O60663 (LMX1B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
LIM homeobox transcription factor 1-beta

Alternative name(s):
LIM/homeobox protein 1.2
Short name=LMX-1.2
LIM/homeobox protein LMX1B

Gene names

Name:

LMX1B

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	402 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.
Subcellular location	Nucleus Potential.
Tissue specificity	Expressed in most tissues. Highest levels in testis, thyroid, duodenum, skeletal muscle, and pancreatic islets.
Involvement in disease	Nail-patella syndrome (NPS) [MIM:161200]: Disease that cause abnormal skeletal patterning and renal dysplasia. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.1 Ref.5 Ref.6 Ref.7 Ref.8
Sequence similarities	Contains 1 homeobox DNA-binding domain. Contains 2 LIM zinc-binding domains.
Sequence caution	The sequence AAC27294.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence AAC39738.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence AAH69601.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence AAI12121.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence AAI13492.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence CAH70295.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence CAI40918.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence EAW87642.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Disease	Disease mutation
Domain	Homeobox LIM domain Repeat
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Activator Developmental protein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	dorsal/ventral pattern formation Inferred from sequence or structural similarity. Source: UniProtKB in utero embryonic development Non-traceable author statement PubMed 12792813. Source: UniProtKB neuron differentiation Inferred from sequence or structural similarity. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from direct assay PubMed 10767331. Source: UniProtKB
Molecular_function	sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro sequence-specific DNA binding transcription factor activity Inferred from direct assay PubMed 10767331. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O60663-1)

Also known as: Long;

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 2 (identifier: O60663-2)

Also known as: Short;

The sequence of this isoform differs from the canonical sequence as follows:
     345-351: Missing.

Isoform 3 (identifier: O60663-3)

The sequence of this isoform differs from the canonical sequence as follows:
     293-293: L → LGQGEPGPGQGL
     345-351: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 402	402	LIM homeobox transcription factor 1-beta		PRO_0000075828
Regions
	Domain	56 – 106	51	LIM zinc-binding 1
	Domain	115 – 168	54	LIM zinc-binding 2
	DNA binding	219 – 278	60	Homeobox
	Compositional bias	282 – 288	7	Poly-Gln
Natural variations
	Alternative sequence	293	1	L → LGQGEPGPGQGL in isoform 3.		VSP_046472
	Alternative sequence	345 – 351	7	Missing in isoform 2 and isoform 3.		VSP_003113
	Natural variant	59	1	C → R in NPS. Ref.7		VAR_015201
	Natural variant	59	1	C → S in NPS. Ref.7		VAR_015202
	Natural variant	75	1	S → F. Corresponds to variant rs2235058 [ dbSNP | Ensembl ].		VAR_047755
	Natural variant	77	1	H → N in NPS. Ref.8		VAR_015190
	Natural variant	77	1	H → Q in NPS. Ref.7		VAR_015203
	Natural variant	77	1	H → Y in NPS. Ref.7		VAR_015204
	Natural variant	80	1	C → R in NPS. Ref.7		VAR_015205
	Natural variant	81	1	L → W in NPS. Ref.8		VAR_015191
	Natural variant	83	1	C → F in NPS. Ref.8		VAR_015192
	Natural variant	83	1	C → G in NPS. Ref.7		VAR_015206
	Natural variant	83	1	C → W in NPS. Ref.8		VAR_015193
	Natural variant	83	1	C → Y in NPS. Ref.7		VAR_015207
	Natural variant	86	1	C → R in NPS. Ref.7		VAR_015208
	Natural variant	103	1	C → W in NPS. Ref.8		VAR_015194
	Natural variant	106	1	D → G in NPS. Ref.7		VAR_015209
	Natural variant	118	1	C → F in NPS. Ref.1		VAR_004198
	Natural variant	118	1	C → Y in NPS. Ref.7 Ref.8		VAR_015195
	Natural variant	137	1	H → Y in NPS. Ref.8		VAR_015196
	Natural variant	140	1	C → Y in NPS. Ref.8		VAR_015197
	Natural variant	143	1	C → S in NPS. Ref.7		VAR_015210
	Natural variant	146	1	C → F in NPS. Ref.7		VAR_015211
	Natural variant	146	1	C → Y in NPS. Ref.7		VAR_015212
	Natural variant	165	1	C → W in NPS. Ref.6		VAR_004199
	Natural variant	223	1	R → Q in NPS. Ref.6 Ref.8 Corresponds to variant rs28939692 [ dbSNP | Ensembl ].		VAR_004200
	Natural variant	236	1	A → P in NPS. Ref.6 Ref.8		VAR_004201
	Natural variant	241	1	S → P in NPS. Ref.6		VAR_004202
	Natural variant	249	1	R → P in NPS. Ref.6		VAR_004203
	Natural variant	252	1	L → P in NPS. Ref.7		VAR_015213
	Natural variant	253	1	A → V in NPS. Ref.6		VAR_004204
	Natural variant	266	1	W → C in NPS. Ref.8		VAR_015198
	Natural variant	269	1	N → K in NPS. Ref.5 Ref.6 Ref.8		VAR_004205

