Homo sapiens gene MR1, encoding major histocompatibility complex, class I-related.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), 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 7 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 0.9 times the average gene in this release. The sequence of this gene is defined by 102 GenBank accessions from 93 cDNA clones, some from kidney (seen 8 times), brain (5), placenta cot 25-normalized (5), 2 pooled tumors (clear cell type) (4), placenta (4), uterus (4), lung (3) and 48 other tissues. We annotate structural defects or features in 15 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 12 distinct gt-ag introns. Transcription produces 10 different mRNAs, 7 alternatively spliced variants and 3 unspliced forms. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 5 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 4 cassette exons, overlapping exons with different boundaries.
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 aAug10).
Function: There are 14 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes (antigen processing and presentation, antigen processing and presentation of peptide antigen via MHC class I, immune response). Proteins are expected to have molecular function (MHC class I receptor activity) and to localize in various compartments (cytoplasm, membrane, endoplasmic reticulum, extracellular region, integral to membrane, MHC class I protein complex, plasma membrane).
Protein coding potential: 7 spliced and the unspliced mRNAs putatively encode good proteins, altogether 8 different isoforms (7 complete, 1 partial), some containing domains Immunoglobulin C1-set domain, Class I Histocompatibility antigen, domains alpha 1 and 2 [Pfam], some transmembrane domains [Psort2]. The remaining 2 mRNA variants (2 unspliced; 1 partial) 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 1, links to other databases and other names
Map: This gene MR1 maps on chromosome 1, at 1q25.3 according to Entrez Gene. In AceView, it covers 23.18 kb, from 181002510 to 181025690 (NCBI 37, August 2010), on the direct strand.
Links to: the SNP view, gene overviews from Entrez Gene 3140, 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 MR1, RP11-309G3.1 or HLALS, LOC3140. It has been described as major histocompatibility complex class I-related gene protein, MHC class I-like antigen MR-1, MHC class-I related-gene protein, class I histocompatibility antigen-like protein, major histocompatibility complex, class I-like sequence.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Mr1 (e= 10-102).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene cutl-14 (e=0.26), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes glubo (e=0.52), AT5G51920 (e=0.52), 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
MR1 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 1.55 6.21 5.40 3.33 6.65 1.10 8.78 8.78 2.52 0.72 3.57 2.90 5.04 2.52 8.19 3.33 8.78 8.78 1.45 7.64 4.71 18.8 5.79 0.83 0.59 1.55 14.3 1.78 6.65 7.64 1.91 14.3 3.82 2.90 2.90 1.18 3.82 2.70 3.57 3.33 2.35 8.78 2.90 5.40 7.64 6.65 0.32 0.39 1.35 10.8 4.10 1.55 0.68 11.6 8.19 6.21 1.78 2.90 1.55 13.3 9.41 5.79 6.21 1.78 10.1 1.66 5.79 5.04 0.48 0.59 2.90 3.57 1.78 2.05 2.90 1.45 4.39 3.82 0.45 2.19 5.04 9.41 2.52 1.91 1.26 2.70 2.70 12.4 2.52 1.35 6.65 2.52 6.65 3.82 1.18 7.13 2.52 2.70 10.1 3.10 1.18 0.48 18.8 10.1 8.78 3.82 6.65 0.48 6.65 6.21 5.79 10.1 2.70 1.26 4.10 6.65 2.52 2.52 3.57 1.91 4.10 1.78 5.79 1.78 1.45 9.41 2.35 5.40 16.4 8.19 6.65 14.3 10.8 5.04 0.34 2.19 0.39 2.35 2.90 7.13 3.57 8.78 1.26 7.64 4.39 3.33 1.45 1.26 1.55 6.65 4.10 17.6 11.6 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions 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 HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene