H-InvDB x AHG DB
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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000503051 Accession number: BC144652 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to C-type lectin domain family 4 member F isoform 2.
 
 

Transcript original information
Accession number BC144652.1
CAGE tag ID NA
EST ID NA
Clone Number MGC:178200 IMAGE:9053183
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (CLEC4F) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (CLEC4F);
Sequence data provider NA
Annotation project NA
Length of cDNA 1780[bp] (No. of exon:7)[A:538 T:389 G:451 C:402]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Brain, cerebellum, PCR rescued clones
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA NA
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) NA
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0002141
Genomic location  G-integra Help Chromosome 2
Location 2p13.3
Position 71036251- 71047686
Strand -
Possible duplicated location(s) NA
Gene structure 7 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:165530
KEGG GENES KEGG GENES(165530)
GeneCard GeneCardCLEC4F*GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS G-integraG-integra cDNA-genome alignmentcDNA-genome alignment

Predicted CDS information
HIP ID HIP000259563
Predicted CDS 32..1705;  557[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.73
Database links RefSeq NP_001244956
UniProt NA
CCDS NA

Motif information
ORF

length(557),orf(32:1705)
MDGEAVRFCTDNQCVSLHPQEVDSVAMAPAAPKIPRLVQATPAFMAVTLV
FSLVTLFVVVQQQTRPVPKPVQAVILGDNITGHLPFEPNNHHHFGREAEM
RELIQTFKGHMENSSAWVVEIQMLKCRVDNVNSQLQVLGDHLGNTNADIQ
MVKGVLKDATTLSLQTQMLRSSLEGTNAEIQRLKEDLEKADALTFQTLNF
LKSSLENTSIELHVLSRGLENANSEIQMLNASLETANTQAQLANSSLKNA
NAEIYVLRGHLDSVNDLRTQNQVLRNSLEGANAEIQGLKENLQNTNALNS
QTQAFIKSSFDNTSAEIQFLRGHLERAGDEIHVLKRDLKMVTAQTQKANG
RLDQTDTQIQVFKSEMENVNTLNAQIQVLNGHMKNASREIQTLKQGMKNA
SALTSQTQMLDSNLQKASAEIQRLRGDLENTKALTMEIQQEQSRLKTLHV
VITSQEQLQRTQSQLLQMVLQGWKFNGGSLYYFSSVKKSWHEAEQFCVSQ
GAHLASVASKEEQAFLVEFTSKVYYWIGLTDRGTEGSWRWTDGTPFNAAQ
NKAATRG*
a.a.
length
InterPro Name
length(100), motif(450:549) 100 IPR016186 C-type lectin-like [Domain]
length(94), motif(456:549) 94 IPR016187 C-type lectin fold [Domain]
length(84), motif(469:552) 84 IPR001304 C-type lectin [Domain]
length(72), motif(476:547) 72 IPR001304 C-type lectin [Domain]
length(64), motif(487:550) 64 IPR001304 C-type lectin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000503051
H-Inv cluster ID Locus viewHIX0002141
Accession number BC144652.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Similar to C-type lectin domain family 4 member F isoform 2.
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (NP_001244956)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens protein.
Experimental evidence Protein evidence
PubMed ID NA
Gene family/group Gene family H-Inv gene family/group ID NA
Gene family/group name NA
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol CLEC4F
HGNC aliases "C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"
HGNC name C-type lectin domain family 4, member F
DDBJ CLEC4F
UniProt NA
EC number NA
GGDB
(GlycoGene Database)
Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000259563
No. of interaction 20
Interaction partner(s) HIP000016685HIP000027819HIP000028809HIP000039325HIP000046193HIP000057436HIP000059239HIP000063071HIP000065568HIP000065690HIP000097985HIP000108733HIP000112838HIP000114160HIP000119302HIP000168026HIP000177012HIP000361080HIP000381996HIP000381996
BIND NA
DIP 111772E; 
MINT MINT-2879054;  MINT-2879073; 
HPRD 03333; 
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:165530
KEGG GENES KEGG GENES(165530)
GeneCard GeneCardCLEC4F*GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Auto-annotated
Notes NA
Related H-InvDB links Gene familyGene family;  Similarity Search ToolSimilarity Search Tool;  TACTTACT
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA


