Q9U489 (LIN41_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein lin-41

Alternative name(s):
Abnormal cell lineage protein 41

Gene names

Name:	lin-41
ORF Names:	C12C8.3

Organism

Caenorhabditis elegans [Reference proteome]

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Protostomia › Ecdysozoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

Protein attributes

Sequence length	1147 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Heterochronic protein which acts downstream let-7 in temporal patterning. Represses lin-29 during late larval stages, which prevents terminal differentiation of hypodermal seam cells and promotes their division. Also governs the timing and extent of male tail tip morphogenesis. Ref.1 Ref.4
Subcellular location	Cytoplasm Ref.1.
Developmental stage	Expressed in body wall muscles, pharyngeal muscles and most neurons at all stages from late embryogenesis until adulthood. Expressed in hypodermal seam cells until the L4 stage. Ref.1 Ref.3
Induction	Negatively regulated by the microRNA (miRNA) let-7 which causes degradation of the mRNA encoding this protein. This requires a let-7 complementary site (LCS) in the 3'-UTR of the mRNA encoding this protein. Ref.1 Ref.3
Sequence similarities	Belongs to the TRIM/RBCC family. Contains 1 B box-type zinc finger. Contains 1 filamin repeat. Contains 6 NHL repeats. Contains 1 RING-type zinc finger.

Ontologies

Keywords
Cellular component	Cytoplasm
Coding sequence diversity	Alternative splicing
Domain	Coiled coil Repeat Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Developmental protein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	epidermal cell fate specification Inferred from mutant phenotype Ref.1. Source: UniProtKB gamete generation Inferred from mutant phenotype Ref.1. Source: WormBase multicellular organismal protein metabolic process Inferred from mutant phenotype Ref.1. Source: WormBase protein ubiquitination involved in ubiquitin-dependent protein catabolic process Inferred from sequence or structural similarity. Source: WormBase regulation of development, heterochronic Inferred from mutant phenotype Ref.1. Source: WormBase regulation of epidermal cell differentiation Inferred from mutant phenotype Ref.1. Source: WormBase tail tip morphogenesis Inferred from mutant phenotype Ref.4. Source: UniProtKB
Cellular_component	cytoplasm Inferred from direct assay Ref.1. Source: UniProtKB
Molecular_function	ubiquitin-protein ligase activity Inferred from sequence or structural similarity. Source: WormBase zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform b (identifier: Q9U489-1)

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.

Isoform a (identifier: Q9U489-2)

The sequence of this isoform differs from the canonical sequence as follows:
     452-455: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1147	1147	Protein lin-41		PRO_0000279514
Regions
	Repeat	723 – 817	95	Filamin
	Repeat	832 – 875	44	NHL 1
	Repeat	879 – 922	44	NHL 2
	Repeat	926 – 969	44	NHL 3
	Repeat	974 – 1017	44	NHL 4
	Repeat	1022 – 1065	44	NHL 5
	Repeat	1107 – 1147	41	NHL 6
	Zinc finger	114 – 155	42	RING-type
	Zinc finger	366 – 412	47	B box-type; atypical
	Coiled coil	565 – 618	54	Potential
	Compositional bias	71 – 74	4	Poly-Pro
	Compositional bias	345 – 434	90	Gln-rich
Natural variations
	Alternative sequence	452 – 455	4	Missing in isoform a.		VSP_023468

