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Q9JKS4 (LDB3_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 110. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
LIM domain-binding protein 3
Alternative name(s):
Protein cypher
Protein oracle
Z-band alternatively spliced PDZ-motif protein
Gene names
Name:Ldb3
Synonyms:Kiaa0613
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length723 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

May function as an adapter in striated muscle to couple protein kinase C-mediated signaling via its LIM domains to the cytoskeleton. Ref.1

Subunit structure

Interacts via its LIM domains with various PKC isoforms. Interacts via its PDZ domain with the ACTN2 C-terminal region. Interacts with MYOZ1, MYOZ2 and MYOZ3. Ref.1 UniProtKB O75112

Subcellular location

Cytoplasmperinuclear region. Cell projectionpseudopodium. Cytoplasmcytoskeleton. CytoplasmmyofibrilsarcomereZ line. Note: Localized to the cytoplasm around nuclei and pseudopodia of undifferentiated cells and detected throughout the myotubes of differentiated cells. Colocalizes with ACTN2 at the Z-lines. Ref.1

Tissue specificity

Expressed primarily in adult heart and skeletal muscle, and detected at lower levels in lung. Isoforms are expressed in a tissue-specific manner. Isoform 1, isoform 3 and isoform 5 are expressed in heart, whereas isoform 2, isoform 4 and isoform 6 are expressed in skeletal muscle. Ref.1 Ref.2 Ref.3 Ref.4

Developmental stage

Initially expressed in a myocardium-specific manner at 8.5-9 dpc and remains cardiac-restricted until day 12. Strongly expressed throughout heart in all stages examined. At 12.5 dpc expressed at low levels in non-cardiac striated muscles. By day E14.5 expressed at high levels in both cardiac and skeletal muscle, and also strongly expressed in striated muscles of tongue, thoracic and abdominal muscles, leg and diaphragm. The various isoforms are developmentally regulated in both skeletal and cardiac muscle. Isoform 5 and isoform 6, which are barely detectable during embryogenesis are up-regulated postnatally. In heart, isoform 3 is up-regulated developmentally, whereas the predominant isoform 1 is expressed throughout development and into adulthood. In skeletal muscle, the predominant isoform 2 is gradually replaced by isoform 4 postnatally. Ref.1 Ref.4

Sequence similarities

Contains 3 LIM zinc-binding domains.

Contains 1 PDZ (DHR) domain.

Sequence caution

The sequence BAB23128.1 differs from that shown. Reason: Sequencing errors.

The sequence BAD32258.1 differs from that shown. Reason: Erroneous initiation.

Alternative products

This entry describes 6 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 Ref.1 (identifier: Q9JKS4-1)

Also known as: Cypher1c; Oracle 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 2 Ref.4 (identifier: Q9JKS4-2)

Also known as: Cypher1s;

The sequence of this isoform differs from the canonical sequence as follows:
     108-227: DPALDTNGSL...KASGAGLLGG → VVANSPANAD...SDFSGASPLA
Isoform 3 Ref.2 Ref.4 (identifier: Q9JKS4-3)

Also known as: Cypher3c; Oracle 2;

The sequence of this isoform differs from the canonical sequence as follows:
     296-357: Missing.
Isoform 4 Ref.4 (identifier: Q9JKS4-4)

Also known as: Cypher3s;

The sequence of this isoform differs from the canonical sequence as follows:
     108-227: DPALDTNGSL...KASGAGLLGG → VVANSPANAD...SDFSGASPLA
     296-357: Missing.
Isoform 5 Ref.4 (identifier: Q9JKS4-5)

Also known as: Cypher2c;

The sequence of this isoform differs from the canonical sequence as follows:
     296-327: STPIEHAPVCTSQATSPLLPASAQSPAAASPI → RERFETERNSPRFAKLRNWHHGLSAQILNVKS
     328-723: Missing.
Isoform 6 Ref.1 Ref.2 (identifier: Q9JKS4-6)