MR1 5' 3' encoded on plus strand of chromosome 1 from 181,002,510 to 181,025,690 56 11454 12483 4820 6710 18003 a [NM] 11454 10 4820 6710 18003 b 11454 12483 10780 18003 c 11454 12483 d h-u j-u 11454 12483 261 e i-u 96 12483 4820 f 147 255 12483 10780 18003 g 1 2kb 0 91 bp exon 422 bp [gt-ag] intron 2 GenBank accessions 54 RNA-seq supporting reads 9 UHR pooled cells 12 Brain 4 Blood 28 Neuroblastoma 1 Other (also 4 Primates bodymap) 188 bp exon 188 bp exon 243 bp uORF 188 bp exon 14977 bp [gt-ag] intron 52 GenBank accessions 11402 RNA-seq supporting reads 2249 UHR pooled cells 511 Brain 5532 Blood 2973 Neuroblastoma 137 Other (also 967 Primates bodymap) 243 bp uORF 261 bp exon 261 bp exon 698 bp [gt-ag] intron 45 GenBank accessions 12438 RNA-seq supporting reads 2557 UHR pooled cells 456 Brain 6208 Blood 3138 Neuroblastoma 79 Other (also 1536 Primates bodymap) 276 bp exon 276 bp exon 1948 bp [gt-ag] intron 20 GenBank accessions 4800 RNA-seq supporting reads 1157 UHR pooled cells 214 Brain 2111 Blood 1276 Neuroblastoma 42 Other (also 1871 Primates bodymap) 276 bp exon 276 bp exon 1062 bp [gt-ag] intron 12 GenBank accessions 6698 RNA-seq supporting reads 1543 UHR pooled cells 294 Brain 2794 Blood 2008 Neuroblastoma 59 Other (also 1870 Primates bodymap) 105 bp exon 105 bp exon 1547 bp [gt-ag] intron 28 GenBank accessions 17975 RNA-seq supporting reads 3798 UHR pooled cells 790 Brain 8033 Blood 5213 Neuroblastoma 141 Other (also 2040 Primates bodymap) 324 bp exon 324 bp exon 13 accessions, NM_001531.1 some from brain glioblastoma (seen once) breast cancer (once) kidney (once), mammary gland (cancer tissue) (once) normal nasopharynx (once) Validated 3' end, 2 accessions 324 bp exon 70 bp exon 70 bp exon 14977 bp [gt-ag] intron 52 GenBank accessions 11402 RNA-seq supporting reads 2249 UHR pooled cells 511 Brain 5532 Blood 2973 Neuroblastoma 137 Other (also 967 Primates bodymap) 261 bp exon 833 bp [gt-ag] intron 7 GenBank accessions 3 RNA-seq supporting reads 2 Blood 1 Neuroblastoma 141 bp exon 1948 bp [gt-ag] intron 20 GenBank accessions 4800 RNA-seq supporting reads 1157 UHR pooled cells 214 Brain 2111 Blood 1276 Neuroblastoma 42 Other (also 1871 Primates bodymap) 276 bp exon 1062 bp [gt-ag] intron 12 GenBank accessions 6698 RNA-seq supporting reads 1543 UHR pooled cells 294 Brain 2794 Blood 2008 Neuroblastoma 59 Other (also 1870 Primates bodymap) 105 bp exon 1547 bp [gt-ag] intron 28 GenBank accessions 17975 RNA-seq supporting reads 3798 UHR pooled cells 790 Brain 8033 Blood 5213 Neuroblastoma 141 Other (also 2040 Primates bodymap) 298 bp exon 9 accessions, some from breast carcinoma (seen once) chondrosarcoma cell line (once) embryonal carcinoma, cell line (once) testis (once), testis embryonal carcinoma (once) Validated 3' end, 2 accessions 298 bp exon 92 bp exon 92 bp exon 14977 bp [gt-ag] intron 52 GenBank accessions 11402 RNA-seq supporting reads 2249 UHR pooled cells 511 Brain 5532 Blood 2973 Neuroblastoma 137 Other (also 967 Primates bodymap) 261 bp exon 698 bp [gt-ag] intron 45 GenBank accessions 12438 RNA-seq supporting reads 2557 UHR pooled cells 456 Brain 6208 Blood 3138 Neuroblastoma 79 Other (also 1536 Primates bodymap) 276 bp exon 3286 bp [gt-ag] intron 15 GenBank accessions 10765 RNA-seq supporting reads 1979 UHR pooled cells 421 Brain 5665 Blood 2621 Neuroblastoma 79 Other (also 57 Primates bodymap) 105 bp exon 1547 bp [gt-ag] intron 28 GenBank accessions 17975 RNA-seq supporting reads 3798 UHR pooled cells 790 Brain 8033 Blood 5213 Neuroblastoma 141 Other (also 2040 Primates bodymap) 1329 bp exon 34 accessions, some from placenta cot 25-normalized (seen 5 times) 2 pooled tumors (clear cell type) (4) kidney (4), lung (3) placenta (3) capped 5' end, 2 