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Protein

Protein lin-28

Gene

lin-28

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Heterochronic protein which controls the choice of stage specific cell fates. Regulates the timing of the second larval stage events (L2 events) in the hypodermis. May negatively regulate the larval to adult transition via the suppression of the microRNA (miRNA) let-7 during L3.15 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi144 – 1441Zinc 1By similarity
Metal bindingi147 – 1471Zinc 1By similarity
Metal bindingi153 – 1531Zinc 1By similarity
Metal bindingi158 – 1581Zinc 1By similarity
Metal bindingi168 – 1681Zinc 2By similarity
Metal bindingi171 – 1711Zinc 2By similarity
Metal bindingi176 – 1761Zinc 2By similarity
Metal bindingi181 – 1811Zinc 2By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri143 – 16018CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri166 – 18318CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: InterPro
  • enzyme binding Source: WormBase
  • mRNA 3'-UTR binding Source: WormBase
  • mRNA binding Source: WormBase
  • mRNA CDS binding Source: WormBase
  • pre-miRNA binding Source: WormBase
  • primary miRNA binding Source: WormBase
  • zinc ion binding Source: InterPro

GO - Biological processi

  • cell fate specification Source: UniProtKB
  • dosage compensation Source: WormBase
  • multicellular organism development Source: UniProtKB-KW
  • negative regulation of primary miRNA processing Source: WormBase
  • pre-miRNA processing Source: WormBase
  • regulation of development, heterochronic Source: WormBase
  • regulation of transcription, DNA-templated Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Protein lin-28
Alternative name(s):
Abnormal cell lineage protein 28
Gene namesi
Name:lin-28
ORF Names:F02E9.2
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome I

Organism-specific databases

WormBaseiF02E9.2a; CE24879; WBGene00003014; lin-28.
F02E9.2b; CE24880; WBGene00003014; lin-28.

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • nucleus Source: WormBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi55 – 551G → S in n1119; loss of function. 1 Publication
Mutagenesisi87 – 871M → I in ga73; when associated with Q-91. 1 Publication
Mutagenesisi91 – 911R → Q in ga73; when associated with I-87. 1 Publication
Mutagenesisi128 – 1281G → E in ma157. 1 Publication
Mutagenesisi128 – 1281G → R in sy283. 1 Publication
Mutagenesisi133 – 1331P → S in ve9. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 227227Protein lin-28PRO_0000253799Add
BLAST

Proteomic databases

EPDiP92186.
PaxDbiP92186.
PRIDEiP92186.

PTM databases

iPTMnetiP92186.

Expressioni

Developmental stagei

Expressed at the first larval stage (L1) in several cell types including hypodermis, muscle, neurons and seam cells. Down-regulated at L2, and absent from L3 and L4.4 Publications

Inductioni

Negatively regulated by the miRNA lin-4 which causes degradation of the mRNA encoding this protein. This requires a lin-4 complementary element (LCE) in the 3'-UTR of the mRNA encoding this protein. Also negatively regulated independent of lin-4 and this is counteracted by the action of lin-14. Positively regulated by TGF-beta signaling.4 Publications

Gene expression databases

BgeeiWBGene00003014.

Interactioni

GO - Molecular functioni

  • enzyme binding Source: WormBase

Protein-protein interaction databases

DIPiDIP-40151N.
IntActiP92186. 3 interactions.
STRINGi6239.F02E9.2a.

