Human Gene BMS1 (uc001jaj.3) Description and Page Index
  Description: Homo sapiens BMS1 ribosome biogenesis factor (BMS1), mRNA.
RefSeq Summary (NM_014753): This gene likely encodes a ribosome assembly protein. A similar protein in yeast functions in 35S-rRNA processing, which includes a series of cleavage steps critical for formation of 40S ribosomes. Related pseudogenes exist on chromosomes 2, 9, 10, 15, 16, and 22.[provided by RefSeq, Mar 2009]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. ##Evidence-Data-START## Transcript exon combination :: SRR1803617.240369.1, SRR1803611.73866.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000374518.6/ ENSP00000363642.4 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr10:43,277,954-43,330,385 Size: 52,432 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr10:43,279,843-43,326,544 Size: 46,702 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr10:43,277,954-43,330,385)mRNA (may differ from genome)Protein (1282 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Ribosome biogenesis protein BMS1 homolog; AltName: Full=Ribosome assembly protein BMS1 homolog;
FUNCTION: May act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus (By similarity).
SUBCELLULAR LOCATION: Nucleus, nucleolus (By similarity).
SIMILARITY: Belongs to the BMS1/TSR1 family. BMS1 subfamily.
SEQUENCE CAUTION: Sequence=BAA11504.2; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): BMS1
CDC HuGE Published Literature: BMS1
Positive Disease Associations: Diabetic Nephropathies , Hypertension , Neuroblastoma , Supranuclear Palsy, Progressive , Vitamin D
Related Studies:
  1. Diabetic Nephropathies
    , , . [PubMed 0]
  2. Hypertension
    , , . [PubMed 0]
  3. Neuroblastoma
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: BMS1
Diseases sorted by gene-association score: aplasia cutis congenita, nonsyndromic* (1600), aplasia cutis congenita* (440)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.01 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 330.50 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -145.10358-0.405 Picture PostScript Text
3' UTR -1109.233841-0.289 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012948 - AARP2CN
IPR007034 - BMS1_TSR1_C
IPR000795 - ProtSyn_GTP-bd

Pfam Domains:
PF04950 - 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal
PF08142 - AARP2CN (NUC121) domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q14692
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0034511 U3 snoRNA binding

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000479 endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0030686 90S preribosome

-  Descriptions from all associated GenBank mRNAs
  AK308420 - Homo sapiens cDNA, FLJ98368.
BC043345 - Homo sapiens BMS1 homolog, ribosome assembly protein (yeast), mRNA (cDNA clone MGC:49890 IMAGE:6062924), complete cds.
D80009 - Homo sapiens KIAA0187 mRNA.
BC150252 - Homo sapiens BMS1 homolog, ribosome assembly protein (yeast), mRNA (cDNA clone MGC:166808 IMAGE:9007274), complete cds.
KJ898093 - Synthetic construct Homo sapiens clone ccsbBroadEn_07487 BMS1 gene, encodes complete protein.
AB385294 - Synthetic construct DNA, clone: pF1KA0187, Homo sapiens BMS1 gene for ribosome biogenesis protein BMS1 homolog, complete cds, without stop codon, in Flexi system.
DQ592769 - Homo sapiens piRNA piR-59881, complete sequence.
JD465092 - Sequence 446116 from Patent EP1572962.
JD221509 - Sequence 202533 from Patent EP1572962.
JD565471 - Sequence 546495 from Patent EP1572962.
JD182428 - Sequence 163452 from Patent EP1572962.
JD498063 - Sequence 479087 from Patent EP1572962.
JD080486 - Sequence 61510 from Patent EP1572962.
JD527024 - Sequence 508048 from Patent EP1572962.
JD518459 - Sequence 499483 from Patent EP1572962.
JD182371 - Sequence 163395 from Patent EP1572962.
JD036765 - Sequence 17789 from Patent EP1572962.
JD036764 - Sequence 17788 from Patent EP1572962.
JD320124 - Sequence 301148 from Patent EP1572962.
JD077545 - Sequence 58569 from Patent EP1572962.
JD492803 - Sequence 473827 from Patent EP1572962.
JD183038 - Sequence 164062 from Patent EP1572962.
JD193786 - Sequence 174810 from Patent EP1572962.
JD436974 - Sequence 417998 from Patent EP1572962.
JD278505 - Sequence 259529 from Patent EP1572962.
JD290430 - Sequence 271454 from Patent EP1572962.
JD528400 - Sequence 509424 from Patent EP1572962.
JD286350 - Sequence 267374 from Patent EP1572962.
JD225881 - Sequence 206905 from Patent EP1572962.
JD377614 - Sequence 358638 from Patent EP1572962.
JD028287 - Sequence 9311 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q14692 (Reactome details) participates in the following event(s):

R-HSA-6790906 EMG1 of the SSU processome methylates pseudouridine-1248 of 18S rRNA yielding N(1)-methylpseudouridine-1248
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: BMS1L, BMS1_HUMAN, KIAA0187, NM_014753, NP_055568, Q14692, Q5QPT5, Q86XJ9
UCSC ID: uc001jaj.3
RefSeq Accession: NM_014753
Protein: Q14692 (aka BMS1_HUMAN)
CCDS: CCDS7199.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_014753.3
exon count: 23CDS single in 3' UTR: no RNA size: 8048
ORF size: 3849CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6592.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.