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Neurochondrin

 NCDN_HUMAN              Reviewed;         729 AA.
Q9UBB6; D3DPR9; Q9UBY2; Q9Y4A6; Q9Y4D9;
18-MAR-2008, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
12-SEP-2018, entry version 129.
RecName: Full=Neurochondrin;
Name=NCDN; Synonyms=KIAA0607;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], AND TISSUE SPECIFICITY.
TISSUE=Brain;
PubMed=10524216; DOI=10.1016/S0167-4781(99)00120-7;
Mochizuki R., Ishizuka Y., Yanai K., Murakami K., Koga Y.,
Fukamizu A.;
"Molecular cloning and expression of human neurochondrin-1 and -2.";
Biochim. Biophys. Acta 1446:397-402(1999).
[2]
ERRATUM.
PubMed=10684983;
Mochizuki R., Ishizuka Y., Yanai K., Murakami K., Koga Y.,
Fukamizu A.;
Biochim. Biophys. Acta 1490:367-368(2000).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16710414; DOI=10.1038/nature04727;
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D.,
Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A.,
Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F.,
McDonald L., Evans R., Phillips K., Atkinson A., Cooper R., Jones C.,
Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P.,
Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K.,
Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G.,
Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D.,
Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G.,
Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J.,
Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R.,
Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D.,
Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G.,
Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M.,
Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J.,
Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M.,
Loveland J., Lovell J., Lush M.J., Lyne R., Martin S.,
Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S.,
Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C.,
Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z.,
Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E.,
Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A.,
Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R.,
Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V.,
Beck S., Rogers J., Bentley D.R.;
"The DNA sequence and biological annotation of human chromosome 1.";
Nature 441:315-321(2006).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
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 (SEP-2005) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Uterus;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[6]
PARTIAL NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3), AND TISSUE
SPECIFICITY.
TISSUE=Brain;
PubMed=9628581; DOI=10.1093/dnares/5.1.31;
Nagase T., Ishikawa K., Miyajima N., Tanaka A., Kotani H., Nomura N.,
Ohara O.;
"Prediction of the coding sequences of unidentified human genes. IX.
The complete sequences of 100 new cDNA clones from brain which can
code for large proteins in vitro.";
DNA Res. 5:31-39(1998).
[7]
FUNCTION, AND INTERACTION WITH MCHR1.
PubMed=16945926; DOI=10.1074/jbc.M602889200;
Francke F., Ward R.J., Jenkins L., Kellett E., Richter D.,
Milligan G., Baechner D.;
"Interaction of neurochondrin with the melanin-concentrating hormone
receptor 1 interferes with G protein-coupled signal transduction but
not agonist-mediated internalization.";
J. Biol. Chem. 281:32496-32507(2006).
[8]
ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS
SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19413330; DOI=10.1021/ac9004309;
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
Mohammed S.;
"Lys-N and trypsin cover complementary parts of the phosphoproteome in
a refined SCX-based approach.";
Anal. Chem. 81:4493-4501(2009).
[9]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[10]
ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, ACETYLATION [LARGE SCALE
ANALYSIS] AT ALA-2 (ISOFORM 2), CLEAVAGE OF INITIATOR METHIONINE
[LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE
ANALYSIS] (ISOFORM 2), AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE
SCALE ANALYSIS].
PubMed=22814378; DOI=10.1073/pnas.1210303109;
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
Aldabe R.;
"N-terminal acetylome analyses and functional insights of the N-
terminal acetyltransferase NatB.";
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[12]
VARIANTS [LARGE SCALE ANALYSIS] GLU-392 AND LEU-392.
PubMed=16959974; DOI=10.1126/science.1133427;
Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D.,
Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S.,
Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J.,
Dawson D., Willson J.K.V., Gazdar A.F., Hartigan J., Wu L., Liu C.,
Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N.,
Vogelstein B., Kinzler K.W., Velculescu V.E.;
"The consensus coding sequences of human breast and colorectal
cancers.";
Science 314:268-274(2006).
-!- FUNCTION: Probably involved in signal transduction, in the nervous
system, via increasing cell surface localization of GRM5 and
positively regulating its signaling (By similarity). Required for
the spatial learning process. Acts as a negative regulator of
Ca(2+)-calmodulin-dependent protein kinase 2 (CaMK2)
phosphorylation. May play a role in modulating melanin-
concentrating hormone-mediated functions via its interaction with
MCHR1 that interferes with G protein-coupled signal transduction.
May be involved in bone metabolism. May also be involved in
neurite outgrowth. {ECO:0000250, ECO:0000269|PubMed:16945926}.
-!- SUBUNIT: Interacts with SEMA4C, DIAPH1 (via FH3 domain) and GRM5
(By similarity). Interacts with MCHR1. {ECO:0000250,
ECO:0000269|PubMed:16945926}.