Also known as: Cypher2s;

The sequence of this isoform differs from the canonical sequence as follows:
     108-227: DPALDTNGSL...KASGAGLLGG → VVANSPANAD...SDFSGASPLA
     296-327: STPIEHAPVCTSQATSPLLPASAQSPAAASPI → RERFETERNSPRFAKLRNWHHGLSAQILNVKS
     328-723: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 723723LIM domain-binding protein 3
PRO_0000075768

Regions

Domain1 – 8484PDZ
Domain545 – 60359LIM zinc-binding 1
Domain604 – 66360LIM zinc-binding 2
Domain664 – 72360LIM zinc-binding 3

Natural variations

Alternative sequence108 – 227120DPALD…GLLGG → VVANSPANADYQERFNPSVL KDSALSTHKPIEVKGLGGKA TIIHAQYNTPISMYSQDAIM DAIAGQAQAQGSDFSGASPL A in isoform 2, isoform 4 and isoform 6. Ref.1 Ref.2 Ref.4
VSP_051903
Alternative sequence296 – 35762Missing in isoform 3 and isoform 4. Ref.3 Ref.4
VSP_051904
Alternative sequence296 – 32732STPIE…AASPI → RERFETERNSPRFAKLRNWH HGLSAQILNVKS in isoform 5 and isoform 6. Ref.1 Ref.2 Ref.4
VSP_051905
Alternative sequence328 – 723396Missing in isoform 5 and isoform 6. Ref.1 Ref.2 Ref.4
VSP_051906

Experimental info

Sequence conflict108 – 14538DPALD…SSFSQ → VVANSPANADYQERFNPSVL KGLSSVLKGLSSVHPQAH in BAB23128. Ref.6
Sequence conflict4501S → T in AAD42950. Ref.1
Sequence conflict4501S → T in AAO26188. Ref.4
Sequence conflict4501S → T in AAO26189. Ref.4
Sequence conflict5121R → W in BAD32258. Ref.5
Isoform 2:
Sequence conflict176 – 18813AQGSD…ASPLA → AQGSDFSG in AAO26189. Ref.4

Secondary structure

................... 723
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Cypher1c) (Oracle 1) [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: CC67D38AC2FFA6B6

FASTA72376,432
        10         20         30         40         50         60 
MSYSVTLTGP GPWGFRLQGG KDFNMPLTIS RITPGSKAAQ SQLSQGDLVV AIDGVNTDTM 

        70         80         90        100        110        120 
THLEAQNKIK SASYNLSLTL QKSKRPIPIS TTAPPIQSPL PVIPHQKDPA LDTNGSLATP 

       130        140        150        160        170        180 
SPSPEARASP GALEFGDTFS SSFSQTSVCS PLMEASGPVL PLGSPVAKAS SEGAQGSVSP 

       190        200        210        220        230        240 
KVLPGPSQPR QYNNPIGLYS AETLREMAQM YQMSLRGKAS GAGLLGGSLP VKDLAVDSAS 

       250        260        270        280        290        300 
PVYQAVIKTQ SKPEDEADEW ARRSSNLQSR SFRILAQMTG TEYMQDPDEE ALRRSSTPIE 

       310        320        330        340        350        360 
HAPVCTSQAT SPLLPASAQS PAAASPIAAS PTLATAAATH AAAASAAGPA ASPVENPRPQ 

       370        380        390        400        410        420 
ASAYSPAAAA SPAPSAHTSY SEGPAAPAPK PRVVTTASIR PSVYQPVPAS SYSPSPGANY 

       430        440        450        460        470        480 
SPTPYTPSPA PAYTPSPAPT YTPSPAPTYS PSPAPAYTPS PAPNYTPTPS AAYSGGPSES 

       490        500        510        520        530        540 
ASRPPWVTDD SFSQKFAPGK STTTVSKQTL PRGAPAYNPT GPQVTPLARG TFQRAERFPA 