Sequences

	Sequence		Length	Mass (Da)
	Isoform b [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 2B94B8AD81C4DD8A	FASTA	1,147	124,232
	10 20 30 40 50 60 MATIVPCSLE KEEGAPSGPR RLQTEIDVDA NDSGNELSMG GSSSEGDSMS HHRGEHSPNH 70 80 90 100 110 120 HHQDNHLGSG PPPPQFTGSL FDTPPSMIQS PQQQPQFQFN TGFGLGLPQD SFRCSVCSKS 130 140 150 160 170 180 STIGVLPFVC AHKTCQSCYQ MTPSSYDRRA CKLCGAVSTA TANFTSQMYL SPTLPSPPRG 190 200 210 220 230 240 ALMSDCSTPT MNNHINSSTP LHQPRAFSFS LSGMPGSPSP VMGARMPSSA GGLMMRPIGF 250 260 270 280 290 300 PDSDSSLTSW SPLQQPSQLS INNLSSIGGH QQQSPMLMQN VFDSLAVNDD TPVFSPLSPT 310 320 330 340 350 360 NTSMHMPPSL MASPDVPKHS ATIAPPRNSM CSTPRLQLAT PMSSQSQQTF PIPSPLGSQP 370 380 390 400 410 420 QQQQPMGPIQ CQGCESKISF AYCMQCQEAL CIHCVQAHQR VRATKQHAFV ELQQLMATLM 430 440 450 460 470 480 SRAVQPQQAQ QYTQNVGGSV RQALGSVGSG DVFFSGHVSG VENDSIGSGE SSPRSSSVCG 490 500 510 520 530 540 THDSVIIGIC ENCPHSVLLC AICVAQHPGK HRVQPLGDIR VAVGEVVNES QLLQWQCEKT 550 560 570 580 590 600 GDTIKQIIDG IVTNATTAEN EIRAAFDTHV NALEERRKEL LKRVETVKNL KLSVLISQAE 610 620 630 640 650 660 SLQSKQIDLQ QAIQTATKLM DSSDCDEMVL RQVFEKLASC QMGNEGTEPN NNILNVLMLA 670 680 690 700 710 720 CQVNEDDRLK FTAPQDGILL NKARQFGNIE SGPCAKNSSI VGDSFKKAIR ERQTVIYVQL 730 740 750 760 770 780 RDACGDLLSS SIAATQPTSQ ALLPHQEPHS HLEQAMPTSD VQAFVISPDG STVEVTMTPR 790 800 810 820 830 840 ENGIVALSYY PSIEGSYTLN ILVKGTPISG CPTTMDIRRG RNYDEIAAKG PILTFGKEGS 850 860 870 880 890 900 GDGELCRPWG ICVDQRGRVI VADRSNNRVQ IFDKDGNFIS KFGTSGNRPG QFDRPAGITT 910 920 930 940 950 960 NSLNNIVVAD KDNHRVQVFD ENGMFLLKFG DRGRAVGYFN YPWGVATNSH NAIAVSDTRN 970 980 990 1000 1010 1020 HRVQIFTPQG QFVRKCGFDS AYFFKNLDSP RGLCYLPDGQ LLITDFNNHR LAVLSPRNMS 1030 1040 1050 1060 1070 1080 EMKVYGSEGD GDGMFVRPQG VVIDPEGHIL VCDSRNNRVQ VFASDDMRFI GSFGLGPVPN 1090 1100 1110 1120 1130 1140 SGFQMPQELP APYSSLGGPF GAPAFSSAPT PLTPSPRQLL DRPTDLAVGP DGRIYVVDFG NNCIRVF
	Isoform a [UniParc]. Checksum: 6CC70D53E3BC4E08	FASTA	1,143	123,751
	10 20 30 40 50 60 MATIVPCSLE KEEGAPSGPR RLQTEIDVDA NDSGNELSMG GSSSEGDSMS HHRGEHSPNH 70 80 90 100 110 120 HHQDNHLGSG PPPPQFTGSL FDTPPSMIQS PQQQPQFQFN TGFGLGLPQD SFRCSVCSKS 130 140 150 160 170 180 STIGVLPFVC AHKTCQSCYQ MTPSSYDRRA CKLCGAVSTA TANFTSQMYL SPTLPSPPRG 190 200 210 220 230 240 ALMSDCSTPT MNNHINSSTP LHQPRAFSFS LSGMPGSPSP VMGARMPSSA GGLMMRPIGF 250 260 270 280 290 300 PDSDSSLTSW SPLQQPSQLS INNLSSIGGH QQQSPMLMQN VFDSLAVNDD TPVFSPLSPT 310 320 330 340 350 360 NTSMHMPPSL MASPDVPKHS ATIAPPRNSM CSTPRLQLAT PMSSQSQQTF PIPSPLGSQP 370 380 390 400 410 420 QQQQPMGPIQ CQGCESKISF AYCMQCQEAL CIHCVQAHQR VRATKQHAFV ELQQLMATLM 430 440 450 460 470 480 SRAVQPQQAQ QYTQNVGGSV RQALGSVGSG DGHVSGVEND SIGSGESSPR SSSVCGTHDS 490 500 510 520 530 540 VIIGICENCP HSVLLCAICV AQHPGKHRVQ PLGDIRVAVG EVVNESQLLQ WQCEKTGDTI 550 560 570 580 590 600 KQIIDGIVTN ATTAENEIRA AFDTHVNALE ERRKELLKRV ETVKNLKLSV LISQAESLQS 610 620 630 640 650 660 KQIDLQQAIQ TATKLMDSSD CDEMVLRQVF EKLASCQMGN EGTEPNNNIL NVLMLACQVN 670 680 690 700 710 720 EDDRLKFTAP QDGILLNKAR QFGNIESGPC AKNSSIVGDS FKKAIRERQT VIYVQLRDAC 730 740 750 760 770 780 GDLLSSSIAA TQPTSQALLP HQEPHSHLEQ AMPTSDVQAF VISPDGSTVE VTMTPRENGI 790 800 810 820 830 840 VALSYYPSIE GSYTLNILVK GTPISGCPTT MDIRRGRNYD EIAAKGPILT FGKEGSGDGE 850 860 870 880 890 900 LCRPWGICVD QRGRVIVADR SNNRVQIFDK DGNFISKFGT SGNRPGQFDR PAGITTNSLN 910 920 930 940 950 960 NIVVADKDNH RVQVFDENGM FLLKFGDRGR AVGYFNYPWG VATNSHNAIA VSDTRNHRVQ 