Subcellular localization information  Last modified:27-May-2015
WoLF PSORT plasma membrane;  cytosol;  mitochondria;  Other; 
Target P Not predicted
SOSUI membrane protein
TMHMM membrane protein
PTS1 Not targeted
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP) GTOP Last modified:27-May-2015
Start End PDB_ID E-value Identity Coverage SCOP_ID
470 547 1ja3A 1e-23 25.6 78/115 d.169.1.1
Related H-InvDB links GTOP GTOP

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
2 .. 2 G/C rs199899515 - 5'UTR
38 .. 38 G/A rs143957481 - CDS Nonsynonymous[Gly3Ser]
45 .. 45 C/T rs202048172 - CDS Nonsynonymous[Ala5Val]
50 .. 50 C/T rs111692180 - CDS Nonsynonymous[Arg7Cys]
85 .. 85 C/A rs150690320 - CDS Nonsynonymous[His18Gln]
107 .. 107 G/A rs200287098 - CDS Nonsynonymous[Ala26Thr]
114 .. 114 C/G rs149541128 - CDS Nonsynonymous[Ala28Gly]
171 .. 171 T/G rs76558637 - CDS Nonsynonymous[Val47Gly]
203 .. 203 G/C rs147008752 - CDS Nonsynonymous[Val58Leu]
208 .. 208 G/A rs200390148 - CDS Synonymous[Val59Val]
250 .. 250 C/T rs17006361 - CDS Synonymous[Ala73Ala]
251 .. 251 G/A rs140483573 - CDS Nonsynonymous[Val74Ile]
333 .. 333 G/A rs2075221 - CDS Nonsynonymous[Arg101Gln]
387 .. 387 T/C rs146659719 - CDS Nonsynonymous[Val119Ala]
404 .. 404 A/C rs116477018 - CDS Nonsynonymous[Lys125Gln]
430 .. 430 G/A rs183733688 - CDS Synonymous[Ser133Ser]
468 .. 468 A/G rs61754946 - CDS Nonsynonymous[Asn146Ser]
481 .. 481 G/C rs141757870 - CDS Nonsynonymous[Gln150His]
483 .. 483 T/C rs117307369 - CDS Nonsynonymous[Met151Thr]
515 .. 515 T/C rs200651188 - CDS Synonymous[Leu162Leu]
547 ^ 548 -/C rs34256142 - CDS
585 .. 585 A/G rs111606232 - CDS Nonsynonymous[Glu185Gly]
604 .. 604 T/C rs190522067 - CDS Synonymous[Asp191Asp]
619 .. 619 G/T rs138316123 - CDS Nonsynonymous[Gln196His]
621 .. 621 C/T rs149379407 - CDS Nonsynonymous[Thr197Met]
648 .. 648 A/G rs201869143 - CDS Nonsynonymous[Glu206Gly]
671 .. 671 G/A rs150218766 - CDS Nonsynonymous[Val214Met]
693 .. 693 A/C rs200019956 - CDS Nonsynonymous[Asn221Thr]
714 .. 714 T/G rs146602856 - CDS Nonsynonymous[Met228Arg]
735 .. 735 C/T rs78458500 - CDS Nonsynonymous[Thr235Met]
760 .. 760 C/T rs142040724 - CDS Synonymous[Ala243Ala]
763 .. 763 T/C rs113852847 - CDS Synonymous[Asn244Asn]
773 .. 773 A/G rs139690383 - CDS Nonsynonymous[Lys248Glu]
778 .. 778 C/T rs142908853 - CDS Synonymous[Asn249Asn]
782 .. 782 A/G rs62622841 - CDS Nonsynonymous[Asn251Asp]
816 .. 816 A/T rs78241995 - CDS Nonsynonymous[Asp262Val]
920 .. 920 G/A rs188433625 - CDS Nonsynonymous[Ala297Thr]
928 .. 928 C/T rs144405556 - CDS Synonymous[Asn299Asn]
932 .. 932 C/T rs199515969 - CDS AA-STOP[Gln301*]
