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

Gene ID: 389421, updated on 4-Nov-2022

Summary

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
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Genomic context

See LIN28B in Genome Data Viewer
Location:
6q16.3-q21
Exon count:
7
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (104937026..105083332)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (106133122..106259422)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (105404982..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 Sharpr-MPRA regulatory region 9880 Neighboring gene poly(A) binding protein cytoplasmic 4 pseudogene Neighboring gene LIN28B antisense RNA 1 Neighboring gene RNA, U6 small nuclear 1106, pseudogene Neighboring gene blood vessel epicardial substance Neighboring gene BVES antisense RNA 1 Neighboring gene popeye domain containing 3

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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
 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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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_001004317.4NP_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
    Q5TCM4, Q6ZN17
    Related
    ENSP00000344401.4, ENST00000345080.5
    Conserved Domains (2) summary
    cd04458
    Location:31101
    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:120165
    AIR1; Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
  2. NM_001410939.1NP_001397868.1  protein lin-28 homolog B isoform 2

    Status: REVIEWED

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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_006715477.3XP_006715540.2  protein lin-28 homolog B isoform X1

    Conserved Domains (1) summary
    cd04458
    Location:50120
    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. ...
  2. XM_011535818.4XP_011534120.1  protein lin-28 homolog B isoform X2

    UniProtKB/TrEMBL
    A0A1B0GVD3
    Related
    ENSP00000490468.1, ENST00000637759.1
    Conserved Domains (2) summary
    PTZ00368
    Location:128173
    PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    cd04458
    Location:39109
    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
    106133122..106259422
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)