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Q8TDQ1 (CLM1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | 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:
CMRF35-like molecule 1

Short name=CLM-1
Alternative name(s):
CD300 antigen-like family member F
Immune receptor expressed on myeloid cells 1
Short name=IREM-1
Immunoglobulin superfamily member 13
Short name=IgSF13
NK inhibitory receptor
CD_antigen=CD300f
Gene names
Name:CD300LF
Synonyms:CD300F, CLM1, IGSF13, IREM1, NKIR
ORF Names:UNQ3105/PRO10111
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length290 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Acts as an inhibitory receptor for myeloid cells and mast cells. Inhibits osteoclast formation. Ref.2

Subunit structure

Interacts with PTPN6/SHP-1 in a tyrosine phosphorylation dependent manner. Ref.1 Ref.2

Subcellular location

Cell membrane; Single-pass type I membrane protein Potential.

Tissue specificity

Highly expressed in spleen, peripheral blood leukocyte and monocyte, and lung. Weakly expressed in thymus, heart, brain, placenta, liver, skeletal muscle, kidney, pancreas, prostate, testis, ovary, small intestine or colon. Expressed selectively in monocytes and monocyte-related cells. Ref.1 Ref.2

Post-translational modification

Phosphorylated on tyrosine. Ref.1

Sequence similarities

Belongs to the CD300 family.

Contains 1 Ig-like V-type (immunoglobulin-like) domain.

Ontologies

Alternative products

This entry describes 6 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q8TDQ1-1)

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 (identifier: Q8TDQ1-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-14: MPLLTLYLLLFWLS → MWLPQLDLMRVISAKSQ
     128-128: A → ASTPAPTTPTSTTFTA
     187-221: AAGMSPEQVLQPLEGDLCYADLTLQLAGTSPQKAT → GTAAPGGRPLLCRPDPAAGRNLPAKGYHEAFLCPG
     222-290: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q8TDQ1-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-14: MPLLTLYLLLFWLS → MWLPQLDLMRVISAKSQ
     150-162: HKLLKLSVLLPLI → YCSPWRATSAMQT
     163-290: Missing.
Isoform 4 (identifier: Q8TDQ1-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-14: MPLLTLYLLLFWLS → MWLPQLDLMRVISAKSQ
     149-191: RHKLLKLSVL...KYQQKAAGMS → SSRDVPRAGT...GYHEAFLCPG
     192-290: Missing.
Note: No experimental confirmation available.
Isoform 5 (identifier: Q8TDQ1-5)

The sequence of this isoform differs from the canonical sequence as follows:
     150-244: HKLLKLSVLL...EYVTMASLPK → SEGSQAANYR...GYHEAFLCPG
     245-290: Missing.
Note: No experimental confirmation available.
Isoform 6 (identifier: Q8TDQ1-6)

The sequence of this isoform differs from the canonical sequence as follows:
     1-14: MPLLTLYLLLFWLS → MWLPQLDLMRVISAKSQ

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1919 Ref.8
Chain20 – 290271CMRF35-like molecule 1
PRO_0000247825

Regions

Topological domain20 – 156137Extracellular Potential
Transmembrane157 – 17721Helical; Potential
Topological domain178 – 290113Cytoplasmic Potential
Domain20 – 126107Ig-like V-type

Sites

Site2051Phosphatase-binding

Amino acid modifications

Glycosylation881N-linked (GlcNAc...) Potential
Disulfide bond40 ↔ 108 Ref.9
Disulfide bond54 ↔ 62 Ref.9

Natural variations

Alternative sequence1 – 1414MPLLT…LFWLS → MWLPQLDLMRVISAKSQ in isoform 2, isoform 3, isoform 4 and isoform 6.
VSP_020056
Alternative sequence1281A → ASTPAPTTPTSTTFTA in isoform 2.
VSP_020057
Alternative sequence149 – 19143RHKLL…AAGMS → SSRDVPRAGTAAPGGRPLLC RPDPAAGRNLPAKGYHEAFL CPG in isoform 4.
VSP_020058
Alternative sequence150 – 24495HKLLK…ASLPK → SEGSQAANYRPAAHQAQAPE AQCPPAPHLHHIAAAFGGRL TLGLEDDEVPAESSRDVPRA GTAAPGGRPLLCRPDPAAGR NLPAKGYHEAFLCPG in isoform 5.
VSP_020059
Alternative sequence150 – 16213HKLLK…LLPLI → YCSPWRATSAMQT in isoform 3.
VSP_020060
Alternative sequence163 – 290128Missing in isoform 3.
VSP_020061
Alternative sequence187 – 22135AAGMS…PQKAT → GTAAPGGRPLLCRPDPAAGR NLPAKGYHEAFLCPG in isoform 2.
VSP_020062
Alternative sequence192 – 29099Missing in isoform 4.
VSP_020063
Alternative sequence222 – 29069Missing in isoform 2.
VSP_020064
Alternative sequence245 – 29046Missing in isoform 5.
VSP_020065
Natural variant191V → A. Ref.1 Ref.2 Ref.3 Ref.4 Ref.5 Ref.7
Corresponds to variant rs35489971 [ dbSNP | Ensembl ].
VAR_039128
Natural variant2181Q → R. Ref.1 Ref.2 Ref.3 Ref.4
Corresponds to variant rs2034310 [ dbSNP | Ensembl ].
VAR_027152