-!- INTERACTION:
Q08117:AES; NbExp=3; IntAct=EBI-1053490, EBI-717810;
Q5JST6:EFHC2; NbExp=5; IntAct=EBI-1053490, EBI-2349927;
Q9BSI4:TINF2; NbExp=2; IntAct=EBI-1053490, EBI-717399;
-!- SUBCELLULAR LOCATION: Cytoplasm, cytosol. Cell projection,
dendrite. Note=Localizes to somatic regions of neurons.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=3;
Name=1; Synonyms=NCDN1, Neurochondrin-1;
IsoId=Q9UBB6-1; Sequence=Displayed;
Name=2; Synonyms=NCDN2, Neurochondrin-2;
IsoId=Q9UBB6-2; Sequence=VSP_032315;
Note=Initiator Met-1 is removed. Contains a N-acetylalanine at
position 2. {ECO:0000244|PubMed:22814378};
Name=3;
IsoId=Q9UBB6-3; Sequence=VSP_032316;
Note=Incomplete sequence. No experimental confirmation
available.;
-!- TISSUE SPECIFICITY: Abundantly expressed in whole adult brain and
in all individual brain regions examined, including spinal cord.
Weakly expressed in ovary, testis, fetal brain and small
intestine. {ECO:0000269|PubMed:10524216,
ECO:0000269|PubMed:9628581}.
-!- SIMILARITY: Belongs to the neurochondrin family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAD05029.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AB018739; BAA85384.2; -; mRNA.
EMBL; AB018740; BAA85385.2; -; mRNA.
EMBL; AB027514; BAA77830.1; -; Genomic_DNA.
EMBL; AB027514; BAA77831.1; -; Genomic_DNA.
EMBL; AC004865; AAD05029.1; ALT_SEQ; Genomic_DNA.
EMBL; CH471059; EAX07410.1; -; Genomic_DNA.
EMBL; CH471059; EAX07411.1; -; Genomic_DNA.
EMBL; CH471059; EAX07412.1; -; Genomic_DNA.
EMBL; BC024592; AAH24592.1; -; mRNA.
EMBL; AB011179; BAA25533.1; -; mRNA.
CCDS; CCDS30672.1; -. [Q9UBB6-2]
CCDS; CCDS392.1; -. [Q9UBB6-1]
RefSeq; NP_001014839.1; NM_001014839.1. [Q9UBB6-1]
RefSeq; NP_001014841.1; NM_001014841.1. [Q9UBB6-2]
RefSeq; NP_055099.1; NM_014284.2. [Q9UBB6-1]
UniGene; Hs.121870; -.
ProteinModelPortal; Q9UBB6; -.
BioGrid; 116768; 51.
IntAct; Q9UBB6; 15.
STRING; 9606.ENSP00000348394; -.
iPTMnet; Q9UBB6; -.
PhosphoSitePlus; Q9UBB6; -.
BioMuta; NCDN; -.
EPD; Q9UBB6; -.
MaxQB; Q9UBB6; -.
PaxDb; Q9UBB6; -.
PeptideAtlas; Q9UBB6; -.
PRIDE; Q9UBB6; -.
ProteomicsDB; 83925; -.
ProteomicsDB; 83926; -. [Q9UBB6-2]
ProteomicsDB; 83927; -. [Q9UBB6-3]
DNASU; 23154; -.
Ensembl; ENST00000356090; ENSP00000348394; ENSG00000020129. [Q9UBB6-1]
Ensembl; ENST00000373243; ENSP00000362340; ENSG00000020129. [Q9UBB6-1]
Ensembl; ENST00000373253; ENSP00000362350; ENSG00000020129. [Q9UBB6-2]
GeneID; 23154; -.
KEGG; hsa:23154; -.
UCSC; uc001bza.3; human. [Q9UBB6-1]
CTD; 23154; -.
EuPathDB; HostDB:ENSG00000020129.15; -.
GeneCards; NCDN; -.
HGNC; HGNC:17597; NCDN.
HPA; HPA023676; -.
MIM; 608458; gene.
neXtProt; NX_Q9UBB6; -.
OpenTargets; ENSG00000020129; -.
PharmGKB; PA134963729; -.
eggNOG; KOG2611; Eukaryota.
eggNOG; ENOG410XRYT; LUCA.
GeneTree; ENSGT00390000013601; -.
HOGENOM; HOG000113742; -.
HOVERGEN; HBG097452; -.
InParanoid; Q9UBB6; -.
OMA; YIQATIR; -.
OrthoDB; EOG091G04JK; -.
PhylomeDB; Q9UBB6; -.
TreeFam; TF323752; -.