970 980 990 1000 1010 1020 IFTPQGQFVR KCGFDSAYFF KNLDSPRGLC YLPDGQLLIT DFNNHRLAVL SPRNMSEMKV 1030 1040 1050 1060 1070 1080 YGSEGDGDGM FVRPQGVVID PEGHILVCDS RNNRVQVFAS DDMRFIGSFG LGPVPNSGFQ 1090 1100 1110 1120 1130 1140 MPQELPAPYS SLGGPFGAPA FSSAPTPLTP SPRQLLDRPT DLAVGPDGRI YVVDFGNNCI RVF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor." Slack F.J., Basson M., Liu Z., Ambros V., Horvitz H.R., Ruvkun G. Mol. Cell 5:659-669(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND B), FUNCTION, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, DOWN-REGULATION BY LET-7.
[2]	"Genome sequence of the nematode C. elegans: a platform for investigating biology." The C. elegans sequencing consortium Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING. Strain: Bristol N2.
[3]	"Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation." Bagga S., Bracht J., Hunter S., Massirer K., Holtz J., Eachus R., Pasquinelli A.E. Cell 122:553-563(2005) [PubMed] [Europe PMC] [Abstract] Cited for: DEVELOPMENTAL STAGE, DOWN-REGULATION BY LET-7.
[4]	"Novel gain-of-function alleles demonstrate a role for the heterochronic gene lin-41 in C. elegans male tail tip morphogenesis." Del Rio-Albrechtsen T., Kiontke K., Chiou S.-Y., Fitch D.H.A. Dev. Biol. 297:74-86(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF195610 mRNA. Translation: AAF15529.1. AF195611 mRNA. Translation: AAF15530.1. Z81467 Genomic DNA. Translation: CAC42255.1. Z81467 Genomic DNA. Translation: CAC42254.1.
RefSeq	NP_001020998.1. NM_001025827.4. NP_001020999.1. NM_001025828.4.
UniGene	Cel.5222.
3D structure databases
ProteinModelPortal	Q9U489.
SMR	Q9U489. Positions 824-1079.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9U489. 11 interactions.
STRING	6239.C12C8.3a.
Proteomic databases
PaxDb	Q9U489.
PRIDE	Q9U489.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	C12C8.3a.1; C12C8.3a.1; C12C8.3. C12C8.3a.2; C12C8.3a.2; C12C8.3.
GeneID	172760.
KEGG	cel:CELE_C12C8.3.
UCSC	C12C8.3b. c. elegans.
Organism-specific databases
CTD	172760.
WormBase	C12C8.3a; CE27062; WBGene00003026; lin-41. C12C8.3b; CE27063; WBGene00003026; lin-41.
Phylogenomic databases
eggNOG	COG3391.
GeneTree	ENSGT00550000074377.
HOGENOM	HOG000022179.
InParanoid	Q9U489.
KO	K12035.
OMA	ESGPCAK.
Family and domain databases
Gene3D	2.120.10.30. 1 hit. 2.60.40.10. 1 hit.
InterPro	IPR011042. 6-blade_b-propeller_TolB-like. IPR003649. Bbox_C. IPR001298. Filamin. IPR017868. Filamin/ABP280_repeat-like. IPR013783. Ig-like_fold. IPR014756. Ig_E-set. IPR001258. NHL_repeat. IPR013017. NHL_repeat_subgr. IPR000315. Znf_B-box. IPR001841. Znf_RING. [Graphical view]
Pfam	PF00630. Filamin. 1 hit. PF01436. NHL. 6 hits. [Graphical view]
SMART	SM00502. BBC. 1 hit. SM00336. BBOX. 2 hits. SM00557. IG_FLMN. 1 hit. SM00184. RING. 1 hit. [Graphical view]
SUPFAM	SSF81296. Ig_E-set. 1 hit.
PROSITE	PS50194. FILAMIN_REPEAT. 1 hit. PS51125. NHL. 6 hits. PS50119. ZF_BBOX. 1 hit. PS00518. ZF_RING_1. False negative. PS50089. ZF_RING_2. False negative. [Graphical view]
ProtoNet	Search...
Other
NextBio	876903.

Entry information

Entry name

LIN41_CAEEL

Accession

Primary (citable) accession number: Q9U489
Secondary accession number(s): Q9U490

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	May 1, 2000
Last modified:	May 29, 2013
This is version 101 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project