Experimental info

Mutagenesis2051Y → F: No interaction with PTPN6. Ref.2
Mutagenesis2491Y → F: Interaction with PTPN6. Ref.2
Mutagenesis2841Y → F: Interaction with PTPN6. Ref.2
Sequence conflict371T → A in AAZ81566. Ref.5
Sequence conflict641I → V in AAZ81566. Ref.5
Sequence conflict781D → N in AAP42153. Ref.2
Sequence conflict1351T → I in AAP42152. Ref.2
Sequence conflict1381S → F in AAM19099. Ref.1
Sequence conflict2121L → Q in AAP42152. Ref.2
Sequence conflict2681H → R in AAP57942. Ref.2

Secondary structure

......................... 290
Helix Strand Turn

Details...

Sequences

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

Last modified May 18, 2010. Version 3.
Checksum: 27AA95664B82B945

FASTA29032,335
        10         20         30         40         50         60 
MPLLTLYLLL FWLSGYSIVT QITGPTTVNG LERGSLTVQC VYRSGWETYL KWWCRGAIWR 

        70         80         90        100        110        120 
DCKILVKTSG SEQEVKRDRV SIKDNQKNRT FTVTMEDLMK TDADTYWCGI EKTGNDLGVT 

       130        140        150        160        170        180 
VQVTIDPAPV TQEETSSSPT LTGHHLDNRH KLLKLSVLLP LIFTILLLLL VAASLLAWRM 

       190        200        210        220        230        240 
MKYQQKAAGM SPEQVLQPLE GDLCYADLTL QLAGTSPQKA TTKLSSAQVD QVEVEYVTMA 

       250        260        270        280        290 
SLPKEDISYA SLTLGAEDQE PTYCNMGHLS SHLPGRGPEE PTEYSTISRP 

« Hide

Isoform 2 [UniParc].

Checksum: C67579996CFFA382
Show »

FASTA23926,480
Isoform 3 [UniParc].

Checksum: 8D46CA836B7E8AAE
Show »

FASTA16518,684
Isoform 4 [UniParc].

Checksum: 9274E383F4A98236
Show »

FASTA19421,427
Isoform 5 [UniParc].

Checksum: 8CB8B81FCB47821A
Show »

FASTA24426,671
Isoform 6 [UniParc].

Checksum: C8AC14CA781BCFC4
Show »

FASTA29332,628

References

« Hide 'large scale' references
[1]"IgSF13, a novel human inhibitory receptor of the immunoglobulin superfamily, is preferentially expressed in dendritic cells and monocytes."
Sui L., Li N., Liu Q., Zhang W., Wan T., Wang B., Luo K., Sun H., Cao X.
Biochem. Biophys. Res. Commun. 319:920-928(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, INTERACTION WITH PTPN6, PHOSPHORYLATION, VARIANTS ALA-19 AND ARG-218.
[2]"IREM-1 is a novel inhibitory receptor expressed by myeloid cells."
Alvarez-Errico D., Aguilar H., Kitzig F., Brckalo T., Sayos J., Lopez-Botet M.
Eur. J. Immunol. 34:3690-3701(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 3 AND 6), FUNCTION, TISSUE SPECIFICITY, INTERACTION WITH PTPN6, SITE, MUTAGENESIS OF TYR-205; TYR-249 AND TYR-284, VARIANTS ALA-19 AND ARG-218.
[3]"The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment."
Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E. expand/collapse author list , Heldens S., Huang A., Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D., Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L., Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C., Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J., Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.
Genome Res. 13:2265-2270(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANTS ALA-19 AND ARG-218.
[4]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 5), VARIANTS ALA-19 AND ARG-218.
Tissue: Small intestine and Umbilical cord blood.
[5]Lin L., Nong W., Zhou G., Ke R., Shen C., Zhong G., Zheng Z., Liang M., Tang Z., Wen S., Li H., Yang S.
Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT ALA-19.
[6]"DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage."
Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L. expand/collapse author list , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C.
Nature 440:1045-1049(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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] (ISOFORM 4), VARIANT ALA-19.
Tissue: Lung.
[8]"Signal peptide prediction based on analysis of experimentally verified cleavage sites."
Zhang Z., Henzel W.J.
Protein Sci. 13:2819-2824(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 20-34.
[9]"The crystal structure of the extracellular domain of the inhibitor receptor expressed on myeloid cells IREM-1."
Marquez J.A., Galfre E., Dupeux F., Flot D., Moran O., Dimasi N.
J. Mol. Biol. 367:310-318(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 21-140, DISULFIDE BONDS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF251706 mRNA. Translation: AAM19099.1.
AF375480 mRNA. Translation: AAP42152.1.
AF375481 mRNA. Translation: AAP42153.1.
AY303545 mRNA. Translation: AAP57942.1.
AY358545 mRNA. Translation: AAQ88909.1.
AK092757 mRNA. Translation: BAC03966.1.
AK315165 mRNA. Translation: BAG37609.1.
DQ153249 mRNA. Translation: AAZ81566.1.
AC016888 Genomic DNA. No translation available.
AC064805 Genomic DNA. No translation available.
BC028199 mRNA. Translation: AAH28199.1.
RefSeqNP_620587.2. NM_139018.4.
UniGeneHs.567706.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2NMSX-ray2.60A21-140[»]
ProteinModelPortalQ8TDQ1.
SMRQ8TDQ1. Positions 19-129.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid127005. 1 interaction.
IntActQ8TDQ1. 1 interaction.
MINTMINT-8020158.

