Homo sapiens complex locus NPDC1andFUT7, encoding fucosyltransferase 7 (alpha (1,3) fucosyltransferase) and neural proliferation, differentiation and control, 1.
SUMMARY back to top
RefSeq summary
[FUT7] The protein encoded by this gene is a Golgi stack membrane protein that is involved in the creation of sialyl-Lewis X antigens. The encoded protein can direct the synthesis of the E-selectin-binding sialyl-Lewis X moiety. [provided by RefSeq].

RefSeq annotates 2 representative transcripts from 2 genes that we see as a complex (NM included in AceView variants .d and .e), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 17 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap, and it merges 2 different NCBI genes.
Expression: According to AceView, this gene is expressed at very high level, 5.2 times the average gene in this release. The sequence of this gene is defined by 593 GenBank accessions from 549 cDNA clones, some from brain (seen 93 times), pancreas (31), prostate (28), hippocampus (25), uterus (25), testis normal (23), lung (21) and 149 other tissues. We annotate structural defects or features in 15 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 17 distinct gt-ag introns. Transcription produces 22 different mRNAs, 17 alternatively spliced variants and 5 unspliced forms. There are 4 probable alternative promotors, 6 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 2 cassette exons, overlapping exons with different boundaries, splicing versus retention of 6 introns. 1405 bp of this gene are antisense to spliced gene C9orf139, raising the possibility of regulated alternate expression.
2 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD).
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant dAug10).
Function: There are 31 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Burkitt lymphoma; Cell Transformation, Neoplastic; Hypertension; Leukemia, Promyelocytic, Acute; Pancreatic Neoplasms) and proposed to participate in pathway (Glycosphingolipid biosynthesis - lacto and neolacto series). Proteins are expected to have molecular function (transferase activity, transferring glycosyl groups) and to localize in various compartments (Golgi membrane, nuclear membrane, Golgi cisterna membrane, integral to membrane). Putative protein interactors have been described (CCND1, CCND2, CCND3, CDK2, E2F1, HNRNPK, KRTAP4-12, MADD, MDFI, NPDC1ANDFUT7, PLSCR1, TFDP1, TLR10).
Protein coding potential: 16 spliced and 3 unspliced mRNAs putatively encode good proteins, altogether 19 different isoforms (11 complete, 4 COOH complete, 4 partial), some containing domains Glycosyltransferase family 10 (fucosyltransferase), Neural proliferation differentiation control-1 protein (NPDC1) [Pfam], some transmembrane domains, a prenylation domain [Psort2]. The remaining 3 mRNA variants (1 spliced, 2 unspliced; 1 partial) appear not to encode good proteins.
2 isoforms are annotated using as Met a Kozak-compatible non-AUG start, thereby gaining a minimum of 122 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by phosphorylation; ubiquitination, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 9, links to other databases and other names
Map: This gene NPDC1andFUT7 maps on chromosome 9, at 9q34.3 according to Entrez Gene. In AceView, it covers 16.52 kb, from 139941150 to 139924626 (NCBI 37, August 2010), on the reverse strand.
Links to: , manual annotations from GAD, KEGG_00601, PhosphoSite, the SNP view, SNP view, gene overviews from Entrez Gene 2529, 56654, GeneCards, expression data from ECgene, UniGene Hs.457, Hs.719906, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as NPDC1andFUT7, FucT-VII, RP11-229P13.1, CAB, CAB-, CAB1, CAB-1, DKFZp586J0523, FUT7, NPDC1 or LOC2529, LOC56654. It has been described as alpha-(1,3)-fucosyltransferase, fuc-TVII, fucosyltransferase VII, selectin ligand synthase, selectin-ligand synthase, galactoside 3-L-fucosyltransferase, neural proliferation differentiation and control protein 1, NPDC-1.
EC number: This gene encodes protein number: 2.4.1.-.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Entpd2andNpdc1 (e=7 10-82).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene cab-1 (e=3 10-06), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes FUT12andAT1G49700 (e=2 10-13), FUT11 (e=10-11), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
Downstream sequence
aAug10 3541 bp 524 aa 1664 bp 302 bp 2kb possibly including promoter 5977 bp 1kb
bAug10 2057 bp 391 aa 669 bp 212 bp 2kb including Promoter 7191 bp 1kb
cAug10 1034 bp 344 aa 2kb 6366 bp 1kb
dAug10 2584 bp 342 aa 1019 bp 536 bp 105 bp 2kb possibly including promoter 2837 bp 1kb
eAug10 2002 bp 325 aa 709 bp 315 bp 2kb including Promoter 7242 bp 1kb
fAug10 1407 bp 298 aa 190 bp 320 bp 2kb including Promoter 8601 bp 1kb
gAug10 1564 bp 267 aa 189 bp 571 bp 2kb including Promoter 6716 bp 1kb
hAug10 1335 bp 236 aa 78 bp 546 bp 2kb possibly including promoter 14647 bp 1kb
iAug10-unspliced 1245 bp 215 aa 598 bp 2kb possibly including promoter 1245 bp 1kb
jAug10 735 bp 208 aa 96 bp 12 bp 2kb probably including promoter 5431 bp 1kb
kAug10 763 bp 194 aa 179 bp 2kb probably including promoter 5383 bp 1kb
lAug10-unspliced 457 bp 151 aa 2kb probably including promoter 457 bp 1kb
mAug10 882 bp 142 aa 452 bp 2kb 1184 bp 1kb
nAug10 718 bp 141 aa 85 bp 207 bp 2kb probably including promoter 5261 bp 1kb
oAug10 800 bp 131 aa 190 bp 214 bp 2kb probably including promoter 3604 bp 1kb
pAug10-unspliced 490 bp 118 aa 131 bp 2kb 490 bp 1kb
qAug10 361 bp 116 aa 9 bp 2kb 698 bp 1kb
rAug10 645 bp 75 aa 266 bp 151 bp 36 bp 2kb possibly including promoter 751 bp 1kb
sAug10 335 bp 61 aa 149 bp 2kb 2407 bp 1kb
tAug10-unspliced 567 bp 86 aa 30 bp 276 bp 2kb including Promoter 567 bp 1kb
uAug10-unspliced 392 bp 38 aa 224 bp 51 bp 2kb 392 bp 1kb
vaAug10 108 bp 36 aa 2kb 178 bp 1kb

Gene neighbors and Navigator on chromosome 9q34.3 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications        
Annotated mRNA diagrams back to top
Bibliography:               31 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i-u, .j, .k, .l-u, .m, .n, .o, .p-u, .q, .r, .s, .t-u, .u-u, .va Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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