       550        560        570        580        590        600 
SSRTPLCGHC NNVIRGPFLV AMGRSWHPEE FNCAYCKTSL ADVCFVEEQN NVYCERCYEQ 

       610        620        630        640        650        660 
FFAPICAKCN TKIMGEVMHA LRQTWHTTCF VCAACKKPFG NSLFHMEDGE PYCEKDYINL 

       670        680        690        700        710        720 
FSTKCHGCDF PVEAGDKFIE ALGHTWHDTC FICAVCHVNL EGQPFYSKKD KPLCKKHAHA 


INV 

« Hide

Isoform 2 (Cypher1s) [UniParc].

Checksum: B8969D96ECC7C7C5
Show »

FASTA68472,752
Isoform 3 (Cypher3c) (Oracle 2) [UniParc].

Checksum: 5DEFEEE78D45532F
Show »

FASTA66170,751
Isoform 4 (Cypher3s) [UniParc].

Checksum: ABC92BB80C3B9903
Show »

FASTA62267,071
Isoform 5 (Cypher2c) [UniParc].

Checksum: 603BEF5D6152B848
Show »

FASTA32735,108
Isoform 6 (Cypher2s) [UniParc].

Checksum: 65B11275409291B6
Show »

FASTA28831,427

References

« Hide 'large scale' references
[1]"Cypher, a striated muscle-restricted PDZ and LIM domain-containing protein, binds to alpha-actinin-2 and protein kinase C."
Zhou Q., Ruiz-Lozano P., Martone M.E., Chen J.
J. Biol. Chem. 274:19807-19813(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 6), INTERACTION WITH ACTN2 AND PKC, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
Strain: NIH Swiss.
Tissue: Heart and Skeletal muscle.
[2]"ZASP: a new Z-band alternatively spliced PDZ-motif protein."
Faulkner G., Pallavicini A., Formentin E., Comelli A., Ievolella C., Trevisan S., Bortoletto G., Scannapieco P., Salamon M., Mouly V., Valle G., Lanfranchi G.
J. Cell Biol. 146:465-475(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 6), TISSUE SPECIFICITY.
Tissue: Diaphragm.
[3]"Oracle, a novel PDZ-LIM domain protein expressed in heart and skeletal muscle."
Passier R., Richardson J.A., Olson E.N.
Mech. Dev. 92:277-284(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 3), TISSUE SPECIFICITY.
Tissue: Heart.
[4]"Characterization and in vivo functional analysis of splice variants of cypher."
Huang C., Zhou Q., Liang P., Hollander M.S., Sheikh F., Li X., Greaser M., Shelton G.D., Evans S., Chen J.
J. Biol. Chem. 278:7360-7365(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2; 3; 4 AND 5), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
Strain: NIH Swiss.
Tissue: Heart and Skeletal muscle.
[5]"Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries."
Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S., Saga Y., Seino S., Nishimura M., Kaisho T., Hoshino K., Kitamura H., Nagase T., Ohara O., Koga H.
DNA Res. 11:205-218(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Fetal brain.
[6]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 5), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-145.
Strain: C57BL/6J.
Tissue: Embryo, Heart and Urinary bladder.
[7]"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] (ISOFORMS 1; 3 AND 6).
Strain: C57BL/6J.
Tissue: Lung and Mammary gland.
[8]"Solution structure of PDZ domain of mouse cypher protein."
RIKEN structural genomics initiative (RSGI)
Submitted (MAY-2004) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 1-83.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF114378 mRNA. Translation: AAD42950.2.
AF114379 mRNA. Translation: AAD42951.2.
AJ005621 mRNA. Translation: CAB46747.1.
AF228057 mRNA. Translation: AAF33847.1.
AF228058 mRNA. Translation: AAF33848.1.
AY206011 mRNA. Translation: AAO26187.1.
AY206012 mRNA. Translation: AAO26188.1.
AY206013 mRNA. Translation: AAO26189.1.
AY206015 mRNA. Translation: AAO26190.1.
AK172980 mRNA. Translation: BAD32258.1. Different initiation.
AK004020 mRNA. Translation: BAB23128.1. Sequence problems.
AK137181 mRNA. Translation: BAE23262.1.
AK142292 mRNA. Translation: BAE25016.1.
BC099596 mRNA. Translation: AAH99596.1.
BC138793 mRNA. Translation: AAI38794.1.
BC145420 mRNA. Translation: AAI45421.1.
RefSeqNP_001034160.1. NM_001039071.2.
NP_001034161.1. NM_001039072.2.
NP_001034162.1. NM_001039073.2.
NP_001034163.1. NM_001039074.2.
NP_001034164.1. NM_001039075.2.
NP_001034165.1. NM_001039076.2.
NP_036048.3. NM_011918.4.
XP_006519080.1. XM_006519017.1.
UniGeneMm.29733.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1WJLNMR-A1-83[»]
ProteinModelPortalQ9JKS4.
SMRQ9JKS4. Positions 5-83, 533-719.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid204912. 9 interactions.
IntActQ9JKS4. 2 interactions.
MINTMINT-97840.