PTM databases

PhosphoSiteQ8TDQ1.

Polymorphism databases

DMDM296439398.

Proteomic databases

PaxDbQ8TDQ1.
PRIDEQ8TDQ1.

Protocols and materials databases

DNASU146722.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000301573; ENSP00000301573; ENSG00000186074. [Q8TDQ1-5]
ENST00000326165; ENSP00000327075; ENSG00000186074. [Q8TDQ1-1]
ENST00000343125; ENSP00000343751; ENSG00000186074. [Q8TDQ1-4]
ENST00000361254; ENSP00000355294; ENSG00000186074. [Q8TDQ1-2]
ENST00000462044; ENSP00000464223; ENSG00000186074. [Q8TDQ1-3]
ENST00000464910; ENSP00000464257; ENSG00000186074. [Q8TDQ1-6]
ENST00000469092; ENSP00000463743; ENSG00000186074. [Q8TDQ1-4]
ENST00000581500; ENSP00000464610; ENSG00000186074. [Q8TDQ1-2]
GeneID146722.
KEGGhsa:146722.
UCSCuc002jlf.3. human. [Q8TDQ1-6]
uc002jlg.3. human. [Q8TDQ1-1]
uc002jlh.3. human. [Q8TDQ1-5]
uc002jli.3. human. [Q8TDQ1-4]
uc002jlj.1. human. [Q8TDQ1-2]

Organism-specific databases

CTD146722.
GeneCardsGC17M072690.
H-InvDBHIX0021633.
HGNCHGNC:29883. CD300LF.
HPAHPA013712.
MIM609807. gene.
neXtProtNX_Q8TDQ1.
PharmGKBPA142672153.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG75577.
HOVERGENHBG050999.
InParanoidQ8TDQ1.
OrthoDBEOG78PVBM.
PhylomeDBQ8TDQ1.
TreeFamTF334441.

Gene expression databases

ArrayExpressQ8TDQ1.
BgeeQ8TDQ1.
GenevestigatorQ8TDQ1.

Family and domain databases

Gene3D2.60.40.10. 1 hit.
InterProIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR013106. Ig_V-set.
[Graphical view]
PfamPF07686. V-set. 1 hit.
[Graphical view]
SMARTSM00409. IG. 1 hit.
[Graphical view]
PROSITEPS50835. IG_LIKE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ8TDQ1.
GeneWikiCD300LF.
GenomeRNAi146722.
NextBio85431.
PROQ8TDQ1.
SOURCESearch...

Entry information

Entry nameCLM1_HUMAN
AccessionPrimary (citable) accession number: Q8TDQ1
Secondary accession number(s): B2RCL2 expand/collapse secondary AC list , C9JDN3, Q3Y6P0, Q6UX24, Q7Z6A6, Q7Z7I4, Q7Z7I5, Q8N6D0, Q8NAF5
Entry history
Integrated into UniProtKB/Swiss-Prot: July 25, 2006
Last sequence update: May 18, 2010
Last modified: April 16, 2014
This is version 102 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 17

Human chromosome 17: entries, gene names and cross-references to MIM

Human cell differentiation molecules

CD nomenclature of surface proteins of human leucocytes and list of entries