Clec4a1 Gene Detail

Summary

• Symbol
  Clec4a1
• Name
  C-type lectin domain family 4, member a1
• Synonyms
  mDcir4

• Feature Type
  protein coding gene
• IDs
  MGI:3036291
  NCBI Gene: 269799
• Alliance
  genome feature page
• Transcription Start Sites
  17 TSS

Location &
Maps

• Sequence Map
  Chr6:122898807-122911578 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 6, 58.01 cM
• Mapping Data
  1 experiment

Strain
Comparison

• SNPs within 2kb
  427 from dbSNP Build 142
• Strain Annotations
  17

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_3036291	protein coding gene	Chr6:122898807-122911578 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0031236	protein coding gene	Chr6:126043001-126055827 (+)
A/J	MGP_AJ_G0031205	protein coding gene	Chr6:121264775-121278149 (+)
AKR/J	MGP_AKRJ_G0031135	protein coding gene	Chr6:124626174-124638940 (+)
BALB/cJ	MGP_BALBcJ_G0031215	protein coding gene	Chr6:120976651-120993259 (+)
C3H/HeJ	MGP_C3HHeJ_G0030934	protein coding gene	Chr6:124587049-124601050 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0031674	protein coding gene	Chr6:129371478-129385872 (+)
CAROLI/EiJ	no annotation
CAST/EiJ	MGP_CASTEiJ_G0030323	protein coding gene	Chr6:124855312-124868376 (+)
CBA/J	MGP_CBAJ_G0030897	protein coding gene	Chr6:134413990-134426757 (+)
DBA/2J	MGP_DBA2J_G0031053	protein coding gene	Chr6:120196037-120208967 (+)
FVB/NJ	MGP_FVBNJ_G0031006	protein coding gene	Chr6:119134464-119148229 (+)
LP/J	MGP_LPJ_G0031134	protein coding gene	Chr6:126232504-126249533 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0031041	protein coding gene	Chr6:138367064-138388515 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031704	protein coding gene	Chr6:124511902-124524673 (+)
PWK/PhJ	MGP_PWKPhJ_G0030037	protein coding gene	Chr6:119036349-119049486 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0029865	protein coding gene	Chr6:122655376-122668423 (+)
WSB/EiJ	MGP_WSBEiJ_G0030405	protein coding gene	Chr6:124825092-124838850 (+)

Homology

• Human Ortholog
  CLEC4A, C-type lectin domain family 4 member A

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  CLEC4A, C-type lectin domain family 4 member A
  
• Synonyms
  CD367, CLECSF6, DCIR, DDB27, HDCGC13P, hDCIR, LLIR
• Links
  HGNC:13257

  NCBI Gene ID: 50856

  UniProt: Q9UMR7

  
  
• Chr Location
  12p13.31; chr12:8102907-8138607 (+)  GRCh38

---

• MGI Vertebrate Homology
  Clec4a1 stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: CLEC4A
• Gene Tree
  Clec4a1
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  3 phenotype references
  

• All Mutations and Alleles
  6
• Endonuclease-mediated
  2
• Targeted
  4
• Incidental Mutations
  APF
• Find Mice (IMSR)
  18 strains or lines available

Expression

• Assay Results
  706
• cDNA Data
  5

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  28
• RefSeq
  2
• UniProt
  2
• CCDS
  CCDS20507.1

• Ensembl
  ENSMUSG00000049037 (Evidence)
• NCBI Gene
  269799

Representative Sequences			Length	Strain/Species
genomic	269799	NCBI Gene Model | MGI Sequence Detail	12772	C57BL/6J
transcript	NM_199311	RefSeq | MGI Sequence Detail	1592	C57BL/6
polypeptide	NP_955015	RefSeq | MGI Sequence Detail	245	C57BL/6

Protein
Information

• UniProt
  2 Sequences
• InterPro Domains
  IPR033989 CD209-like, C-type lectin-like domain
  IPR016187 C-type lectin fold
  IPR001304 C-type lectin-like
  IPR016186 C-type lectin-like/link domain superfamily
  IPR051379 C-type Lectin Receptor Immune Modulators

Molecular
Reagents

• All nucleic 5

  cDNA 5

  
  

  Microarray probesets 1

References

• Summaries
  All 15

  Phenotypes 3
• Earliest
  J:93065 Flornes LM, et al., Identification of lectin-like receptors expressed by antigen presenting cells and neutrophils and their mapping to a novel gene complex. Immunogenetics. 2004 Oct;56(7):506-17
• Latest
  J:173534 Skarnes WC, et al., A conditional knockout resource for the genome-wide study of mouse gene function. Nature. 2011 Jun 16;474(7351):337-42

TSS for Clec4a1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr2003	Chr6:122898747-122898758 (+)	-54 bp
Tssr58718	Chr6:122898764-122898824 (+)	-13 bp
Tssr58719	Chr6:122899511-122899536 (+)	717 bp
Tssr58720	Chr6:122899555-122899578 (+)	760 bp
Tssr58721	Chr6:122899703-122899715 (+)	902 bp
Tssr58722	Chr6:122900635-122900685 (+)	1,853 bp
Tssr58723	Chr6:122905945-122905971 (+)	7,151 bp
Tssr58724	Chr6:122909149-122909163 (+)	10,349 bp
Tssr58725	Chr6:122909181-122909198 (+)	10,383 bp
Tssr58726	Chr6:122910730-122910750 (+)	11,933 bp
Tssr58727	Chr6:122910807-122910831 (+)	12,012 bp
Tssr58728	Chr6:122910860-122910879 (+)	12,063 bp
Tssr58729	Chr6:122910923-122910935 (+)	12,122 bp
Tssr58730	Chr6:122910942-122910962 (+)	12,145 bp
Tssr58731	Chr6:122910983-122910998 (+)	12,184 bp
Tssr58732	Chr6:122911035-122911085 (+)	12,253 bp
Tssr58733	Chr6:122911101-122911116 (+)	12,302 bp