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Aliases for LIN28B Gene

Aliases for LIN28B Gene

  • Lin-28 Homolog B 2 3 5
  • Lin-28B 3 4
  • CSDD2 3 4
  • Lin-28 Homolog B (C. Elegans) 2
  • Protein Lin-28 Homolog B 3
  • Lin-28.2 3

External Ids for LIN28B Gene

Previous GeneCards Identifiers for LIN28B Gene

  • GC06P105512
  • GC06P105404
  • GC06P102848

Summaries for LIN28B Gene

Entrez Gene Summary for LIN28B Gene

  • 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]

GeneCards Summary for LIN28B Gene

LIN28B (Lin-28 Homolog B) is a Protein Coding gene. Diseases associated with LIN28B include Neuroblastoma and Idiopathic Central Precocious Puberty. Among its related pathways are Cardiac Progenitor Differentiation and Validated targets of C-MYC transcriptional activation. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is LIN28A.

UniProtKB/Swiss-Prot for LIN28B Gene

  • Suppressor of microRNA (miRNA) biogenesis, including that of let-7 and possibly of miR107, miR-143 and miR-200c. Binds primary let-7 transcripts (pri-let-7), including pri-let-7g and pri-let-7a-1, and sequester them in the nucleolus, away from the microprocessor complex, hence preventing their processing into mature miRNA (PubMed:22118463). Does not act on pri-miR21 (PubMed:22118463). The repression of let-7 expression is required for normal development and contributes to maintain the pluripotent state of embryonic stem cells by preventing let-7-mediated differentiation. When overexpressed, recruits ZCCHC11/TUT4 uridylyltransferase to pre-let-7 transcripts, leading to their terminal uridylation and degradation (PubMed:19703396). This activity might not be relevant in vivo, as LIN28B-mediated inhibition of let-7 miRNA maturation appears to be ZCCHC11-independent (PubMed:22118463). Interaction with target pre-miRNAs occurs via an 5-GGAG-3 motif in the pre-miRNA terminal loop. Mediates MYC-induced let-7 repression (By similarity). When overexpressed, isoform 1 stimulates growth of the breast adenocarcinoma cell line MCF-7. Isoform 2 has no effect on cell growth.

Additional gene information for LIN28B Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIN28B Gene

Genomics for LIN28B Gene

GeneHancer (GH) Regulatory Elements for LIN28B Gene

Promoters and enhancers for LIN28B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I104951 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 556.7 +19.3 19303 8.5 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 POLR2B LIN28B LIN28B-AS1 HACE1 GC06M105046 RNU6-1106P
GH06I104612 Enhancer 0.6 FANTOM5 ENCODE 2.8 -323.0 -322950 1.4 USF2 FOXP2 LIN28B HACE1 GC06P104610 GC06M104657
GH06I104940 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 0.8 +4.5 4466 2.1 PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 GLI4 ZNF2 ZNF48 ETS1 LIN28B-AS1 HACE1 LIN28B
GH06I104624 Enhancer 0.8 FANTOM5 ENCODE dbSUPER 1.4 -310.8 -310750 1.8 ZNF146 MAFF LIN28B GC06P104610 GC06M104657
GH06I104995 Enhancer 0.2 FANTOM5 4.9 +58.9 58855 0.1 LIN28B HACE1 GC06M105046 LIN28B-AS1 RNU6-1106P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LIN28B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LIN28B gene promoter:

Genomic Locations for LIN28B Gene

Genomic Locations for LIN28B Gene
chr6:104,936,616-105,083,332
(GRCh38/hg38)
Size:
146,717 bases
Orientation:
Plus strand
chr6:105,404,923-105,531,207
(GRCh37/hg19)

Genomic View for LIN28B Gene

Genes around LIN28B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIN28B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIN28B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIN28B Gene

Proteins for LIN28B Gene

  • Protein details for LIN28B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZN17-LN28B_HUMAN
    Recommended name:
    Protein lin-28 homolog B
    Protein Accession:
    Q6ZN17
    Secondary Accessions:
    • A1L165
    • B2RPN6
    • Q5TCM4

    Protein attributes for LIN28B Gene

    Size:
    250 amino acids
    Molecular mass:
    27084 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for LIN28B Gene

    Alternative splice isoforms for LIN28B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIN28B Gene

Post-translational modifications for LIN28B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LIN28B Gene

No data available for DME Specific Peptides for LIN28B Gene

Domains & Families for LIN28B Gene

Gene Families for LIN28B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for LIN28B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6ZN17

UniProtKB/Swiss-Prot:

LN28B_HUMAN :
  • The tandem zinc fingers, also referred as zinc knuckle domain (ZKD), mediate specific binding to the GGAG/GGUG motif while the CSD shows only limited pyrimidine-rich sequence specificity. Both domains bind single-stranded nucleic acids.
  • Belongs to the lin-28 family.
Domain:
  • The tandem zinc fingers, also referred as zinc knuckle domain (ZKD), mediate specific binding to the GGAG/GGUG motif while the CSD shows only limited pyrimidine-rich sequence specificity. Both domains bind single-stranded nucleic acids.
Family:
  • Belongs to the lin-28 family.
genes like me logo Genes that share domains with LIN28B: view

