5' end of an exon, lacks an alternate in-frame exon, and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (5) lacks two alternate internal segments and has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

Q8C943

Conserved Domains (3) summary

TIGR00834
Location:118 → 1030

ae; anion exchange protein

pfam00955
Location:445 → 958

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 404

Band_3_cyto; Band 3 cytoplasmic domain
NM_001242382.2 → NP_001229311.1 sodium-driven chloride bicarbonate exchanger isoform 6

See identical proteins and their annotated locations for NP_001229311.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (6) lacks a single internal aa compared to isoform 1.

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

Q8C943, R4H243

Conserved Domains (3) summary

TIGR00834
Location:118 → 1060

ae; anion exchange protein

pfam00955
Location:475 → 988

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 434

Band_3_cyto; Band 3 cytoplasmic domain
NM_001242383.2 → NP_001229312.1 sodium-driven chloride bicarbonate exchanger isoform 7

See identical proteins and their annotated locations for NP_001229312.1

Status: VALIDATED

Description

Transcript Variant: This variant (7) uses an alternate in-frame splice junction at the 5' end of an exon and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (7) lacks two alternate internal segments compared to isoform 1.

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

Q8C943

Conserved Domains (1) summary

cl26877
Location:118 → 1030

Band_3_cyto; Band 3 cytoplasmic domain
NM_001362671.2 → NP_001349600.1 sodium-driven chloride bicarbonate exchanger isoform 8

Status: VALIDATED

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

J7H264

Conserved Domains (1) summary

cl26877
Location:117 → 1060

Band_3_cyto; Band 3 cytoplasmic domain
NM_001362672.2 → NP_001349601.1 sodium-driven chloride bicarbonate exchanger isoform 9

Status: VALIDATED

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

J7H264

Conserved Domains (1) summary

cl26877
Location:117 → 1059

Band_3_cyto; Band 3 cytoplasmic domain
NM_001362673.2 → NP_001349602.1 sodium-driven chloride bicarbonate exchanger isoform 10

Status: VALIDATED

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

Q8C943

Conserved Domains (1) summary

cl26877
Location:117 → 1030

Band_3_cyto; Band 3 cytoplasmic domain
NM_001362674.2 → NP_001349603.1 sodium-driven chloride bicarbonate exchanger isoform 11

Status: VALIDATED

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

Q8C943

Conserved Domains (1) summary

cl26877
Location:117 → 1030

Band_3_cyto; Band 3 cytoplasmic domain
NM_001362675.2 → NP_001349604.1 sodium-driven chloride bicarbonate exchanger isoform 12

Status: VALIDATED

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

J7H264

Conserved Domains (1) summary

cl26877
Location:117 → 1060

Band_3_cyto; Band 3 cytoplasmic domain
NM_001362676.2 → NP_001349605.1 sodium-driven chloride bicarbonate exchanger isoform 13

Status: VALIDATED

Source sequence(s)

AL772323, AL928613, AL928804

UniProtKB/TrEMBL

Q8C943

Conserved Domains (1) summary

cl26877
Location:117 → 1030

Band_3_cyto; Band 3 cytoplasmic domain
NM_001422237.1 → NP_001409166.1 sodium-driven chloride bicarbonate exchanger isoform 14

Status: VALIDATED

Source sequence(s)

AL772323, AL928613
NM_001422238.1 → NP_001409167.1 sodium-driven chloride bicarbonate exchanger isoform 15

Status: VALIDATED

Source sequence(s)

AL772323, AL928613
NM_001422239.1 → NP_001409168.1 sodium-driven chloride bicarbonate exchanger isoform 16

Status: VALIDATED

Source sequence(s)

AL772323, AL928613
NM_033552.4 → NP_291030.2 sodium-driven chloride bicarbonate exchanger isoform 2

See identical proteins and their annotated locations for NP_291030.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) lacks an alternate internal segment and has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AL772323, AL928613, AL928804

Consensus CDS

CCDS16064.1

UniProtKB/TrEMBL

Q8C943

Related

ENSMUSP00000099796.4, ENSMUST00000102735.10

Conserved Domains (3) summary

TIGR00834
Location:118 → 1031

ae; anion exchange protein

pfam00955
Location:446 → 959

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 405

Band_3_cyto; Band 3 cytoplasmic domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

61876815..62157087

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030252258.2 → XP_030108118.1 sodium-driven chloride bicarbonate exchanger isoform X4

Conserved Domains (1) summary

pfam00955
Location:1 → 469

HCO3_cotransp; HCO3- transporter family
XM_036162733.1 → XP_036018626.1 sodium-driven chloride bicarbonate exchanger isoform X3

UniProtKB/TrEMBL

Q8C943

Conserved Domains (1) summary

cl26877
Location:117 → 1029

Band_3_cyto; Band 3 cytoplasmic domain
XM_017319349.3 → XP_017174838.1 sodium-driven chloride bicarbonate exchanger isoform X2

UniProtKB/TrEMBL

Q8C943

Conserved Domains (1) summary

cl26877
Location:117 → 1029

Band_3_cyto; Band 3 cytoplasmic domain
XM_011239858.4 → XP_011238160.1 sodium-driven chloride bicarbonate exchanger isoform X1

UniProtKB/TrEMBL

J7H264

Conserved Domains (1) summary

cl26877
Location:117 → 1059

Band_3_cyto; Band 3 cytoplasmic domain