accessions Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 4 accessions 1329 bp exon 82 bp exon 82 bp exon 14977 bp [gt-ag] intron 52 GenBank accessions 11402 RNA-seq supporting reads 2249 UHR pooled cells 511 Brain 5532 Blood 2973 Neuroblastoma 137 Other (also 967 Primates bodymap) 261 bp exon 698 bp [gt-ag] intron 45 GenBank accessions 12438 RNA-seq supporting reads 2557 UHR pooled cells 456 Brain 6208 Blood 3138 Neuroblastoma 79 Other (also 1536 Primates bodymap) 1347 bp exon 8 accessions, some from adrenal adenoma (seen once) adrenal gland (once) embryonic stem cells embryoid bodiesderived from H1 H7 and H9 cells (once) kidney (once), nervous tumor (once) 1347 bp exon 584 bp exon 584 bp exon 4 accessions, some from anaplastic oligodendroglioma (seen 2 times) brain (2), kidney (2) 584 bp exon 390 bp exon 390 bp exon 1 accession from colon normal 390 bp exon 144 bp exon 144 bp exon 14977 bp [gt-ag] intron 52 GenBank accessions 11402 RNA-seq supporting reads 2249 UHR pooled cells 511 Brain 5532 Blood 2973 Neuroblastoma 137 Other (also 967 Primates bodymap) 261 bp exon 698 bp [gt-ag] intron 45 GenBank accessions 12438 RNA-seq supporting reads 2557 UHR pooled cells 456 Brain 6208 Blood 3138 Neuroblastoma 79 Other (also 1536 Primates bodymap) 276 bp exon 4938 bp [gt-ag] intron 1 GenBank accession 260 RNA-seq supporting reads 61 UHR pooled cells 12 Brain 139 Blood 47 Neuroblastoma 1 Other (also 21 Primates bodymap) 365 bp exon 21 accessions, some from uterus (seen 3 times) small intestine (2), amygdala (once) brain (once), breast tumor tissue (once) capped 5' end, 1 accession 365 bp exon 578 bp exon 578 bp exon 1 accession 578 bp exon 41 bp exon 4149 bp [gt-ag] intron 1 GenBank accession 95 RNA-seq supporting reads 26 UHR pooled cells 33 Blood 36 Neuroblastoma 261 bp exon 261 bp exon 150 bp uORF 261 bp exon 261 bp exon 698 bp [gt-ag] intron 45 GenBank accessions 12438 RNA-seq supporting reads 2557 UHR pooled cells 456 Brain 6208 Blood 3138 Neuroblastoma 79 Other (also 1536 Primates bodymap) 276 bp exon 276 bp exon 1948 bp [gt-ag] intron 20 GenBank accessions 4800 RNA-seq supporting reads 1157 UHR pooled cells 214 Brain 2111 Blood 1276 Neuroblastoma 42 Other (also 1871 Primates bodymap) 208 bp exon 208 bp exon 1 accession capped 5' end, 1 accession 208 bp exon 65 bp exon 2922 bp [gt-ag] intron 1 GenBank accession 146 RNA-seq supporting reads 18 UHR pooled cells 8 Brain 95 Blood 21 Neuroblastoma 4 Other (also 10 Primates bodymap) 116 bp exon 11939 bp [gt-ag] intron 1 GenBank accession 254 RNA-seq supporting reads 22 UHR pooled cells 6 Brain 178 Blood 46 Neuroblastoma 2 Other (also 43 Primates bodymap) 261 bp exon 261 bp exon 698 bp [gt-ag] intron 45 GenBank accessions 12438 RNA-seq supporting reads 2557 UHR pooled cells 456 Brain 6208 Blood 3138 Neuroblastoma 79 Other (also 1536 Primates bodymap) 276 bp exon 3286 bp [gt-ag] intron 15 GenBank accessions 10765 RNA-seq supporting reads 1979 UHR pooled cells 421 Brain 5665 Blood 2621 Neuroblastoma 79 Other (also 57 Primates bodymap) 105 bp exon 1547 bp [gt-ag] intron 28 GenBank accessions 17975 RNA-seq supporting reads 3798 UHR pooled cells 790 Brain 8033 Blood 5213 Neuroblastoma 141 Other (also 2040 Primates bodymap) 60 bp exon 1 accession from thymus 60 bp exon 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 1521 bp 341 aa 212 bp 283 bp 240 bp 2kb possibly including promoter 22175 bp 1kb
bAug10 1151 bp 296 aa 257 bp 2kb probably including promoter 21518 bp 1kb
cAug10 2063 bp 249 aa 25 bp 1288 bp 2kb including Promoter 22571 bp 1kb
dAug10 1690 bp 220 aa 15 bp 1012 bp 2kb probably including promoter 17365 bp 1kb
eAug10 1046 bp 214 aa 77 bp 324 bp 2kb including Promoter 21659 bp 1kb
fAug10 786 bp 199 aa 187 bp 147 bp 2kb including Promoter 7581 bp 1kb
