Slc6a17 solute carrier family 6 (neurotransmitter transporter), member 17 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Slc6a17provided by MGI
Official Full Name: solute carrier family 6 (neurotransmitter transporter), member 17provided by MGI
Primary source: MGI:MGI:2442535
See related: Ensembl:ENSMUSG00000027894 AllianceGenome:MGI:2442535
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: Ntt4; D130012J15Rik
Summary: Predicted to enable symporter activity. Involved in brain development. Predicted to be located in cell projection; plasma membrane; and postsynapse. Predicted to be active in GABA-ergic synapse; glutamatergic synapse; and synaptic vesicle membrane. Is expressed in several structures, including nervous system. Human ortholog(s) of this gene implicated in autosomal recessive intellectual developmental disorder 48. Orthologous to human SLC6A17 (solute carrier family 6 member 17). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in cortex adult (RPKM 51.2), frontal lobe adult (RPKM 44.9) and 8 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 F2.3; 3 46.83 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (107374864..107425334, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (107467548..107518018, complement)

Chromosome 3 - NC_000069.7 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?

Importance of glutamine in synaptic vesicles revealed by functional studies of SLC6A17 and its mutations pathogenic for intellectual disability.
Title: Importance of glutamine in synaptic vesicles revealed by functional studies of SLC6A17 and its mutations pathogenic for intellectual disability.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Endonuclease-mediated (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Slc6a17 (e-PCR), detects polymorphism
- UniSTS:547356

D3Mit103 (e-PCR), detects polymorphism
- UniSTS:129501

AW490886 (e-PCR)
- UniSTS:178916

18.MMHAP5FLF3.seq (e-PCR)
- UniSTS:123387

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables symporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in L-leucine transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in L-leucine transport	ISO Inferred from Sequence Orthology more info
involved_in L-leucine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in alanine transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in alanine transport	ISO Inferred from Sequence Orthology more info
involved_in alanine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in brain development	IDA Inferred from Direct Assay more info	PubMed
involved_in glycine transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycine transport	ISO Inferred from Sequence Orthology more info
involved_in glycine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in neurotransmitter transport	IEA Inferred from Electronic Annotation more info
involved_in neutral amino acid transport	ISO Inferred from Sequence Orthology more info
involved_in neutral amino acid transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in proline transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in proline transport	ISO Inferred from Sequence Orthology more info
involved_in proline transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in sodium ion transport	IEA Inferred from Electronic Annotation more info
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in GABA-ergic synapse	ISO Inferred from Sequence Orthology more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in postsynapse	IEA Inferred from Electronic Annotation more info
is_active_in synapse	ISO Inferred from Sequence Orthology more info
is_active_in synaptic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle	ISO Inferred from Sequence Orthology more info
located_in synaptic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
is_active_in synaptic vesicle membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: sodium-dependent neutral amino acid transporter SLC6A17

Names: orphan sodium- and chloride-dependent neurotransmitter transporter NTT4

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_001293689.1 → NP_001280618.1 sodium-dependent neutral amino acid transporter SLC6A17 isoform 1

See identical proteins and their annotated locations for NP_001280618.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).

Source sequence(s)

AC124727, AK083807, AY155578

Consensus CDS

CCDS79998.1

UniProtKB/Swiss-Prot

B2RUH5, Q8BJI1, Q8C057, Q8CGQ9

UniProtKB/TrEMBL

A0A0R4J252

Related

ENSMUSP00000129379.2, ENSMUST00000169449.8

Conserved Domains (1) summary

cd11521
Location:60 → 648

SLC6sbd_NTT4; Na(+)-dependent neurotransmitter transporter 4; solute-binding domain
NM_172271.2 → NP_758475.1 sodium-dependent neutral amino acid transporter SLC6A17 isoform 2

See identical proteins and their annotated locations for NP_758475.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AY155578

Consensus CDS

CCDS38591.1

UniProtKB/TrEMBL

A0A0R4J087, A0A0R4J252

Related

ENSMUSP00000029499.9, ENSMUST00000029499.15

Conserved Domains (1) summary

cd11521
Location:60 → 645

SLC6sbd_NTT4; Na(+)-dependent neurotransmitter transporter 4; solute-binding domain

RNA

NR_121629.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 3' structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK032262, AY155578

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_000069.7 Reference GRCm39 C57BL/6J

Range

107374864..107425334 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006501407.4 → XP_006501470.1 sodium-dependent neutral amino acid transporter SLC6A17 isoform X1

See identical proteins and their annotated locations for XP_006501470.1

UniProtKB/Swiss-Prot

B2RUH5, Q8BJI1, Q8C057, Q8CGQ9

UniProtKB/TrEMBL

A0A0R4J252

Related

ENSMUSP00000131888.2, ENSMUST00000168211.2

Conserved Domains (1) summary

cd11521
Location:60 → 648

SLC6sbd_NTT4; Na(+)-dependent neurotransmitter transporter 4; solute-binding domain
XM_006501406.4 → XP_006501469.1 sodium-dependent neutral amino acid transporter SLC6A17 isoform X1

See identical proteins and their annotated locations for XP_006501469.1

UniProtKB/Swiss-Prot

B2RUH5, Q8BJI1, Q8C057, Q8CGQ9

UniProtKB/TrEMBL

A0A0R4J252

Conserved Domains (1) summary

cd11521
Location:60 → 648

SLC6sbd_NTT4; Na(+)-dependent neurotransmitter transporter 4; solute-binding domain