Human Gene LSM14B (uc010gjy.1) Description and Page Index
  Description: Homo sapiens LSM14B, SCD6 homolog B (S. cerevisiae) (LSM14B), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr20:60,697,517-60,710,434 Size: 12,918 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr20:60,697,723-60,708,517 Size: 10,795 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:60,697,517-60,710,434)mRNA (may differ from genome)Protein (385 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: LS14B_HUMAN
DESCRIPTION: RecName: Full=Protein LSM14 homolog B; AltName: Full=Protein FAM61B; AltName: Full=RNA-associated protein 55B; Short=hRAP55B;
FUNCTION: May play a role in control of mRNA translation (By similarity).
SUBUNIT: Component of a ribonucleoprotein (RNP) complex (By similarity).
SIMILARITY: Belongs to the LSM14 family.
SIMILARITY: Contains 1 DFDF domain.

-  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: 39.79 RPKM in Testis
Total median expression: 773.15 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 -119.70206-0.581 Picture PostScript Text
3' UTR -432.421230-0.352 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
IPR025762 - DFDF
IPR019050 - FDF_dom
IPR025761 - FFD_box
IPR025609 - Lsm14_N
IPR010920 - LSM_dom
IPR025768 - TFG_box

Pfam Domains:
PF09532 - FDF domain
PF12701 - Scd6-like Sm domain
PF14438 - Ataxin 2 SM domain

ModBase Predicted Comparative 3D Structure on Q9BX40
FrontTopSide
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 BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding

Biological Process:
GO:0006417 regulation of translation
GO:0007275 multicellular organism development


-  Descriptions from all associated GenBank mRNAs
  BC057387 - Homo sapiens LSM14B, SCD6 homolog B (S. cerevisiae), mRNA (cDNA clone MGC:52030 IMAGE:5724236), complete cds.
BC035702 - Homo sapiens LSM14 homolog B (SCD6, S. cerevisiae), mRNA (cDNA clone IMAGE:5551204).
CU691202 - Synthetic construct Homo sapiens gateway clone IMAGE:100021326 5' read LSM14B mRNA.
KJ903862 - Synthetic construct Homo sapiens clone ccsbBroadEn_13256 LSM14B gene, encodes complete protein.
AK058202 - Homo sapiens cDNA FLJ25473 fis, clone TST09650.
AK298748 - Homo sapiens cDNA FLJ52017 complete cds, moderately similar to Protein FAM61B.
JD393520 - Sequence 374544 from Patent EP1572962.
JD135354 - Sequence 116378 from Patent EP1572962.
JD493824 - Sequence 474848 from Patent EP1572962.
JD188902 - Sequence 169926 from Patent EP1572962.
JD052481 - Sequence 33505 from Patent EP1572962.
JD365570 - Sequence 346594 from Patent EP1572962.
JD123470 - Sequence 104494 from Patent EP1572962.
JD059950 - Sequence 40974 from Patent EP1572962.
JD544535 - Sequence 525559 from Patent EP1572962.
JD340517 - Sequence 321541 from Patent EP1572962.
JD109155 - Sequence 90179 from Patent EP1572962.
AF165185 - Homo sapiens FT005 (FT005) mRNA, complete cds.
JD231520 - Sequence 212544 from Patent EP1572962.
JD359019 - Sequence 340043 from Patent EP1572962.
BC054888 - Homo sapiens LSM14B, SCD6 homolog B (S. cerevisiae), mRNA (cDNA clone IMAGE:6565452).
JD497230 - Sequence 478254 from Patent EP1572962.
JD444499 - Sequence 425523 from Patent EP1572962.
JD232422 - Sequence 213446 from Patent EP1572962.
KJ903863 - Synthetic construct Homo sapiens clone ccsbBroadEn_13257 LSM14B gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: C20orf40, FAM61B, LS14B_HUMAN, NM_144703, NP_653304, Q6PFW8, Q96LH8, Q9BX40, RAP55B
UCSC ID: uc010gjy.1
RefSeq Accession: NM_144703
Protein: Q9BX40 (aka LS14B_HUMAN)
CCDS: CCDS46626.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_144703.2
exon count: 9CDS single in 3' UTR: no RNA size: 2618
ORF size: 1158CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2516.00frame shift in genome: no % Coverage: 99.08
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.