Function for LIN28B Gene

Molecular function for LIN28B Gene

UniProtKB/Swiss-Prot Function:
Suppressor of microRNA (miRNA) biogenesis, including that of let-7 and possibly of miR107, miR-143 and miR-200c. Binds primary let-7 transcripts (pri-let-7), including pri-let-7g and pri-let-7a-1, and sequester them in the nucleolus, away from the microprocessor complex, hence preventing their processing into mature miRNA (PubMed:22118463). Does not act on pri-miR21 (PubMed:22118463). The repression of let-7 expression is required for normal development and contributes to maintain the pluripotent state of embryonic stem cells by preventing let-7-mediated differentiation. When overexpressed, recruits ZCCHC11/TUT4 uridylyltransferase to pre-let-7 transcripts, leading to their terminal uridylation and degradation (PubMed:19703396). This activity might not be relevant in vivo, as LIN28B-mediated inhibition of let-7 miRNA maturation appears to be ZCCHC11-independent (PubMed:22118463). Interaction with target pre-miRNAs occurs via an 5-GGAG-3 motif in the pre-miRNA terminal loop. Mediates MYC-induced let-7 repression (By similarity). When overexpressed, isoform 1 stimulates growth of the breast adenocarcinoma cell line MCF-7. Isoform 2 has no effect on cell growth.
UniProtKB/Swiss-Prot Induction:
Might be negatively regulated by the microRNA let-7b.

Phenotypes From GWAS Catalog for LIN28B Gene

Gene Ontology (GO) - Molecular Function for LIN28B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IDA,IEA 19703396
GO:0005515 protein binding IPI 19703396
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LIN28B: view
genes like me logo Genes that share phenotypes with LIN28B: view

Human Phenotype Ontology for LIN28B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LIN28B Gene

MGI Knock Outs for LIN28B:

Animal Model Products

miRNA for LIN28B Gene

miRTarBase miRNAs that target LIN28B

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LIN28B Gene

Localization for LIN28B Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIN28B Gene

Nucleus. Nucleus, nucleolus. Cytoplasm. Note=Predominantly nucleolar (PubMed:22118463). In Huh7 cells, predominantly cytoplasmic, with only a subset of cells exhibiting strong nuclear staining; however, the specificity of the polyclonal antibody used in these experiments has not been not documented (PubMed:16971064). {ECO:0000269 PubMed:16971064, ECO:0000269 PubMed:22118463}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LIN28B gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LIN28B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IEA,IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with LIN28B: view

Pathways & Interactions for LIN28B Gene

genes like me logo Genes that share pathways with LIN28B: view

Pathways by source for LIN28B Gene

2 Cell Signaling Technology pathways for LIN28B Gene

Gene Ontology (GO) - Biological Process for LIN28B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0010587 miRNA catabolic process IMP 19703396
GO:0031047 gene silencing by RNA IEA --
GO:0031054 pre-miRNA processing IMP 19703396
GO:0031123 RNA 3-end processing IMP 19703396
genes like me logo Genes that share ontologies with LIN28B: view

No data available for SIGNOR curated interactions for LIN28B Gene

Drugs & Compounds for LIN28B Gene

No Compound Related Data Available

Transcripts for LIN28B Gene

Unigene Clusters for LIN28B Gene

Lin-28 homolog B (C. elegans):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LIN28B Gene

No ASD Table

Relevant External Links for LIN28B Gene

GeneLoc Exon Structure for
LIN28B
ECgene alternative splicing isoforms for
LIN28B

Expression for LIN28B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LIN28B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LIN28B Gene

This gene is overexpressed in Testis (x21.6), Brain - Hypothalamus (x4.2), and Brain - Frontal Cortex (BA9) (x4.0).

Protein differential expression in normal tissues from HIPED for LIN28B Gene

This gene is overexpressed in Placenta (65.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LIN28B Gene



Protein tissue co-expression partners for LIN28B Gene

NURSA nuclear receptor signaling pathways regulating expression of LIN28B Gene:

LIN28B

SOURCE GeneReport for Unigene cluster for LIN28B Gene:

Hs.23616

mRNA Expression by UniProt/SwissProt for LIN28B Gene:

Q6ZN17-LN28B_HUMAN
Tissue specificity: Expressed at high levels in the placenta and, at mucher lower, in testis and fetal liver (PubMed:16971064). Isoform 1 is only detected in placenta and in moderately and poorly differentiated hepatocellular carcinoma cells (at protein level). Isoform 2 is detected in fetal liver, non-tumor liver tissues, as well as well-differentiated tumor tissues (at protein level). Tends to be up-regulated in triple-negative (ER-,PR-,HER2-) breast tumors, as well as in liver, ovarian, and thyroid carcinomas (PubMed:22118463).