ChiTaRS; NCDN; human.
GeneWiki; NCDN; -.
GenomeRNAi; 23154; -.
PRO; PR:Q9UBB6; -.
Proteomes; UP000005640; Chromosome 1.
Bgee; ENSG00000020129; Expressed in 146 organ(s), highest expression level in middle frontal gyrus.
CleanEx; HS_NCDN; -.
ExpressionAtlas; Q9UBB6; baseline and differential.
Genevisible; Q9UBB6; HS.
GO; GO:0005829; C:cytosol; IDA:HPA.
GO; GO:0030425; C:dendrite; ISS:UniProtKB.
GO; GO:0016020; C:membrane; HDA:UniProtKB.
GO; GO:0043025; C:neuronal cell body; ISS:UniProtKB.
GO; GO:0045453; P:bone resorption; IEA:Ensembl.
GO; GO:0031175; P:neuron projection development; ISS:UniProtKB.
GO; GO:0048168; P:regulation of neuronal synaptic plasticity; IEA:Ensembl.
InterPro; IPR016024; ARM-type_fold.
InterPro; IPR008709; Neurochondrin.
PANTHER; PTHR13109; PTHR13109; 1.
Pfam; PF05536; Neurochondrin; 1.
SUPFAM; SSF48371; SSF48371; 1.
1: Evidence at protein level;
Acetylation; Alternative splicing; Cell projection; Complete proteome;
Cytoplasm; Methylation; Phosphoprotein; Polymorphism;
Reference proteome.
INIT_MET 1 1 Removed. {ECO:0000244|PubMed:19413330,
ECO:0000244|PubMed:22814378}.
CHAIN 2 729 Neurochondrin.
/FTId=PRO_0000324617.
MOD_RES 2 2 N-acetylserine.
{ECO:0000244|PubMed:19413330,
ECO:0000244|PubMed:22814378}.
MOD_RES 2 2 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
MOD_RES 75 75 Asymmetric dimethylarginine.
{ECO:0000250|UniProtKB:Q9Z0E0}.
MOD_RES 448 448 Phosphoserine.
{ECO:0000250|UniProtKB:O35095}.
VAR_SEQ 1 17 Missing (in isoform 2). {ECO:0000305}.
/FTId=VSP_032315.
VAR_SEQ 1 11 MSCCDLAAAGQ -> ALGEDFAARGRSL (in isoform
3). {ECO:0000305}.
/FTId=VSP_032316.
VARIANT 392 392 V -> E (in a colorectal cancer sample;
somatic mutation; dbSNP:rs753974779).
{ECO:0000269|PubMed:16959974}.
/FTId=VAR_039849.
VARIANT 392 392 V -> L (in a colorectal cancer sample;
somatic mutation).
{ECO:0000269|PubMed:16959974}.
/FTId=VAR_039850.
SEQUENCE 729 AA; 78864 MW; FA8D46B06CE1F5AB CRC64;
MSCCDLAAAG QLGKASIMAS DCEPALNQAE GRNPTLERYL GALREAKNDS EQFAALLLVT
KAVKAGDIDA KTRRRIFDAV GFTFPNRLLT TKEAPDGCPD HVLRALGVAL LACFCSDPEL
AAHPQVLNKI PILSTFLTAR GDPDDAARRS MIDDTYQCLT AVAGTPRGPR HLIAGGTVSA
LCQAYLGHGY GFDQALALLV GLLAAAETQC WKEAEPDLLA VLRGLSEDFQ KAEDASKFEL
CQLLPLFLPP TTVPPECYRD LQAGLARILG SKLSSWQRNP ALKLAARLAH ACGSDWIPAG
SSGSKFLALL VNLACVEVRL ALEETGTEVK EDVVTACYAL MELGIQECTR CEQSLLKEPQ
KVQLVSVMKE AIGAVIHYLL QVGSEKQKEP FVFASVRILG AWLAEETSSL RKEVCQLLPF
LVRYAKTLYE EAEEANDLSQ QVANLAISPT TPGPTWPGDA LRLLLPGWCH LTVEDGPREI
LIKEGAPSLL CKYFLQQWEL TSPGHDTSVL PDSVEIGLQT CCHIFLNLVV TAPGLIKRDA
CFTSLMNTLM TSLPALVQQQ GRLLLAANVA TLGLLMARLL STSPALQGTP ASRGFFAAAI
LFLSQSHVAR ATPGSDQAVL ALSPEYEGIW ADLQELWFLG MQAFTGCVPL LPWLAPAALR
SRWPQELLQL LGSVSPNSVK PEMVAAYQGV LVELARANRL CREAMRLQAG EETASHYRMA
ALEQCLSEP


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