Sytl4 synaptotagmin-like 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sytl4provided by MGI
Official Full Name: synaptotagmin-like 4provided by MGI
Primary source: MGI:MGI:1351606
See related: Ensembl:ENSMUSG00000031255 AllianceGenome:MGI:1351606
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: Gph; Slp4
Summary: Enables neurexin family protein binding activity and phospholipid binding activity. Acts upstream of or within exocytosis and negative regulation of insulin secretion. Located in secretory granule. Is extrinsic component of membrane. Is expressed in diencephalon lateral wall ventricular layer; endocrine gland; foregut-midgut junction; and paravertebral ganglion. Orthologous to human SYTL4 (synaptotagmin like 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in genital fat pad adult (RPKM 13.0), bladder adult (RPKM 1.7) and 3 other tissues See more
Orthologs: human all
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Genomic context

Location:: X E3; X 55.47 cM

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	X	NC_000086.8 (132837134..132882569, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	X	NC_000086.7 (133936385..133981821, complement)

Chromosome X - NC_000086.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Granuphilin and exophilin7, differentially regulate the exocytosis of either stably or minimally docked granules, respectively.
Title: The Rab27a effector exophilin7 promotes fusion of secretory granules that have not been docked to the plasma membrane.
granuphilin binds to syntaxin-2 and syntaxin-3 as well as syntaxin-1a, it likely mediates granule docking through interactions with those multiple syntaxins on the plasma membrane.
Title: Loss of granuphilin and loss of syntaxin-1A cause differential effects on insulin granule docking and fusion.
It is shown that the granuphilin promoter is a target of SREBP-1c, a transcription factor that controls fatty acid synthesis, and MafA, a beta cell differentiation factor
Title: Granuphilin is activated by SREBP-1c and involved in impaired insulin secretion in diabetic mice.
granuphilin promotes the plasma membrane targeting of insulin granules via interaction with syntaxin 1a
Title: Rab27 effector granuphilin promotes the plasma membrane targeting of insulin granules via interaction with syntaxin 1a.
Synaptotagmin-like protein 4 (Slp4)/granuphilin-a contains an N-terminal Slp homology domain (SHD) (PMID: 11327731). The SHD of Slp4 specifically and directly binds the GTP-bound form of Rab3A, Rab8, and Rab27A.
Title: The Slp homology domain of synaptotagmin-like proteins 1-4 and Slac2 functions as a novel Rab27A binding domain.

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Variation

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Alleles

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

Targeted (1) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

px-72c6 (e-PCR)
- UniSTS:258458

Sytl4 (e-PCR), detects polymorphism
- UniSTS:525516

NoName (e-PCR)
- UniSTS:238075

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables neurexin family protein binding	IBA Inferred from Biological aspect of Ancestor more info
enables neurexin family protein binding	IDA Inferred from Direct Assay more info	PubMed
enables phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in exocytosis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within exocytosis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of insulin secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in lysosome localization	ISO Inferred from Sequence Orthology more info
involved_in multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of insulin secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in plasma membrane repair	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of exocytosis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein secretion	ISO Inferred from Sequence Orthology more info
involved_in regulation of plasma membrane repair	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in apical plasma membrane	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
located_in endosome	ISO Inferred from Sequence Orthology more info
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
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 secretory granule	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: synaptotagmin-like protein 4

Names: exophilin-2; granuphilin-a; granuphilin-b

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_001290717.1 → NP_001277646.1 synaptotagmin-like protein 4 isoform 2

See identical proteins and their annotated locations for NP_001277646.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks three alternate exons, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1. Variants 2 and 3 encode the same isoform (2).

Source sequence(s)

AB025258, AK161582, AL691421, BX510358

Consensus CDS

CCDS72429.1

UniProtKB/Swiss-Prot

Q9R0Q1

Related

ENSMUSP00000108922.3, ENSMUST00000113297.9

Conserved Domains (2) summary

cd04029
Location:359 → 483

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins
NM_001290718.1 → NP_001277647.1 synaptotagmin-like protein 4 isoform 2

See identical proteins and their annotated locations for NP_001277647.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR and lacks three alternate exons, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1. Variants 2 and 3 encode the same isoform (2).

Source sequence(s)

AB025258, AK030401, BX510358

Consensus CDS

CCDS72429.1

UniProtKB/Swiss-Prot

Q9R0Q1

Conserved Domains (2) summary

cd04029
Location:359 → 483

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins
NM_001290719.1 → NP_001277648.1 synaptotagmin-like protein 4 isoform 3

See identical proteins and their annotated locations for NP_001277648.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks multiple 3' coding exons and its transcription extends past a splice site used in variant 1, resulting in a different 3' coding region and 3' UTR. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AB025258, AL691421, BX510358

Consensus CDS

CCDS81169.1

UniProtKB/Swiss-Prot

Q9R0Q1

Related

ENSMUSP00000108919.2, ENSMUST00000113294.8

Conserved Domains (2) summary

cd04029
Location:359 → 483

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins
NM_013757.2 → NP_038785.1 synaptotagmin-like protein 4 isoform 1

See identical proteins and their annotated locations for NP_038785.1

Status: VALIDATED

Description

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

Source sequence(s)

AB025258, BX510358

Consensus CDS

CCDS30388.1

UniProtKB/Swiss-Prot

B1AVI8, B1AVI9, Q8R321, Q9R0Q0, Q9R0Q1

UniProtKB/TrEMBL

Q549X6

Related

ENSMUSP00000033608.9, ENSMUST00000033608.15

Conserved Domains (4) summary

cd04020
Location:498 → 663

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:359 → 483

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily

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_000086.8 Reference GRCm39 C57BL/6J

Range

132837134..132882569 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006528551.4 → XP_006528614.1 synaptotagmin-like protein 4 isoform X1

See identical proteins and their annotated locations for XP_006528614.1

UniProtKB/Swiss-Prot

B1AVI8, B1AVI9, Q8R321, Q9R0Q0, Q9R0Q1

UniProtKB/TrEMBL

Q549X6

Conserved Domains (4) summary

cd04020
Location:498 → 663

C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4

cd04029
Location:359 → 483

C2A_SLP-4_5; C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5

cd15764
Location:58 → 107

FYVE_Slp4; FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins

cl22851
Location:8 → 121

PHD_SF; PHD finger superfamily