Seroatlas · Human Serome Atlas

LIN28B

Protein lin-28 homolog B

Also known as: CSDD2, FLJ16517, LN28B_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q6ZN17
Gene: LIN28B
Ensembl: ENSG00000187772
Chromosome: 6
Canonical length: 250 aa
Protein class: Predicted intracellular proteins
Subcellular location: Nucleoplasm,Nucleoli,Cytosol

OverviewNCBI 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]

Canonical amino-acid sequenceUniProt

250 residues, UniProt reviewed canonical sequence.

>Q6ZN17|LIN28B
     1  MAEGGASKGG GEEPGKLPEP AEEESQVLRG TGHCKWFNVR MGFGFISMIN REGSPLDIPV
    61  DVFVHQSKLF MEGFRSLKEG EPVEFTFKKS SKGLESIRVT GPGGSPCLGS ERRPKGKTLQ
   121  KRKPKGDRCY NCGGLDHHAK ECSLPPQPKK CHYCQSIMHM VANCPHKNVA QPPASSQGRQ
   181  EAESQPCTST LPREVGGGHG CTSPPFPQEA RAEISERSGR SPQEASSTKS SIAPEEQSKK
   241  GPSVQKRKKT

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LIN28B can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.53
Highest tissue expression: 62 nTPM

Expression across tissuesHPA

Tissue

placenta: 62 nTPM
testis: 3.9 nTPM
retina: 1.4 nTPM
bone marrow: 0.5 nTPM
hypothalamus: 0.3 nTPM
cerebral cortex: 0.2 nTPM

Single-cell type

extravillous trophoblasts: 287 nCPM
cytotrophoblasts: 241 nCPM
migrating cytotrophoblasts: 219 nCPM
syncytiotrophoblasts: 141 nCPM
retinal ganglion cells: 120 nCPM
corticotrophs: 69 nCPM

Immune cell

basophil: 0.3 nTPM
neutrophil: 0.3 nTPM
naive B-cell: 0.1 nTPM
plasmacytoid DC: 0.1 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM

Brain region

cerebral cortex: 6.1 nTPM
basal ganglia: 5.1 nTPM
hypothalamus: 4.8 nTPM
amygdala: 4.1 nTPM
white matter: 4 nTPM
medulla oblongata: 3.9 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.57
gnomAD pLI: 0.56
gnomAD missense Z: 1.28
DepMap mean gene effect: 0.01
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads LIN28B as an antibody target. Whether an autoantibody or antibody against LIN28B could matter depends on whether native LIN28B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LIN28B is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label LIN28B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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