gAug10 883 bp 178 aa 327 bp 19 bp 2kb probably including promoter 21275 bp 1kb
hAug10-unspliced 584 bp 103 aa 145 bp 127 bp 2kb possibly including promoter 584 bp 1kb
iAug10-unspliced 578 bp 73 aa 186 bp 170 bp 2kb probably including promoter 578 bp 1kb
jAug10-unspliced 390 bp 73 aa 167 bp 2kb 390 bp 1kb

Gene neighbors and Navigator on chromosome 1q25.3 back to top
R XPR1andKIAA1614 C R P R R MR1 C R P R IER5 C R P R G P C I R P STX6 100kb 0 zeyfobu, 18 accessions XPR1andKIAA1614, 439 accessions 17 variants vorbu, 3 accessions, 2 variants weebu, 1 accession MR1, 98 accessions, 10 variants reru, 71 accessions IER5, 248 accessions worbu, 6 accessions, 2 variants LOC100287948, 1 accession CACNA1E, 113 accessions 7 variants rykeybo, 1 accession blajerbu, 1 accession chykley, 1 accession rukeybo, 2 accessions rarkeybo, 2 accessions pleelobu, 2 accessions starlee, 2 accessions plerlobu, 1 accession smarabo, 1 accession mukamo, 2 accessions, 2 variants reekeybo, 1 accession plorlobu, 1 accession ploylobu, 1 accession skalobu, 1 accession skylobu, 1 accession sakeybo, 3 accessions dusybo, 1 accession sukeybo, 1 accession flyjerbu, 1 accession sokeybo, 1 accession smyrabo, 2 accessions skarlobu, 1 accession skeelobu, 1 accession chokley, 1 accession stawlee, 2 accessions flujerbu, 1 accession slylobu, 1 accession smawrabo, 2 accessions slulobu, 1 accession slolobu, 1 accession fasybo, 1 accession chawkley, 1 accession fusybo, 1 accession slorlobu, 1 accession farsybo, 1 accession smylobu, 1 accession flarjerbu, 3 accessions seykeybo, 3 accessions wawbu, 5 accessions smerlobu, 3 accessions soykeybo, 2 accessions smorlobu, 2 accessions fleevoybo, 1 accession snylobu, 1 accession gusybo, 3 accessions snarlobu, 1 accession snarabo, 3 accessions tarkeybo, 1 accession sneelobu, 2 accessions garsybo, 1 accession gawsybo, 1 accession snerlobu, 1 accession sneylobu, 1 accession tawkeybo, 2 accessions florjerbu, 1 accession spulobu, 3 accessions glojerbu, 1 accession flervoybo, 1 accession fleyvoybo, 2 accessions vykeybo, 1 accession vukeybo, 1 accession sporlobu, 1 accession spoylobu, 3 accessions stalobu, 1 accession stylobu, 1 accession verkeybo, 1 accession jawsybo, 1 accession veykeybo, 1 accession bosybo, 1 accession bersybo, 1 accession rokeybo, 2 accessions flajerbu, 1 accession plarlobu, 1 accession plawlobu, 2 accessions pleylobu, 1 accession rerkeybo, 1 accession reykeybo, 1 accession skulobu, 1 accession skawlobu, 1 accession skerlobu, 1 accession skeylobu, 1 accession sawkeybo, 2 accessions flarvoybo, 1 accession slalobu, 1 accession vawbu, 1 accession dosybo, 1 accession darsybo, 1 accession slarlobu, 1 accession sleelobu, 1 accession smeerabo, 2 accessions flojerbu, 1 accession sloylobu, 1 accession smalobu, 1 accession wubu, 4 accessions smolobu, 1 accession cheekley, 2 accessions smeelobu, 3 accessions smoylobu, 1 accession glakoybu, 1 accession smoyrabo, 3 accessions mekamo, 2 accessions, 2 variants mokuyo, 1 accession snalobu, 1 accession mokamo, 2 accessions, 2 variants tykeybo, 1 accession tukeybo, 2 accessions snolobu, 1 accession gosybo, 2 accessions cherkley, 2 accessions gersybo, 3 accessions spalobu, 4 accessions floyjerbu, 1 accession teykeybo, 2 accessions spolobu, 1 accession sparlobu, 1 accession speelobu, 5 accessions woybu, 3 accessions toykeybo, 1 accession sperlobu, 1 accession veekeybo, 1 accession zybu, 1 accession stulobu, 2 accessions jeesybo, 1 accession stolobu, 1 accession starlobu, 1 accession stolee, 2 accessions STX6, 374 accessions, 9 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               14 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h-u, .i-u, .j-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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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