Human Gene LIN28B (uc003pqv.2) Description and Page Index
  Description: Homo sapiens lin-28 homolog B (C. elegans) (LIN28B), mRNA.
RefSeq Summary (NM_001004317): The protein encoded by this gene belongs to the lin-28 family, which is characterized by the presence of a cold-shock domain and a pair of CCHC zinc finger domains. This gene is highly expressed in testis, fetal liver, placenta, and in primary human tumors and cancer cell lines. It is negatively regulated by microRNAs that target sites in the 3' UTR, and overexpression of this gene in primary tumors is linked to the repression of let-7 family of microRNAs and derepression of let-7 targets, which facilitates cellular transformation. [provided by RefSeq, Jun 2012]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: DQ127228.1, BC137526.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968968, SAMEA2142853 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000345080.5/ ENSP00000344401.4 RefSeq Select criteria :: based on conservation ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr6:105,404,923-105,531,207 Size: 126,285 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr6:105,405,126-105,526,658 Size: 121,533 Coding Exon Count: 4 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:105,404,923-105,531,207)mRNA (may differ from genome)Protein (250 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: LN28B_HUMAN
DESCRIPTION: RecName: Full=Protein lin-28 homolog B; Short=Lin-28B;
FUNCTION: Acts as a suppressor of microRNA (miRNA) biogenesis by specifically binding the precursor let-7 (pre-let-7), a miRNA precursor. Acts by binding pre-let-7 and recruiting ZCCHC11/TUT4 uridylyltransferase, leading to the terminal uridylation of pre- let-7. Uridylated pre-let-7 miRNAs fail to be processed by Dicer and undergo degradation. Specifically recognizes the 5'-GGAG-3' motif in the terminal loop of pre-let-7. Also recognizes and binds non pre-let-7 pre-miRNAs that contain the 5'-GGAG-3' motif in the terminal loop, leading to their terminal uridylation and subsequent degradation. Mediates MYC-mediated let-7 repression. Isoform 1, when overexpressed, stimulates growth of the breast adenocarcinoma cell line MCF-7. Isoform 2 has no effect on cell growth.
SUBUNIT: Interacts with ZCCHC11/TUT4.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Predominantly cytoplasmic at G1 phase, accumulates in the nucleus in S and G2 phases. The frequency of nuclear localization in S and in G2 phases is 60% and 30%, respectively.
TISSUE SPECIFICITY: High expression in testis, fetal liver, placenta and in hepatocellular carcinoma (HCC). Isoform 1 is only detected in moderately and poorly differentiated HCC tissues and placenta (at protein level). Isoform 2 is detected in fetal liver, non-tumor liver tissues, as well as well-differentiated tumor tissues (at protein level).
INDUCTION: Might be negatively regulated by the microRNA let-7b.
MISCELLANEOUS: Overexpressed in primary tumors (overall frequency approximately 15%), overexpression being linked to repression of let-7 family miRNAs and derepression of let-7 targets. Facilitates cellular transformation in vitro, and overexpression is associated with advanced disease across multiple tumor types.
SIMILARITY: Belongs to the lin-28 family.
SIMILARITY: Contains 2 CCHC-type zinc fingers.
SIMILARITY: Contains 1 CSD (cold-shock) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LIN28B
CDC HuGE Published Literature: LIN28B
Positive Disease Associations: Body Height , height , Menarche , menarche (age at onset) , menarche and menopause (age at onset) , Neuroblastoma , timing of puberty , Waist Circumference
Related Studies:
  1. Body Height
    , , . [PubMed 0]
  2. Body Height
    , , . [PubMed 0]
  3. Body Height
    Guillaume Lettre et al. Nature genetics 2008, Identification of ten loci associated with height highlights new biological pathways in human growth., Nature genetics. [PubMed 18391950]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: LIN28B
Diseases sorted by gene-association score: neuroblastoma* (9), neuroblastoma, susceptibility (8), idiopathic central precocious puberty (7), oral cavity cancer (7), hepatocellular carcinoma (2), juvenile myelomonocytic leukemia (2)
* = 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: 2.25 RPKM in Testis
Total median expression: 3.66 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 -49.12203-0.242 Picture PostScript Text
3' UTR -1212.214549-0.266 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
IPR011129 - Cold_shock_prot
IPR002059 - CSP_DNA-bd
IPR012340 - NA-bd_OB-fold
IPR016027 - NA-bd_OB-fold-like
IPR001878 - Znf_CCHC

Pfam Domains:
PF00098 - Zinc knuckle
PF00313 - 'Cold-shock' DNA-binding domain
PF14392 - Zinc knuckle

SCOP Domains:
50249 - Nucleic acid-binding proteins
57756 - Retrovirus zinc finger-like domains

Protein Data Bank (PDB) 3-D Structure
MuPIT help

4A4I
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q6ZN17
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 orthologNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
   FlyBaseWormBase 
   Protein SequenceProtein Sequence 
   AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0010587 miRNA catabolic process
GO:0031047 gene silencing by RNA
GO:0031054 pre-miRNA processing
GO:0031123 RNA 3'-end processing

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK131411 - Homo sapiens cDNA FLJ16517 fis, clone NT2RI3007167.
DQ127228 - Homo sapiens LIN28B mRNA, complete cds.
BC137526 - Homo sapiens lin-28 homolog B (C. elegans), mRNA (cDNA clone MGC:169149 IMAGE:9021526), complete cds.
BC137527 - Homo sapiens lin-28 homolog B (C. elegans), mRNA (cDNA clone MGC:169150 IMAGE:9021527), complete cds.
KJ896209 - Synthetic construct Homo sapiens clone ccsbBroadEn_05603 LIN28B gene, encodes complete protein.
BC127712 - Homo sapiens lin-28 homolog B (C. elegans), mRNA (cDNA clone IMAGE:40127308), partial cds.
BC127713 - Homo sapiens lin-28 homolog B (C. elegans), mRNA (cDNA clone IMAGE:40127309), partial cds.
BC141959 - Homo sapiens cDNA clone IMAGE:40127312.
BC141960 - Homo sapiens lin-28 homolog B (C. elegans), mRNA (cDNA clone IMAGE:40127313), partial cds.
BC150537 - Homo sapiens lin-28 homolog B (C. elegans), mRNA (cDNA clone IMAGE:40127314), partial cds.
BC150538 - Homo sapiens lin-28 homolog B (C. elegans), mRNA (cDNA clone IMAGE:40127315), partial cds.
JD019892 - Sequence 916 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A1L165, B2RPN6, CSDD2, LN28B_HUMAN, NM_001004317, NP_001004317, Q5TCM4, Q6ZN17, uc003pqv.1
UCSC ID: uc003pqv.2
RefSeq Accession: NM_001004317
Protein: Q6ZN17 (aka LN28B_HUMAN)
CCDS: CCDS34504.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001004317.3
exon count: 4CDS single in 3' UTR: no RNA size: 5517
ORF size: 753CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1581.00frame shift in genome: no % Coverage: 99.78
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.