LOCUS       NM_138379               1330 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens T cell immunoglobulin and mucin domain containing 4
            (TIMD4), transcript variant 1, mRNA.
ACCESSION   NM_138379
VERSION     NM_138379.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1330)
  AUTHORS   Wang,Y., Wang,Y., Liu,W., Ding,L., Zhang,X., Wang,B., Tong,Z.,
            Yue,X., Li,C., Xu,L., Wu,Z., Liang,X., Ma,C. and Gao,L.
  TITLE     TIM-4 orchestrates mitochondrial homeostasis to promote lung cancer
            progression via ANXA2/PI3K/AKT/OPA1 axis
  JOURNAL   Cell Death Dis 14 (2), 141 (2023)
   PUBMED   36806050
  REMARK    GeneRIF: TIM-4 orchestrates mitochondrial homeostasis to promote
            lung cancer progression via ANXA2/PI3K/AKT/OPA1 axis.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1330)
  AUTHORS   Qin,D., Liu,P., Zhou,H., Jin,J., Gong,W., Liu,K., Chen,S.,
            Huang,J., Fan,W., Tao,Z. and Xu,Y.
  TITLE     TIM-4 in macrophages contributes to nasal polyp formation through
            the TGF-beta1-mediated epithelial to mesenchymal transition in
            nasal epithelial cells
  JOURNAL   Front Immunol 13, 941608 (2022)
   PUBMED   35990621
  REMARK    GeneRIF: TIM-4 in macrophages contributes to nasal polyp formation
            through the TGF-beta1-mediated epithelial to mesenchymal transition
            in nasal epithelial cells.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1330)
  AUTHORS   Chow,A., Schad,S., Green,M.D., Hellmann,M.D., Allaj,V., Ceglia,N.,
            Zago,G., Shah,N.S., Sharma,S.K., Mattar,M., Chan,J., Rizvi,H.,
            Zhong,H., Liu,C., Bykov,Y., Zamarin,D., Shi,H., Budhu,S.,
            Wohlhieter,C., Uddin,F., Gupta,A., Khodos,I., Waninger,J.J.,
            Qin,A., Markowitz,G.J., Mittal,V., Balachandran,V., Durham,J.N.,
            Le,D.T., Zou,W., Shah,S.P., McPherson,A., Panageas,K., Lewis,J.S.,
            Perry,J.S.A., de Stanchina,E., Sen,T., Poirier,J.T., Wolchok,J.D.,
            Rudin,C.M. and Merghoub,T.
  TITLE     Tim-4+ cavity-resident macrophages impair anti-tumor CD8+ T cell
            immunity
  JOURNAL   Cancer Cell 39 (7), 973-988 (2021)
   PUBMED   34115989
  REMARK    GeneRIF: Tim-4(+) cavity-resident macrophages impair anti-tumor
            CD8(+) T cell immunity.
REFERENCE   4  (bases 1 to 1330)
  AUTHORS   Moon,B., Yang,S., Kim,K., Lee,J., Jeong,D. and Park,D.
  TITLE     EphA2 Interacts with Tim-4 through Association between Its FN3
            Domain and the IgV Domain of Tim-4
  JOURNAL   Cells 10 (6), 1290 (2021)
   PUBMED   34067457
  REMARK    GeneRIF: EphA2 Interacts with Tim-4 through Association between Its
            FN3 Domain and the IgV Domain of Tim-4.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1330)
  AUTHORS   Omori,S., Tsugita,M., Hoshikawa,Y., Morita,M., Ito,F.,
            Yamaguchi,S.I., Xie,Q., Noyori,O., Yamaguchi,T., Takada,A.,
            Saitoh,T., Toyokuni,S., Akiba,H., Nagata,S., Kinoshita,K. and
            Nakayama,M.
  TITLE     Tim4 recognizes carbon nanotubes and mediates phagocytosis leading
            to granuloma formation
  JOURNAL   Cell Rep 34 (6), 108734 (2021)
   PUBMED   33567275
  REMARK    GeneRIF: Tim4 recognizes carbon nanotubes and mediates phagocytosis
            leading to granuloma formation.
REFERENCE   6  (bases 1 to 1330)
  AUTHORS   Santiago,C., Ballesteros,A., Martinez-Munoz,L., Mellado,M.,
            Kaplan,G.G., Freeman,G.J. and Casasnovas,J.M.