PTM databases

PhosphoSiteQ9JKS4.

Proteomic databases

PaxDbQ9JKS4.
PRIDEQ9JKS4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000022327; ENSMUSP00000022327; ENSMUSG00000021798. [Q9JKS4-1]
ENSMUST00000022328; ENSMUSP00000022328; ENSMUSG00000021798. [Q9JKS4-3]
ENSMUST00000022330; ENSMUSP00000022330; ENSMUSG00000021798. [Q9JKS4-5]
ENSMUST00000090040; ENSMUSP00000087494; ENSMUSG00000021798. [Q9JKS4-2]
GeneID24131.
KEGGmmu:24131.
UCSCuc007taz.1. mouse. [Q9JKS4-2]
uc007tba.1. mouse. [Q9JKS4-4]
uc007tbc.1. mouse. [Q9JKS4-1]
uc007tbd.1. mouse. [Q9JKS4-3]
uc007tbe.1. mouse. [Q9JKS4-6]
uc007tbf.1. mouse. [Q9JKS4-5]

Organism-specific databases

CTD11155.
MGIMGI:1344412. Ldb3.
RougeSearch...

Phylogenomic databases

eggNOGNOG286537.
GeneTreeENSGT00740000114891.
HOVERGENHBG051478.
InParanoidB2RSB0.
OMAREMAAMQ.
OrthoDBEOG7HXCQB.
PhylomeDBQ9JKS4.
TreeFamTF106408.

Gene expression databases

ArrayExpressQ9JKS4.
BgeeQ9JKS4.
CleanExMM_LDB3.
GenevestigatorQ9JKS4.

Family and domain databases

Gene3D2.10.110.10. 3 hits.
2.30.42.10. 1 hit.
InterProIPR001478. PDZ.
IPR006643. ZASP.
IPR001781. Znf_LIM.
[Graphical view]
PfamPF00412. LIM. 3 hits.
PF00595. PDZ. 1 hit.
[Graphical view]
SMARTSM00132. LIM. 3 hits.
SM00228. PDZ. 1 hit.
SM00735. ZM. 1 hit.
[Graphical view]
SUPFAMSSF50156. SSF50156. 1 hit.
PROSITEPS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 3 hits.
PS50106. PDZ. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9JKS4.
NextBio304169.
PROQ9JKS4.
SOURCESearch...

Entry information

Entry nameLDB3_MOUSE
AccessionPrimary (citable) accession number: Q9JKS4
Secondary accession number(s): B2RSB0 expand/collapse secondary AC list , B7ZNT6, Q6A038, Q811P2, Q811P3, Q811P4, Q811P5, Q9D130, Q9JKS3, Q9R0Z1, Q9WVH1, Q9WVH2
Entry history
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: October 1, 2000
Last modified: April 16, 2014
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot