Slamf1 MGI Mouse Gene Detail - MGI:1351314 - signaling lymphocytic activation molecule family member 1

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Slamf1 Gene Detail

Symbol

Slamf1
Name

signaling lymphocytic activation molecule family member 1
Synonyms

CD150, CDw150, ESTM51, IPO-3, Slam

Feature Type

protein coding gene
IDs

MGI:1351314
NCBI Gene: 27218
Alliance

gene page
Transcription Start Sites

11 TSS
Candidate for QTL

2 QTL

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Sequence Map

Chr1:171594700-171628752 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 79.54 cM
Mapping Data

6 experiments

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SNPs within 2kb

903 from dbSNP Build 142
Strain Annotations

17

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_1351314	protein coding gene	Chr1:171594695-171628752 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0016770	protein coding gene	Chr1:177605753-177639549 (+)
A/J	MGP_AJ_G0016749	protein coding gene	Chr1:170342642-170379127 (+)
AKR/J	MGP_AKRJ_G0016715	protein coding gene	Chr1:175485358-175520389 (+)
BALB/cJ	MGP_BALBcJ_G0016710	protein coding gene	Chr1:170886715-170927486 (+)
C3H/HeJ	MGP_C3HHeJ_G0016534	protein coding gene	Chr1:176050696-176098292 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0017172	protein coding gene	Chr1:183485106-183525398 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014879	protein coding gene	Chr1:162058879-162094178 (+)
CAST/EiJ	MGP_CASTEiJ_G0016115	protein coding gene	Chr1:175413692-175450833 (+)
CBA/J	MGP_CBAJ_G0016508	protein coding gene	Chr1:190046928-190083186 (+)
DBA/2J	MGP_DBA2J_G0016615	protein coding gene	Chr1:169277971-169316515 (+)
FVB/NJ	MGP_FVBNJ_G0016612	protein coding gene	Chr1:167532619-167566261 (+)
LP/J	MGP_LPJ_G0016686	protein coding gene	Chr1:178685325-178722082 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016639	protein coding gene	Chr1:197310877-197345854 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0017208	protein coding gene	Chr1:175344764-175384039 (+)
PWK/PhJ	MGP_PWKPhJ_G0015900	protein coding gene	Chr1:168656249-168690756 (+)
SPRET/EiJ	no annotation
WSB/EiJ	MGP_WSBEiJ_G0016176	protein coding gene	Chr1:175516076-175552201 (+)

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Human Ortholog

SLAMF1, signaling lymphocytic activation molecule family member 1

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SLAMF1, signaling lymphocytic activation molecule family member 1
Synonyms

CD150, CDw150, SLAM
Links

HGNC:10903

NCBI Gene ID: 6504

neXtProt AC: NX_Q13291

UniProt: Q13291
Chr Location

1q23.3; chr1:160608106-160647044 (-) GRCh38

MGI Vertebrate Homology

Slamf1 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: SLAMF1
Gene Tree

Slamf1

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Phenotype Summary

6 phenotypes from 3 alleles in 4 genetic backgrounds
3 phenotypes from multigenic genotypes
33 phenotype references

Phenotype Overview

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

13
Chemically induced (other)

2
Endonuclease-mediated

5
Targeted

6
Genomic Mutations

3 involving Slamf1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

24 strains or lines available

Homozygous null mice are fertile and display impaired T cell and macrophage cytokine production.

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All GO Annotations

58
GO References

19

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

729
Tissues

1
cDNA Data

24
Literature Summary

4

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

57
RefSeq

8
UniProt

6
CCDS

CCDS15502.1

Ensembl

ENSMUSG00000015316 (Evidence)
NCBI Gene

27218

Representative Sequences				Length	Strain/Species	Flank
	genomic	27218	NCBI Gene Model \| MGI Sequence Detail	34053	C57BL/6J	± kb
	transcript	NM_013730	RefSeq \| MGI Sequence Detail	2688	ZRU/MplStud
	polypeptide	Q9QUM4	UniProt \| EBI \| MGI Sequence Detail	343	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000001833 SLAM family member 1

(term hierarchy)
InterPro Domains

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR010407 Signaling lymphocytic activation molecule, N-terminal
GlyGen

Q9QUM4 10 sites, 1 O-linked glycan (1 site)

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All nucleic 30

Genomic 4

cDNA 25

Primer pair 1

Microarray probesets 5

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MGI:1334421

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Summaries

All 89

Developmental Gene Expression 4

Gene Ontology 19

Phenotypes 33
Earliest

J:227465 Aversa G, et al., Engagement of the signaling lymphocytic activation molecule (SLAM) on activated T cells results in IL-2-independent, cyclosporin A-sensitive T cell proliferation and IFN-gamma production. J Immunol. 1997 May 1;158(9):4036-44
Latest

J:322501 Kohn EM, et al., SLAMF1 Is Dispensable for Vaccine-Induced T Cell Development but Required for Resistance to Fungal Infection. J Immunol. 2022 Mar 15;208(6):1417-1423

TSS for Slamf1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr10084	Chr1:171594463-171594481 (+)	-228 bp
Tssr10085	Chr1:171594493-171594509 (+)	-199 bp
Tssr10086	Chr1:171594691-171594706 (+)	-1 bp
Tssr10087	Chr1:171594712-171594738 (+)	25 bp
Tssr10088	Chr1:171602727-171602730 (+)	8,029 bp
Tssr10089	Chr1:171602932-171602940 (+)	8,236 bp
Tssr10090	Chr1:171604744-171604755 (+)	10,050 bp
Tssr10091	Chr1:171606166-171606207 (+)	11,487 bp
Tssr10092	Chr1:171615547-171615553 (+)	20,850 bp
Tssr10093	Chr1:171627183-171627195 (+)	32,489 bp
Tssr10094	Chr1:171628024-171628035 (+)	33,330 bp

Slamf1 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Nktcn1	Chr1, 76.25 cM	Chr1:168186243-171632257	J:137521	Microarray analysis was performed on thymus RNA from 4 week old NOD.Nkrp1.Nkt1 congenic animals and NOD.Nkrp1 congenic animals to screen candidate genes for Nktcn1. The NOD.Nkrp1 congenic carries C57BL/6J-derived DNA from D6Mit105 (45.5 cM) toD6Mit135 (62.3 cM) on a NOD genetic background. The NOD.Nkrp.Nkt1 congenic carries C57BL/6J-derived DNA from D1Mit369 (73 cM) to D1Mit155 (telomere) on a NOD genetic background in addition to the NOD-derived chromosome 6 interval. The formal QTL designation for Nkt1 is Nktcn1. Nkrp1 is synonymous with Klrb1c. Previously identified lupus susceptibility locus Sle1b (89.5 cM) maps near Nktcn1. Twenty-one genes displaying expression differences between NOD and C57BL/6J mapped to the Nktcn1 region, 15of which are located in the 95% confidence interval. The most promising candidate genes for controlling NKT cell number are Slamf1 (93.3 cM) and Slamf6 (89.5 cM). Gene expression of Slamf1 and Slamf6 was examined in thymic and splenic lymphocytes from congenic animals. It was observed that NOD.Nkrp.Nkt1 animals expressed significantly higher amounts of SLAM proteins on cell sufaces compared to NOD.Nkt1 parentals. Authors hypothesize control of NKT cell numbers may be mediated by differentialexpression of Slamf1 with additionial influence by Slamf6.
Sle1b	Chr1, 75.10 cM		J:94686	Congenic and physical mapping was used to show that Sle1b mapped within an interval containing SLAM family members ordered as Cd244 - Ly9 - Slamf7 - Cd48 - Slamf1 - Cd84 - Slamf6. Haplotype analysis of the aformentioned region were suggestive that the markers contained within the region as contributing to the Sle1b phenotype. The strongest contribution may come from Slamf6.

*cM position of peak correlated region/marker

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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