CLEC3B (C-type lectin domain family 3 member B)

Gene: CLEC3B (C-type lectin domain family 3 member B) Sus scrofa

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Symbol:

CLEC3B

Name:

C-type lectin domain family 3 member B

RGD ID:

14230135

Description:

ENCODES a protein that exhibits calcium ion binding (ortholog); heparin binding (ortholog); INVOLVED IN bone mineralization (ortholog); positive regulation of plasminogen activation (ortholog); skeletal system development (ortholog); ASSOCIATED WITH genetic disease (ortholog); osteoarthritis (ortholog); retinal macular dystrophy 4 (ortholog); FOUND IN cytoplasm (ortholog); extracellular space (ortholog); granular component (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

tetranectin

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	28,219,500 - 28,229,096 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	28,219,241 - 28,229,113 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	31,096,895 - 31,107,071 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

osteoarthritis (ISO)

retinal macular dystrophy 4 (ISO)

Scheuermann's disease (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

bone mineralization (IBA,IEA,ISS)

cellular response to organic substance (IEA)

cellular response to transforming growth factor beta stimulus (IEA)

ossification (IBA,IEA)

positive regulation of plasminogen activation (ISS)

skeletal system development (ISO)

Cellular Component

collagen-containing extracellular matrix (HDA)

cytoplasm (IEA,ISS)

extracellular space (IBA,IEA,ISS)

granular component (IEA,ISS)

Molecular Function

calcium ion binding (IEA,ISS)

carbohydrate binding (IEA)

heparin binding (IEA,ISS)

kringle domain binding (IEA)

protein binding (ISO)

References

Additional References at PubMed

PMID:14681463	PMID:30032202

Genomics

Comparative Map Data

CLEC3B
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	28,219,500 - 28,229,096 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	28,219,241 - 28,229,113 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	31,096,895 - 31,107,071 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CLEC3B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	45,026,303 - 45,036,071 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	45,001,548 - 45,036,071 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	3	45,067,795 - 45,077,563 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	45,042,763 - 45,052,567 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	3	45,005,711 - 45,015,514 (+)	NCBI		Celera
Cytogenetic Map	3	p21.31	NCBI
HuRef	3	45,111,173 - 45,120,977 (+)	NCBI		HuRef
CHM1_1	3	45,017,739 - 45,027,543 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	3	45,042,041 - 45,051,809 (+)	NCBI		T2T-CHM13v2.0

Clec3b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	122,980,011 - 122,986,497 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	9	122,980,011 - 122,986,497 (+)	Ensembl		GRCm39 Ensembl
GRCm38	9	123,150,946 - 123,157,432 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	123,150,946 - 123,157,432 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	123,060,064 - 123,066,550 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	9	122,999,547 - 123,006,125 (+)	NCBI		MGSCv36	mm8
Celera	9	123,602,080 - 123,608,547 (+)	NCBI		Celera
Cytogenetic Map	9	F4	NCBI
cM Map	9	73.91	NCBI

Clec3b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	8	131,687,575 - 131,693,292 (+)	NCBI		GRCr8
mRatBN7.2	8	122,810,120 - 122,815,837 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	8	122,810,149 - 122,815,835 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	8	128,400,421 - 128,406,145 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	126,599,361 - 126,605,084 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	124,427,554 - 124,433,270 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	132,241,016 - 132,248,066 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	132,241,134 - 132,246,694 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	131,394,703 - 131,401,659 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	8	121,922,992 - 121,930,042 (+)	NCBI		Celera
Cytogenetic Map	8	q32	NCBI

Clec3b
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955420	26,665,472 - 26,669,474 (-)	NCBI	ChiLan1.0	ChiLan1.0

CLEC3B
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	2	44,984,162 - 44,994,010 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	44,989,026 - 44,998,777 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	44,927,098 - 44,936,847 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	3	46,038,115 - 46,047,927 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	3	46,038,115 - 46,047,927 (+)	Ensembl	panpan1.1		panPan2

CLEC3B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	20	43,319,786 - 43,332,161 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	20	43,324,231 - 43,332,135 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	20	43,239,918 - 43,248,089 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	20	43,808,958 - 43,817,196 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	20	43,808,965 - 43,817,166 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	20	43,047,906 - 43,056,075 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	20	43,455,546 - 43,463,778 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	20	43,731,532 - 43,739,811 (-)	NCBI		UU_Cfam_GSD_1.0

