Human Gene RBM27 (uc003lnz.4)
  Description: Homo sapiens RNA binding motif protein 27 (RBM27), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:145,583,163-145,668,784 Size: 85,622 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr5:145,583,329-145,665,593 Size: 82,265 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:145,583,163-145,668,784)mRNA (may differ from genome)Protein (1060 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RBM27_HUMAN
DESCRIPTION: RecName: Full=RNA-binding protein 27; AltName: Full=RNA-binding motif protein 27;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus speckle. Note=Incorporated into the nuclear speckles and to speckles proximal to the nuclear periphery. Also localizes to punctate structures in the cytoplasm termed cytospeckles (By similarity).
DOMAIN: The RRM domain mediates integration into cytospeckles (By similarity).
SIMILARITY: Contains 1 C3H1-type zinc finger.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RBM27
CDC HuGE Published Literature: RBM27

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 10.70 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 221.29 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -77.70166-0.468 Picture PostScript Text
3' UTR -789.973191-0.248 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR002483 - PWI
IPR000504 - RRM_dom
IPR000571 - Znf_CCCH

Pfam Domains:
PF00642 - Zinc finger C-x8-C-x5-C-x3-H type (and similar)
PF01480 - PWI domain

SCOP Domains:
101233 - PWI domain
54928 - RNA-binding domain, RBD
90229 - CCCH zinc finger

ModBase Predicted Comparative 3D Structure on Q9P2N5
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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 orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0006397 mRNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AK128738 - Homo sapiens cDNA FLJ16787 fis, clone PLACE6013222, weakly similar to Mus musculus RNA binding motif protein 26 (Rbm26), mRNA.
BX647384 - Homo sapiens mRNA; cDNA DKFZp686P2236 (from clone DKFZp686P2236).
BC029648 - Homo sapiens RNA binding motif protein 27, mRNA (cDNA clone IMAGE:4401038), partial cds.
AB037732 - Homo sapiens mRNA for KIAA1311 protein, partial cds.
JD165616 - Sequence 146640 from Patent EP1572962.
BC009537 - Homo sapiens RNA binding motif protein 27, mRNA (cDNA clone IMAGE:3892831), partial cds.
JD466544 - Sequence 447568 from Patent EP1572962.
JD196217 - Sequence 177241 from Patent EP1572962.
JD129360 - Sequence 110384 from Patent EP1572962.
JD134603 - Sequence 115627 from Patent EP1572962.
JD310379 - Sequence 291403 from Patent EP1572962.
JD373013 - Sequence 354037 from Patent EP1572962.
BC033524 - Homo sapiens RNA binding motif protein 27, mRNA (cDNA clone IMAGE:3458303), partial cds.
AL833706 - Homo sapiens mRNA; cDNA DKFZp667L189 (from clone DKFZp667L189).
BC047011 - Homo sapiens mRNA similar to hypothetical protein A730010I06 (cDNA clone IMAGE:4520147).
JD303092 - Sequence 284116 from Patent EP1572962.
JD344537 - Sequence 325561 from Patent EP1572962.
JD499622 - Sequence 480646 from Patent EP1572962.
JD459614 - Sequence 440638 from Patent EP1572962.
JD238675 - Sequence 219699 from Patent EP1572962.
JD167509 - Sequence 148533 from Patent EP1572962.
AK074316 - Homo sapiens cDNA FLJ23736 fis, clone HEP14948.
JD529912 - Sequence 510936 from Patent EP1572962.
JD423413 - Sequence 404437 from Patent EP1572962.
JD092240 - Sequence 73264 from Patent EP1572962.
JD391500 - Sequence 372524 from Patent EP1572962.
JD046649 - Sequence 27673 from Patent EP1572962.
JD184577 - Sequence 165601 from Patent EP1572962.
JD205902 - Sequence 186926 from Patent EP1572962.
AK026358 - Homo sapiens cDNA: FLJ22705 fis, clone HSI13142.
JD247913 - Sequence 228937 from Patent EP1572962.
JD509476 - Sequence 490500 from Patent EP1572962.
JD261902 - Sequence 242926 from Patent EP1572962.
JD566751 - Sequence 547775 from Patent EP1572962.
JD566337 - Sequence 547361 from Patent EP1572962.
JD303183 - Sequence 284207 from Patent EP1572962.
JD299128 - Sequence 280152 from Patent EP1572962.
JD184296 - Sequence 165320 from Patent EP1572962.
JD494988 - Sequence 476012 from Patent EP1572962.
JD509370 - Sequence 490394 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA1311, NM_018989, NP_061862, Q8IYW9, Q9P2N5, RBM27_HUMAN
UCSC ID: uc003lnz.4
RefSeq Accession: NM_018989
Protein: Q9P2N5 (aka RBM27_HUMAN)
CCDS: CCDS43378.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018989.1
exon count: 21CDS single in 3' UTR: no RNA size: 6555
ORF size: 3183CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6533.00frame shift in genome: no % Coverage: 99.77
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.