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (Long) [UniParc]. Last modified May 1, 2013. Version 3. Checksum: E59FC36C39C7C9A3	FASTA	402	44,917
	10 20 30 40 50 60 MDIATGPESL ERCFPRGQTD CAKMLDGIKM EEHALRPGPA TLGVLLGSDC PHPAVCEGCQ 70 80 90 100 110 120 RPISDRFLMR VNESSWHEEC LQCAACQQAL TTSCYFRDRK LYCKQDYQQL FAAKCSGCME 130 140 150 160 170 180 KIAPTEFVMR ALECVYHLGC FCCCVCERQL RKGDEFVLKE GQLLCKGDYE KEKDLLSSVS 190 200 210 220 230 240 PDESDSVKSE DEDGDMKPAK GQGSQSKGSG DDGKDPRRPK RPRTILTTQQ RRAFKASFEV 250 260 270 280 290 300 SSKPCRKVRE TLAAETGLSV RVVQVWFQNQ RAKMKKLARR HQQQQEQQNS QRLGQEVLSS 310 320 330 340 350 360 RMEGMMASYT PLAPPQQQIV AMEQSPYGSS DPFQQGLTPP QMPGDHMNPY GNDSIFHDID 370 380 390 400 SDTSLTSLSD CFLGSSDVGS LQARVGNPID RLYSMQSSYF AS
	Isoform 2 (Short) [UniParc]. Checksum: 9FFBF8A68E7AC676	FASTA	395	44,102
	10 20 30 40 50 60 MDIATGPESL ERCFPRGQTD CAKMLDGIKM EEHALRPGPA TLGVLLGSDC PHPAVCEGCQ 70 80 90 100 110 120 RPISDRFLMR VNESSWHEEC LQCAACQQAL TTSCYFRDRK LYCKQDYQQL FAAKCSGCME 130 140 150 160 170 180 KIAPTEFVMR ALECVYHLGC FCCCVCERQL RKGDEFVLKE GQLLCKGDYE KEKDLLSSVS 190 200 210 220 230 240 PDESDSVKSE DEDGDMKPAK GQGSQSKGSG DDGKDPRRPK RPRTILTTQQ RRAFKASFEV 250 260 270 280 290 300 SSKPCRKVRE TLAAETGLSV RVVQVWFQNQ RAKMKKLARR HQQQQEQQNS QRLGQEVLSS 310 320 330 340 350 360 RMEGMMASYT PLAPPQQQIV AMEQSPYGSS DPFQQGLTPP QMPGNDSIFH DIDSDTSLTS 370 380 390 LSDCFLGSSD VGSLQARVGN PIDRLYSMQS SYFAS
	Isoform 3 [UniParc]. Checksum: 5FF15E73B7FD552E	FASTA	406	45,080
	10 20 30 40 50 60 MDIATGPESL ERCFPRGQTD CAKMLDGIKM EEHALRPGPA TLGVLLGSDC PHPAVCEGCQ 70 80 90 100 110 120 RPISDRFLMR VNESSWHEEC LQCAACQQAL TTSCYFRDRK LYCKQDYQQL FAAKCSGCME 130 140 150 160 170 180 KIAPTEFVMR ALECVYHLGC FCCCVCERQL RKGDEFVLKE GQLLCKGDYE KEKDLLSSVS 190 200 210 220 230 240 PDESDSVKSE DEDGDMKPAK GQGSQSKGSG DDGKDPRRPK RPRTILTTQQ RRAFKASFEV 250 260 270 280 290 300 SSKPCRKVRE TLAAETGLSV RVVQVWFQNQ RAKMKKLARR HQQQQEQQNS QRLGQGEPGP 310 320 330 340 350 360 GQGLGQEVLS SRMEGMMASY TPLAPPQQQI VAMEQSPYGS SDPFQQGLTP PQMPGNDSIF 370 380 390 400 HDIDSDTSLT SLSDCFLGSS DVGSLQARVG NPIDRLYSMQ SSYFAS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Loss-of-function mutations in the LIM-homeodomain gene, LMX1B, in nail-patella syndrome." Vollrath D., Jaramillo-Babb V.L., Clough M.V., McIntosh I., Scott K.M., Lichter P.R., Richards J.E. Hum. Mol. Genet. 7:1091-1098(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1), VARIANT NPS PHE-118.
[2]	"DNA sequence and analysis of human chromosome 9." Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I. Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 8-402 (ISOFORM 2).
[5]	"Mutations in LMX1B cause abnormal skeletal patterning and renal dysplasia in nail patella syndrome." Dreyer S.D., Zhou G., Baldini A., Winterpacht A., Zabel B., Cole W., Johnson R.L., Lee B. Nat. Genet. 19:47-50(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 24-402 (ISOFORM 2), VARIANT NPS LYS-269.
[6]	"Mutation analysis of LMX1B gene in nail-patella syndrome patients." McIntosh I., Dreyer S.D., Clough M.V., Dunston J.A., Eyaid W., Roig C.M., Montgomery T., Ala-Mello S., Kaitila I., Winterpacht A., Zabel B., Frydman M., Cole W.G., Francomano C.A., Lee B. Am. J. Hum. Genet. 63:1651-1658(1998) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS NPS TRP-165; GLN-223; PRO-236; PRO-241; PRO-249; VAL-253 AND LYS-269.
