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    LIN28B lin-28 homolog B [ Homo sapiens (human) ]

    Gene ID: 389421, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LIN28Bprovided by HGNC
    Official Full Name
    lin-28 homolog Bprovided by HGNC
    Primary source
    HGNC:HGNC:32207
    See related
    Ensembl:ENSG00000187772 MIM:611044; AllianceGenome:HGNC:32207
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CSDD2
    Summary
    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]
    Expression
    Restricted expression toward placenta (RPKM 24.7) See more
    Orthologs
    mouse all
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    Genomic context

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    See LIN28B in Genome Data Viewer
    Location:
    6q16.3-q21
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (104937026..105083332)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (106113007..106259422)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (105388840..105531207)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 Neighboring gene RNA, U6 small nuclear 897, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105307475-105307974 Neighboring gene poly(A) binding protein cytoplasmic 4 pseudogene Neighboring gene MPRA-validated peak5989 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105384704-105385204 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105385205-105385705 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105388624-105389458 Neighboring gene LIN28B antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:105403995-105404932 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:105404933-105405870 Neighboring gene RNA, U6 small nuclear 1106, pseudogene Neighboring gene popeye domain cAMP effector 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17426 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17427 Neighboring gene POPDC1 antisense RNA 1 Neighboring gene popeye domain cAMP effector 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. LIN28B overexpression defines a novel fetal-like subgroup of juvenile myelomonocytic leukemia. Helsmoortel HH, et al. Blood, 2016 Mar 3. PMID 26712910
    2. Lin-28B expression promotes transformation and invasion in human hepatocellular carcinoma. Wang YC, et al. Carcinogenesis, 2010 Sep. PMID 20525879
    3. LIN28B promotes colon cancer migration and recurrence. Pang M, et al. PLoS One, 2014. PMID 25360631, Free PMC Article
    4. Genetic variants in let-7/Lin28 modulate the risk of oral cavity cancer in a Chinese Han population. Zhang Y, et al. Sci Rep, 2014 Dec 11. PMID 25503985, Free PMC Article
    5. RNA binding protein Lin28B confers gastric cancer cells stemness via directly binding to NRP-1. Wang X, et al. Biomed Pharmacother, 2018 Aug. PMID 29787985