Structurei

3D structure databases

ProteinModelPortaliP92186.
SMRiP92186. Positions 52-182.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini52 – 12069CSDAdd
BLAST

Sequence similaritiesi

Belongs to the lin-28 family.Curated
Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation
Contains 1 CSD (cold-shock) domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri143 – 16018CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri166 – 18318CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
GeneTreeiENSGT00840000129853.
HOGENOMiHOG000113330.
InParanoidiP92186.
KOiK18754.
OMAiCPERRRK.
OrthoDBiEOG091G0RTY.
PhylomeDBiP92186.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
4.10.60.10. 1 hit.
InterProiIPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
SM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50158. ZF_CCHC. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform a (identifier: P92186-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSTVVSEGRN DGNNRYSPQD EVEDRLPDVV DNRLTENMRV PSFERLPSPT
60 70 80 90 100
PRYFGSCKWF NVSKGYGFVI DDITGEDLFV HQSNLNMQGF RSLDEGERVS
110 120 130 140 150
YYIQERSNGK GREAYAVSGE VEGQGLKGSR IHPLGRKKAV SLRCFRCGKF
160 170 180 190 200
ATHKAKSCPN VKTDAKVCYT CGSEEHVSSI CPERRRKHRP EQVAAEEAEA
210 220
ARMAAEKSSP TTSDDDIREK NSNSSDE
Length:227
Mass (Da):25,465
Last modified:May 1, 1997 - v1
Checksum:i5E4AE901AD8BAEBC
GO
Isoform b (identifier: P92186-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-16: MSTVVSEGRNDGNNRY → MIEAALENPVPIKSQL
     17-47: Missing.

Note: Gene prediction based on EST data.
Show »
Length:196
Mass (Da):21,783
Checksum:i243358FCC7881C63
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 1616MSTVV…GNNRY → MIEAALENPVPIKSQL in isoform b. CuratedVSP_021122Add
BLAST
Alternative sequencei17 – 4731Missing in isoform b. CuratedVSP_021123Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U75912 mRNA. Translation: AAC47476.1.
U75915 Genomic DNA. Translation: AAB49759.1.
Z81494 Genomic DNA. Translation: CAB61008.1.
Z81494 Genomic DNA. Translation: CAB61009.1.
RefSeqiNP_001021085.1. NM_001025914.4. [P92186-1]
NP_492281.2. NM_059880.5. [P92186-2]
UniGeneiCel.22515.

Genome annotation databases

EnsemblMetazoaiF02E9.2a; F02E9.2a; WBGene00003014. [P92186-1]
GeneIDi172626.
KEGGicel:CELE_F02E9.2.
UCSCiF02E9.2a. c. elegans. [P92186-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U75912 mRNA. Translation: AAC47476.1.
U75915 Genomic DNA. Translation: AAB49759.1.
Z81494 Genomic DNA. Translation: CAB61008.1.
Z81494 Genomic DNA. Translation: CAB61009.1.
RefSeqiNP_001021085.1. NM_001025914.4. [P92186-1]
NP_492281.2. NM_059880.5. [P92186-2]
UniGeneiCel.22515.

3D structure databases

ProteinModelPortaliP92186.
SMRiP92186. Positions 52-182.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-40151N.
IntActiP92186. 3 interactions.
STRINGi6239.F02E9.2a.

PTM databases

iPTMnetiP92186.

Proteomic databases

EPDiP92186.
PaxDbiP92186.
PRIDEiP92186.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiF02E9.2a; F02E9.2a; WBGene00003014. [P92186-1]
GeneIDi172626.
KEGGicel:CELE_F02E9.2.
UCSCiF02E9.2a. c. elegans. [P92186-1]

Organism-specific databases

CTDi38639.
WormBaseiF02E9.2a; CE24879; WBGene00003014; lin-28.
F02E9.2b; CE24880; WBGene00003014; lin-28.

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
GeneTreeiENSGT00840000129853.
HOGENOMiHOG000113330.
InParanoidiP92186.
KOiK18754.
OMAiCPERRRK.
OrthoDBiEOG091G0RTY.
PhylomeDBiP92186.

Miscellaneous databases

PROiP92186.

Gene expression databases

BgeeiWBGene00003014.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
4.10.60.10. 1 hit.
InterProiIPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
SM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50158. ZF_CCHC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLIN28_CAEEL
AccessioniPrimary (citable) accession number: P92186
Secondary accession number(s): Q9U3K6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: May 1, 1997
Last modified: September 7, 2016
This is version 133 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.