[7]	"Restricted distribution of loss-of-function mutations within the LMX1B genes of nail-patella syndrome patients." Clough M.V., Hamlington J.D., McIntosh I. Hum. Mutat. 14:459-465(1999) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS NPS ARG-59; SER-59; GLN-77; TYR-77; ARG-80; GLY-83; TYR-83; ARG-86; GLY-106; TYR-118; SER-143; PHE-146; TYR-146 AND PRO-252.
[8]	"Twenty-two novel LMX1B mutations identified in nail patella syndrome (NPS) patients." Hamlington J.D., Jones C., McIntosh I. Hum. Mutat. 18:458-458(2001) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS NPS ASN-77; TRP-81; PHE-83; TRP-83; TRP-103; TYR-118; TYR-137; TYR-140; GLN-223; PRO-236; CYS-266 AND LYS-269.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF059575 , AF059572, AF059573, AF059574 Genomic DNA. Translation: AAC27294.1. Different initiation. AL161908, AL161731 Genomic DNA. Translation: CAH70294.1. AL161908, AL161731 Genomic DNA. Translation: CAH70295.1. Different initiation. AL161731, AL161908 Genomic DNA. Translation: CAI40917.1. AL161731, AL161908 Genomic DNA. Translation: CAI40918.1. Different initiation. CH471090 Genomic DNA. Translation: EAW87642.1. Different initiation. BC069601 mRNA. Translation: AAH69601.1. Different initiation. BC112120 mRNA. Translation: AAI12121.1. Different initiation. BC113491 mRNA. Translation: AAI13492.1. Different initiation. AF057135 mRNA. Translation: AAC39738.1. Different initiation.
IPI	IPI00030989. IPI00220363. IPI00956472.
RefSeq	NP_001167618.1. NM_001174147.1. NP_002307.2. NM_002316.3.
UniGene	Hs.129133.
3D structure databases
ProteinModelPortal	O60663.
ModBase	Search...
Protein-protein interaction databases
IntAct	O60663. 2 interactions.
STRING	9606.ENSP00000347684.
PTM databases
PhosphoSite	O60663.
Proteomic databases
PaxDb	O60663.
PRIDE	O60663.
Protocols and materials databases
DNASU	4010.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000355497; ENSP00000347684; ENSG00000136944. ENST00000373474; ENSP00000362573; ENSG00000136944. ENST00000425646; ENSP00000390923; ENSG00000136944.
GeneID	4010.
KEGG	hsa:4010.
UCSC	uc004bqj.3. human.
Organism-specific databases
CTD	4010.
GeneCards	GC09P129376.
HGNC	HGNC:6654. LMX1B.
MIM	161200. phenotype. 602575. gene.
neXtProt	NX_O60663.
Orphanet	2614. Nail-patella syndrome.
PharmGKB	PA30417.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG243427.
HOGENOM	HOG000231629.
HOVERGEN	HBG052335.
InParanoid	O60663.
KO	K09371.
OrthoDB	EOG4QFWDN.
PhylomeDB	O60663.
Gene expression databases
ArrayExpress	O60663.
Bgee	O60663.
CleanEx	HS_LMX1B.
Genevestigator	O60663.
GermOnline	ENSG00000136944. Homo sapiens.
Family and domain databases
Gene3D	1.10.10.60. 1 hit. 2.10.110.10. 2 hits.
InterPro	IPR017970. Homeobox_CS. IPR001356. Homeodomain. IPR009057. Homeodomain-like. IPR001781. Znf_LIM. [Graphical view]
Pfam	PF00046. Homeobox. 1 hit. PF00412. LIM. 2 hits. [Graphical view]
SMART	SM00389. HOX. 1 hit. SM00132. LIM. 2 hits. [Graphical view]
SUPFAM	SSF46689. Homeodomain_like. 1 hit.
PROSITE	PS00027. HOMEOBOX_1. 1 hit. PS50071. HOMEOBOX_2. 1 hit. PS00478. LIM_DOMAIN_1. 2 hits. PS50023. LIM_DOMAIN_2. 2 hits. [Graphical view]
ProtoNet	Search...
Other
GenomeRNAi	4010.
NextBio	15732.
SOURCE	Search...

Entry information

Entry name

LMX1B_HUMAN

Accession

Primary (citable) accession number: O60663
Secondary accession number(s): F8W7W6 , O75463, Q5JU95, Q6ISC9

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 1998
Last sequence update:	May 1, 2013
Last modified:	May 1, 2013
This is version 130 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.