    See all (213) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. N[6]-methyladenosine modification of circMARK2 enhances cytoplasmic export and stabilizes LIN28B, contributing to the progression of Wilms tumor.
      Title: N(6)-methyladenosine modification of circMARK2 enhances cytoplasmic export and stabilizes LIN28B, contributing to the progression of Wilms tumor.
    2. Transcriptional repression of the oncofetal LIN28B gene by the transcription factor SOX6.
      Title: Transcriptional repression of the oncofetal LIN28B gene by the transcription factor SOX6.
    3. Regulating Protein-RNA Interactions: Advances in Targeting the LIN28/Let-7 Pathway.
      Title: Regulating Protein-RNA Interactions: Advances in Targeting the LIN28/Let-7 Pathway.
    4. MIR222HG/LIN28B/ATG5 Axis Drives M2 Macrophage Polarization and Proliferation of Hepatocellular Carcinoma Cells.
      Title: MIR222HG/LIN28B/ATG5 Axis Drives M2 Macrophage Polarization and Proliferation of Hepatocellular Carcinoma Cells.
    5. LIN28B promotes differentiation of fully transformed AML cells but is dispensable for fetal leukemia suppression.
      Title: LIN28B promotes differentiation of fully transformed AML cells but is dispensable for fetal leukemia suppression.
    6. A Multi-Omics Approach Reveals Enrichment in Metabolites Involved in the Regulation of the Glutathione Pathway in LIN28B-Dependent Cancer Cells.
      Title: A Multi-Omics Approach Reveals Enrichment in Metabolites Involved in the Regulation of the Glutathione Pathway in LIN28B-Dependent Cancer Cells.
    7. Exosomes derived from cancer-associated fibroblasts promote tumorigenesis, metastasis and chemoresistance of colorectal cancer by upregulating circ_0067557 to target Lin28.
      Title: Exosomes derived from cancer-associated fibroblasts promote tumorigenesis, metastasis and chemoresistance of colorectal cancer by upregulating circ_0067557 to target Lin28.
    8. Association of LIN28B Gene Polymorphisms (rs221634, rs221635, rs314276, rs9404590, and rs12194974) with Non-Hodgkin Lymphoma Susceptibility and Clinical/Pathological Features.
      Title: Association of LIN28B Gene Polymorphisms (rs221634, rs221635, rs314276, rs9404590, and rs12194974) with Non-Hodgkin Lymphoma Susceptibility and Clinical/Pathological Features.
    9. MCTS1 enhances the proliferation of laryngeal squamous cell carcinoma via promoting OTUD6B-1 mediated LIN28B deubiquitination.
      Title: MCTS1 enhances the proliferation of laryngeal squamous cell carcinoma via promoting OTUD6B-1 mediated LIN28B deubiquitination.
    10. LIN28B promotes cell invasion and colorectal cancer metastasis via CLDN1 and NOTCH3.
      Title: LIN28B promotes cell invasion and colorectal cancer metastasis via CLDN1 and NOTCH3.
    Submit: New GeneRIF Correction See all GeneRIFs (156)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A variant in LIN28B is associated with 2D:4D finger-length ratio, a putative retrospective biomarker of prenatal testosterone exposure.
    EBI GWAS Catalog
    Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma.
    EBI GWAS Catalog
    Genetic variation in LIN28B is associated with the timing of puberty.
    EBI GWAS Catalog
    Genome wide association study of age at menarche in the Japanese population.
    EBI GWAS Catalog
    Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.
    EBI GWAS Catalog
    Genome-wide association studies identify loci associated with age at menarche and age at natural menopause.
    EBI GWAS Catalog
    Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche.
    EBI GWAS Catalog
    Genome-wide association study of sexual maturation in males and females highlights a role for body mass and menarche loci in male puberty.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Identification of ten loci associated with height highlights new biological pathways in human growth.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association data identifies two loci influencing age at menarche.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag Interaction of HIV-1 Gag with lin-28 homolog B (LIN28B) is identified in a series of six affinity purification/mass spectrometry screens PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ16517

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in RNA destabilization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in miRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of pre-miRNA processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of primary miRNA processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of miRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in pre-miRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in pre-miRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein lin-28 homolog B
    Names
    Lin-28.2
    lin-28B

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_032815.2 RefSeqGene

      Range
      25083..151308
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001004317.4 → NP_001004317.1  protein lin-28 homolog B isoform 1

      See identical proteins and their annotated locations for NP_001004317.1

      Status: REVIEWED

      Source sequence(s)
      AW674597, DQ127228
      Consensus CDS
      CCDS34504.1
      UniProtKB/Swiss-Prot
      A1L165, B2RPN6, Q5TCM4, Q6ZN17
      UniProtKB/TrEMBL
      A7E2T3
      Related
      ENSP00000344401.4, ENST00000345080.5
      Conserved Domains (2) summary
      cd04458
      Location:31 → 101
      CSP_CDS; Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. ...
      cl26705
      Location:120 → 165
      AIR1; Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

    2. NM_001410939.1 → NP_001397868.1  protein lin-28 homolog B isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL135911, Z95329
      Consensus CDS
      CCDS93980.1
      UniProtKB/TrEMBL
      A0A1B0GVD3
      Related
      ENSP00000490468.1, ENST00000637759.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      104937026..105083332
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006715477.3 → XP_006715540.2  protein lin-28 homolog B isoform X1

      UniProtKB/TrEMBL
      A7E2T3
      Conserved Domains (1) summary
      cd04458
      Location:50 → 120
      CSP_CDS; Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      106113007..106259422
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355416.1 → XP_054211391.1  protein lin-28 homolog B isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZN17.1 GenPept UniProtKB/Swiss-Prot:Q6ZN17

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools