Homo sapiens complex locus YIPF3, encoding Yip1 domain family, member 3.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.b), 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.
Expression: According to AceView, this gene is expressed at high level, 3.4 times the average gene in this release. The sequence of this gene is defined by 391 GenBank accessions from 358 cDNA clones, some from placenta cot 25-normalized (seen 29 times), brain (22), ovary (13), placenta (13), kidney (10), breast (9), eye (9) and 112 other tissues. We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 22 distinct gt-ag introns. Transcription produces 17 alternatively spliced mRNAs. There are 2 probable alternative promotors, 3 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 6 cassette exons, overlapping exons with different boundaries, splicing versus retention of 15 introns.
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 cAug10, dAug10, eAug10, iAug10).
Function: There is one article specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in a process (cell differentiation). Proteins are expected to localize in various compartments (Golgi apparatus, intracellular membrane-bounded organelle, transport vesicle, cytoplasm, integral to membrane, plasma membrane). Putative protein interactors have been described (PLSCR1, YIPF4).
Protein coding potential: 15 spliced mRNAs putatively encode good proteins, altogether 14 different isoforms (10 complete, 4 partial), some containing Yip1 domain [Pfam], some transmembrane domains, a N-myristoylation domain, a coiled coil stretch [Psort2]. The remaining 2 mRNA variants (2 spliced) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 6, links to other databases and other names
Map: This gene YIPF3 maps on chromosome 6, at 6p21.1 according to Entrez Gene. In AceView, it covers 5.22 kb, from 43484728 to 43479506 (NCBI 37, August 2010), on the reverse strand.
Links to: the SNP view, gene overviews from Entrez Gene 25844, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as YIPF3, RP3-337H4.3, KLIP1, FinGER3, C6orf109, dJ337H4.3, DKFZp566C243, LOC25844 or soykleybu, takleybu. It has been described as protein YIPF3, OTTHUMP00000016462, OTTHUMP00000016463, OTTHUMP00000217265, OTTHUMP00000217266, OTTHUMP00000217267, OTTHUMP00000217268, OTTHUMP00000217272, killer lineage protein 1, natural killer cell-specific antigen KLIP1.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Yipf3 (e=3 10-64).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 2J996 (e=2 10-19).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT5G27490 (e=0.002)
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!.
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          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.
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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
unit
pre-mRNA
Downstream sequence
aAug10 1441 bp 356 aa 131 bp 239 bp 2kb probably including promoter 5011 bp 1kb
bAug10 1635 bp 350 aa 183 bp 399 bp 2kb including Promoter 5223 bp 1kb
cAug10 1321 bp 315 aa 365 bp 8 bp 192 bp 2kb probably including promoter 4814 bp 1kb
dAug10 1587 bp 315 aa 342 bp 297 bp 189 bp 2kb probably including promoter 5083 bp 1kb
eAug10 1813 bp 263 aa 881 bp 140 bp 240 bp 2kb including Promoter 4774 bp 1kb
fAug10 1252 bp 261 aa 175 bp 291 bp 2kb possibly including promoter 5107 bp 1kb
gAug10 777 bp 259 aa 2kb probably including promoter 4093 bp 1kb
hAug10 823 bp 226 aa 145 bp 2kb probably including promoter 4192 bp 1kb
iAug10 1528 bp 224 aa 520 bp 333 bp 189 bp 2kb probably including promoter 5035 bp 1kb
jAug10 1453 bp 193 aa 570 bp 301 bp 2kb probably including promoter 5087 bp 1kb
kAug10 513 bp 170 aa 2kb 2976 bp 1kb
lAug10 1873 bp 157 aa 238 bp 1161 bp 81 bp 2kb possibly including promoter 4783 bp 1kb
mAug10 772 bp 115 aa 114 bp 310 bp 2kb probably including promoter 4146 bp 1kb
nAug10 627 bp 113 aa 64 bp 221 bp 2kb probably including promoter 3513 bp 1kb
oAug10 854 bp 112 aa 517 bp 2kb possibly including promoter 1381 bp 1kb
pAug10 1731 bp 78 aa 380 bp 1114 bp 2kb including Promoter 4525 bp 1kb
qAug10 558 bp 83 aa 184 bp 122 bp 2kb including Promoter 843 bp 1kb

Gene neighbors and Navigator on chromosome 6p21.1 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               1 article in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l, .m, .n, .o, .p, .q Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes CI

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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