937 .. 937 C/G rs114209954 - CDS Synonymous[Thr302Thr]
1027 .. 1027 C/T rs186061685 - CDS Synonymous[His332His]
1028 .. 1028 G/A rs150268223 - CDS Nonsynonymous[Val333Met]
1077 .. 1077 A/G rs35381972 + CDS Nonsynonymous[Asn349Ser]
1083 .. 1083 G/A rs722896 + CDS Nonsynonymous[Arg351His]
1087 .. 1087 G/T rs144360819 - CDS Synonymous[Leu352Leu]
1114 .. 1114 A/G rs114477809 - CDS Synonymous[Val361Val]
1137 .. 1137 T/C rs34318515 + CDS Nonsynonymous[Val369Ala]
1143 .. 1143 C/T rs146366027 - CDS Nonsynonymous[Thr371Ile]
1144 .. 1144 C/T rs180671756 - CDS Synonymous[Thr371Thr]
1169 .. 1169 A/C rs115197636 - CDS Nonsynonymous[Asn380His]
1190 .. 1190 A/G rs149210018 - CDS Nonsynonymous[Ser387Gly]
1212 .. 1212 A/C rs137920767 - CDS Nonsynonymous[Lys394Thr]
1234 .. 1234 A/G rs141231276 - CDS Synonymous[Ser401Ser]
1251 .. 1251 C/T rs61740120 - CDS Nonsynonymous[Thr407Ile]
1254 .. 1254 A/G rs150978300 - CDS Nonsynonymous[Gln408Arg]
1264 .. 1264 C/T rs148473537 - CDS Synonymous[Asp411Asp]
1288 .. 1288 C/T rs144178729 - CDS Synonymous[Ala419Ala]
1330 .. 1330 T/C rs199714505 - CDS Synonymous[Ala433Ala]
1347 .. 1347 A/C rs142016693 - CDS Nonsynonymous[Gln439Pro]
1456 .. 1456 C/T rs201125258 - CDS Synonymous[Phe475Phe]
1485 .. 1485 G/C rs150657543 - CDS Nonsynonymous[Ser485Thr]
1494 .. 1494 A/G rs200559066 - CDS Nonsynonymous[Lys488Arg]
1511 .. 1511 G/A rs142013309 - CDS Nonsynonymous[Glu494Lys]
1522 .. 1522 C/T rs138154208 - CDS Synonymous[Cys497Cys]
1523 .. 1523 G/A rs113999331 - CDS Nonsynonymous[Val498Met]
1566 .. 1566 A/T rs145897327 - CDS Nonsynonymous[Glu512Val]
1578 .. 1578 T/C rs34875126 + CDS Nonsynonymous[Leu516Pro]
1599 .. 1599 T/C rs150339964 - CDS Nonsynonymous[Val523Ala]
1600 .. 1600 G/C rs146771126 - CDS Synonymous[Val523Val]
1613 .. 1613 G/A rs201804036 - CDS Nonsynonymous[Gly528Ser]
1624 .. 1624 C/G rs144900238 - CDS Nonsynonymous[Asp531Glu]
1629 .. 1629 G/A rs35001900 + CDS Nonsynonymous[Gly533Asp]
1646 .. 1646 C/T rs148732839 - CDS Nonsynonymous[Arg539Cys]
1647 .. 1647 G/A rs139353507 - CDS Nonsynonymous[Arg539His]
1664 .. 1664 C/G rs143296096 - CDS Nonsynonymous[Pro545Ala]
1676 .. 1676 G/A rs201579889 - CDS Nonsynonymous[Ala549Thr]
1681 .. 1681 G/T rs145732605 - CDS Nonsynonymous[Gln550His]
1701 .. 1701 G/T rs79617432 - CDS Nonsynonymous[Gly557Val]
1728 .. 1728 C/T rs200582927 - 3'UTR
1761 .. 1761 C/T rs60744039 - 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
No data available
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
No data available
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD)
Related H-InvDB links VaryGeneVaryGene Repeat mask viewerRepeat Mask Viewer