Clec3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405118	198,378,987 - 198,386,451 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936695	730,729 - 738,952 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936695	731,184 - 738,752 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLEC3B
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	22	6,501,082 - 6,510,878 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	22	6,501,102 - 6,512,314 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666041	160,658,725 - 160,668,539 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Clec3b
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624730	75,530,770 - 75,536,248 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624730	75,531,320 - 75,535,875 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in CLEC3B
296 total Variants

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	hemolymphoid system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system
High
Medium	5	4	2	4	2	2	2	3
Low	5		1	1		21			1
Below cutoff									1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005669451	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000085	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK240262	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CU915630	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GFLN01042218	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSSCT00000036280 ⟹ ENSSSCP00000041870

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1 Ensembl	13	28,219,500 - 28,229,096 (+)	Ensembl

RefSeq Acc Id:

XM_005669451 ⟹ XP_005669508

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	13	28,219,241 - 28,229,113 (+)	NCBI

Sequence:

show sequence

TGAGCTATGACAACTAGCATGTGTTTTTCAGAATCCTAGAAAATAATAACTGTTGCAGAAGGCG
GAGCCAGGATGCTGGATGGGTGTTCCCCGGCCAGTGAGGCGCTGTGGCTCCCAGACCTTTTGCA
GGCTCTTCTTTGTTTTTGTTTCTTGGCACTCCTGCAGCCAAGTCTGGGAGGGTTTCCTGGACAG
AGGTCCTCGTGGCTGCTGCCTTAAGACGTGCAGCCCAGGCCACAGCTGACAGTGCTCTCTGACC
CAGGCCCACCACAGGCAGCAAGAGCAGCAGCAGCCGTAGTCCCAGCCGGTGCAGCAGCATGGAG
CTTTGGGGGCCCTACTTGCTCCTCTGCCTCTTCTCCCTTCTGACCCAGGTCACTGCTGAGACAC
CTACCCCCAAGGTCAAGAAGCCTGCAAATGCCAAGAAAGATGCCGCAAGCCCAAAGATACTTGA
GGAGCTCAAGACCCAGCTGGACACTCTGGCCCAGGAGGTGGCCCTGCTGAAGGAGCAGCAGGCC
CTGCAGACGGTCTGCCTGAAAGGCACCAAGGTGCACATGAAGTGCTTCCTGGCCTTCGTCCAGG
CGAAGACTTTCCACGAGGCGAGCGAGGACTGTATCTCACGCGGGGGCACCCTGGGCACCCCTAA
GACAGGCTCGGAGAACGATGCCCTGTACGAGTACCTACGGCAGAGCGTGGGCGCAGAGGCTGAG
GTCTGGCTGGGCTTCAACGATATGGCGGATGAGGGCGCCTGGGTGGACATGACCGGCGGCCACA
TCGCCTACAAGAACTGGGAGACAGAGATCACTGCGCAGCCTGATGGCGGCAAGGTGGAGAACTG
CGCCGCCCTGGCTGGCGCGGCCAACGGCAAGTGGTTCGACAAGCGCTGCCGGGACAAGCTGCCC
TACGTCTGCCAGTTCGCCATCGTGTAGCGGGCGAGGCGGGGCGGGGCGGGGCGGGGCGGGGCGG
GGCCGGGGCCGGGGCGGGGCGAGCAGGAGGAGGATCCTGAGCCGCTGGAGGAGCAGTGCTGGGA
CTTTCCCTTCAGGCATCCCTGCCACGCTGGGAGCCTTCTTTTGCAAATAAAGTGGGTGCAGCTT
AGCGGAGA

hide sequence

Protein Sequences


Protein RefSeqs	XP_005669508	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSSCP00000041870
	ENSSSCP00000041870.1
	ENSSSCP00005041582.1
	ENSSSCP00015023466.1
	ENSSSCP00025025371.1
	ENSSSCP00030044729.1
	ENSSSCP00035045093.1
	ENSSSCP00040025790.1
	ENSSSCP00045027087.1
	ENSSSCP00050037842.1
	ENSSSCP00055021718.1
	ENSSSCP00060008050.1
	ENSSSCP00065004776.1
	ENSSSCP00070013742.1