Phenotype-based relationships between genes and organs from Gene ORGANizer for LIN28B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • heart
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • adrenal gland
  • intestine
  • kidney
  • large intestine
  • small intestine
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with LIN28B: view

No data available for Evidence on tissue expression from TISSUES for LIN28B Gene

Orthologs for LIN28B Gene

This gene was present in the common ancestor of animals.

Orthologs for LIN28B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LIN28B 33 34
  • 99.73 (n)
cow
(Bos Taurus)
Mammalia LIN28B 33 34
  • 91.63 (n)
dog
(Canis familiaris)
Mammalia LIN28B 33 34
  • 88.89 (n)
mouse
(Mus musculus)
Mammalia Lin28b 33 16 34
  • 86.64 (n)
rat
(Rattus norvegicus)
Mammalia Lin28b 33
  • 84.55 (n)
oppossum
(Monodelphis domestica)
Mammalia LIN28B 34
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LIN28B 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves LIN28B 33 34
  • 85.54 (n)
lizard
(Anolis carolinensis)
Reptilia LIN28B 34
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lin28b 33
  • 81.87 (n)
Str.9971 33
African clawed frog
(Xenopus laevis)
Amphibia LOC373796 33
zebrafish
(Danio rerio)
Actinopterygii LIN28B 34
  • 72 (a)
OneToOne
LOC799825 33
  • 65.37 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006591 33
  • 50.2 (n)
fruit fly
(Drosophila melanogaster)
Insecta lin-28 33 34
  • 48.57 (n)
worm
(Caenorhabditis elegans)
Secernentea lin-28 34
  • 28 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 41 (a)
OneToMany
Species where no ortholog for LIN28B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LIN28B Gene

ENSEMBL:
Gene Tree for LIN28B (if available)
TreeFam:
Gene Tree for LIN28B (if available)

Paralogs for LIN28B Gene

Paralogs for LIN28B Gene

(1) SIMAP similar genes for LIN28B Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for LIN28B Gene

genes like me logo Genes that share paralogs with LIN28B: view

Variants for LIN28B Gene

Sequence variations from dbSNP and Humsavar for LIN28B Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs386352325 uncertain-significance, not provided 104,957,255(+) C/A coding_sequence_variant, intron_variant, missense_variant
rs1000053999 -- 104,949,521(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000055685 -- 104,950,019(+) T/G genic_upstream_transcript_variant, intron_variant
rs1000102274 -- 105,033,537(+) G/A intron_variant
rs1000103453 -- 104,949,908(+) T/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LIN28B Gene

Variant ID Type Subtype PubMed ID
dgv216e55 CNV gain 17911159
esv2759461 CNV gain 17122850
esv3610248 CNV gain 21293372
esv3610250 CNV gain 21293372
esv3610251 CNV gain 21293372
nsv1142014 OTHER inversion 24896259
nsv604433 CNV loss 21841781
nsv818450 CNV gain 17921354
nsv830754 CNV gain 17160897
nsv970156 CNV duplication 23825009

Variation tolerance for LIN28B Gene

Residual Variation Intolerance Score: 35.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.58; 12.49% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIN28B Gene

Human Gene Mutation Database (HGMD)
LIN28B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIN28B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIN28B Gene

Disorders for LIN28B Gene

MalaCards: The human disease database

(5) MalaCards diseases for LIN28B Gene - From: HGMD, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
neuroblastoma
  • neuroblastoma, susceptibility to
idiopathic central precocious puberty
oral cavity cancer
  • malignant neoplasm of anterior portion of floor of mouth
juvenile myelomonocytic leukemia
  • jmml
hepatocellular carcinoma
  • hcc
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LIN28B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LIN28B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LIN28B Gene

Publications for LIN28B Gene

  1. LIN28B in constitutional delay of growth and puberty. (PMID: 20350940) Tommiska J … Dunkel L (The Journal of clinical endocrinology and metabolism 2010) 3 22 44 58
  2. Identification and characterization of lin-28 homolog B (LIN28B) in human hepatocellular carcinoma. (PMID: 16971064) Guo Y … Aburatani H (Gene 2006) 3 4 22 58
  3. Lin28A and Lin28B inhibit let-7 microRNA biogenesis by distinct mechanisms. (PMID: 22118463) Piskounova E … Gregory RI (Cell 2011) 3 4 58
  4. Associations between the pubertal timing-related variant in LIN28B and BMI vary across the life course. (PMID: 20962026) Ong KK … Hardy R (The Journal of clinical endocrinology and metabolism 2011) 3 44 58
  5. A variant in LIN28B is associated with 2D:4D finger-length ratio, a putative retrospective biomarker of prenatal testosterone exposure. (PMID: 20303062) Medland SE … Evans DM (American journal of human genetics 2010) 3 44 58

Products for LIN28B Gene

Sources for LIN28B Gene

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