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

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: mouse all
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Genomic context

Location:: 6q16.3-q21

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (104937026..105083332)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (106113007..106259422)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (105404982..105531207)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
The transposable element-derived transcript of LIN28B has a placental origin and is not specific to tumours.
Title: The transposable element-derived transcript of LIN28B has a placental origin and is not specific to tumours.

Submit: New GeneRIF Correction See all GeneRIFs (155)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL008739 (e-PCR)
- UniSTS:94730

RH121687 (e-PCR)
- UniSTS:134426

SHGC-58271 (e-PCR)
- UniSTS:46938

SHGC-80846 (e-PCR)
- UniSTS:102497

D6S2097 (e-PCR)
- UniSTS:38642

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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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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

NG_032815.2 RefSeqGene

Range

25083..151308

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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, A7E2T3

Related

ENSP00000490468.1, ENST00000637759.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

104937026..105083332

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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. ...