RefSeq Acc Id:

XP_005669508 ⟸ XM_005669451

- UniProtKB:

F1SRC8 (UniProtKB/TrEMBL), A0A4X1TEJ3 (UniProtKB/TrEMBL), A0A8D0KDH5 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MELWGPYLLLCLFSLLTQVTAETPTPKVKKPANAKKDAASPKILEELKTQLDTLAQEVALLKEQ
QALQTVCLKGTKVHMKCFLAFVQAKTFHEASEDCISRGGTLGTPKTGSENDALYEYLRQSVGAE
AEVWLGFNDMADEGAWVDMTGGHIAYKNWETEITAQPDGGKVENCAALAGAANGKWFDKRCRDK
LPYVCQFAIV

hide sequence

RefSeq Acc Id:

ENSSSCP00000041870 ⟸ ENSSSCT00000036280

Protein Domains

C-type lectin

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSSCG00000011299	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSSSCG00005041713	UniProtKB/TrEMBL
	ENSSSCG00015043923	UniProtKB/TrEMBL
	ENSSSCG00025044099	UniProtKB/TrEMBL
	ENSSSCG00030069358	UniProtKB/TrEMBL
	ENSSSCG00035077190	UniProtKB/TrEMBL
	ENSSSCG00040045663	UniProtKB/TrEMBL
	ENSSSCG00045022831	UniProtKB/TrEMBL
	ENSSSCG00050064846	UniProtKB/TrEMBL
	ENSSSCG00055013865	UniProtKB/TrEMBL
	ENSSSCG00060014897	UniProtKB/TrEMBL
	ENSSSCG00065008675	UniProtKB/TrEMBL
	ENSSSCG00070008582	UniProtKB/TrEMBL
Ensembl Transcript	ENSSSCT00000036280	ENTREZGENE
	ENSSSCT00000036280.4	UniProtKB/TrEMBL
	ENSSSCT00005066986.1	UniProtKB/TrEMBL
	ENSSSCT00015058533.1	UniProtKB/TrEMBL
	ENSSSCT00025059834.1	UniProtKB/TrEMBL
	ENSSSCT00030097051.1	UniProtKB/TrEMBL
	ENSSSCT00035105108.1	UniProtKB/TrEMBL
	ENSSSCT00040061333.1	UniProtKB/TrEMBL
	ENSSSCT00045038954.1	UniProtKB/TrEMBL
	ENSSSCT00050088281.1	UniProtKB/TrEMBL
	ENSSSCT00055027298.1	UniProtKB/TrEMBL
	ENSSSCT00060019779.1	UniProtKB/TrEMBL
	ENSSSCT00065011602.1	UniProtKB/TrEMBL
	ENSSSCT00070016589.1	UniProtKB/TrEMBL
Gene3D-CATH	3.10.100.10	UniProtKB/TrEMBL
InterPro	C-type_lectin-like	UniProtKB/TrEMBL
	C-type_lectin-like/link_sf	UniProtKB/TrEMBL
	C-type_lectin_CS	UniProtKB/TrEMBL
	CTDL_fold	UniProtKB/TrEMBL
KEGG Report	ssc:100620511	UniProtKB/TrEMBL
NCBI Gene	CLEC3B	ENTREZGENE
PANTHER	TETRANECTIN	UniProtKB/TrEMBL
	TETRANECTIN-RELATED	UniProtKB/TrEMBL
Pfam	Lectin_C	UniProtKB/TrEMBL
PROSITE	C_TYPE_LECTIN_1	UniProtKB/TrEMBL
	C_TYPE_LECTIN_2	UniProtKB/TrEMBL
SMART	CLECT	UniProtKB/TrEMBL
Superfamily-SCOP	SSF56436	UniProtKB/TrEMBL
	Triple coiled coil domain of C-type lectins	UniProtKB/TrEMBL
UniProt	A0A4X1TEJ3	ENTREZGENE, UniProtKB/TrEMBL
	A0A8D0KDH5	ENTREZGENE, UniProtKB/TrEMBL
	F1SRC8	ENTREZGENE, UniProtKB/TrEMBL
VGNC ID	VGNC:86754	ENTREZGENE

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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