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Identifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. We applied a proteogenomics strategy to detect un-annotated protein-coding regions in mouse genome. High-accuracy tandem mass spectrometry (MS/MS) data from diverse mouse samples were generated by LTQ-Orbitrap mass spectrometer in house. Two searchable diagnostic proteomic...
The first complete mammalian genomic sequence reported thus far in the Notch gene family, including a putative promoter region and 30 exons of the human NOTCH4 gene spanning 56.8 kb of DNA, were sequenced. The NOTCH4 locus contains a TATA-less promoter with two putative transcription initiation sites (Inr), three RBP-Jκ sites, and two GATA recognition sites. Two cDNA isoforms, NOTCH4(L) and NOTCH4(S),were...
To elucidate the complete gene structure and to identify new genes involved in the development ofHLAclass I antigen-associated diseases in the class I region of the human major histocompatibility complex on chromosome 6, a YAC clone (745D12) covering the 146-kb segment around theIkBLandMICAloci was isolated from a YAC library constructed from the B-cell line, BOLETH. A physical map of this region...
A cosmid contig was constructed from a YAC clone with a 220-kb insert that spans the centromeric side of the human MHC class II region, corresponding to the mousetcomplex. The gene order was identified to beHSET–HKE1.5–HKE2–HKE3–RING1–HKE6–HKE 4 (RING5).The genomic sequence of a 42,801-bp long region encoded by one cosmid clone in theRING1, HKE6,andHKE4subregions was determined by the shotgun method...
To elucidate the detailed gene organization of the human leukocyte antigen (HLA) class I region on chromosome 6, seven contiguous cosmid genomic clones covering the 237-kb segment around the HLA-B and -C loci were subjected to DNA sequencing by the shotgun strategy to give a single contig of 236,822 bp from the MICA gene (58.2 kb centromeric of HLA-B) to 90.8 kb telomeric of HLA-C. This region was...
cDNA clones corresponding to theHKE4andHKE6genes at the centromeric end of the HLA region on human chromosome 6p21.3 were isolated and characterized. The predicted amino acid sequences of HKE4 and HKE6 exhibited 81.5 and 85.6% identity to the mouse homologues, Ke4 and Ke6, respectively.HKE4may encode a membrane protein with histidine-rich charge clusters. HKE6 possesses remarkable amino acid sequence...
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