  TITLE     Structures of T cell immunoglobulin mucin protein 4 show a
            metal-Ion-dependent ligand binding site where phosphatidylserine
            binds
  JOURNAL   Immunity 27 (6), 941-951 (2007)
   PUBMED   18083575
  REMARK    GeneRIF: Structures of T cell immunoglobulin mucin protein 4 show a
            metal-Ion-dependent ligand binding site where phosphatidylserine
            binds.
REFERENCE   7  (bases 1 to 1330)
  AUTHORS   Kobayashi,N., Karisola,P., Pena-Cruz,V., Dorfman,D.M., Jinushi,M.,
            Umetsu,S.E., Butte,M.J., Nagumo,H., Chernova,I., Zhu,B.,
            Sharpe,A.H., Ito,S., Dranoff,G., Kaplan,G.G., Casasnovas,J.M.,
            Umetsu,D.T., Dekruyff,R.H. and Freeman,G.J.
  TITLE     TIM-1 and TIM-4 glycoproteins bind phosphatidylserine and mediate
            uptake of apoptotic cells
  JOURNAL   Immunity 27 (6), 927-940 (2007)
   PUBMED   18082433
  REMARK    GeneRIF: TIM-4 and TIM-1 are immunologically restricted members of
            the group of receptors whose recognition of PS is critical for the
            efficient clearance of apoptotic cells and prevention of
            autoimmunity.
REFERENCE   8  (bases 1 to 1330)
  AUTHORS   Liu,T., He,S.H., Zheng,P.Y., Zhang,T.Y., Wang,B.Q. and Yang,P.C.
  TITLE     Staphylococcal enterotoxin B increases TIM4 expression in human
            dendritic cells that drives naive CD4 T cells to differentiate into
            Th2 cells
  JOURNAL   Mol Immunol 44 (14), 3580-3587 (2007)
   PUBMED   17439824
  REMARK    GeneRIF: The results demonstrate that Staphylococcus aureus derived
            Staphylococcal enterotoxin B promotes the TIM4 production in human
            dendritic cells.
REFERENCE   9  (bases 1 to 1330)
  AUTHORS   Xia,Y.P., Cui,T.P. and Wu,J.M.
  TITLE     [Study on relationship between polymorphism sites of TIM4 and
            allergic asthma in the population of Han nationality from Hubei
            province of China]
  JOURNAL   Zhonghua Yi Xue Yi Chuan Xue Za Zhi 24 (2), 213-216 (2007)
   PUBMED   17407086
  REMARK    GeneRIF: The polymorphism of 8570G > A in TIM4 may be associated
            with allergic asthma in the population of Han nationality from
            Hubei province of China.
            GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   10 (bases 1 to 1330)
  AUTHORS   Page,N.S., Jones,G. and Stewart,G.J.
  TITLE     Genetic association studies between the T cell immunoglobulin mucin
            (TIM) gene locus and childhood atopic dermatitis
  JOURNAL   Int Arch Allergy Immunol 141 (4), 331-336 (2006)
   PUBMED   16940744
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BC008988.1, AC008491.6 and AA843555.1.
            
            On Nov 23, 2018 this sequence version replaced NM_138379.2.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR5189664.3602.1, SRR5189664.461.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000274532.7/ ENSP00000274532.2
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-746               BC008988.1         30-775
            747-760             AC008491.6         129398-129411       c
            761-1263            BC008988.1         790-1292
            1264-1330           AA843555.1         16-82               c
FEATURES             Location/Qualifiers
     source          1..1330
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q33.3"
     gene            1..1330
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /note="T cell immunoglobulin and mucin domain containing
                     4"
                     /db_xref="GeneID:91937"
                     /db_xref="HGNC:HGNC:25132"
                     /db_xref="MIM:610096"
     exon            1..86
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /inference="alignment:Splign:2.1.0"
     CDS             29..1165
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; T-cell immunoglobulin and mucin
                     domain-containing protein 4; TIM-4; TIMD-4; T-cell
                     membrane protein 4; T-cell immunoglobulin mucin receptor
                     4"
                     /codon_start=1
                     /product="T-cell immunoglobulin and mucin
                     domain-containing protein 4 isoform 1 precursor"
                     /protein_id="NP_612388.2"
                     /db_xref="CCDS:CCDS4332.1"
                     /db_xref="GeneID:91937"
                     /db_xref="HGNC:HGNC:25132"
                     /db_xref="MIM:610096"
                     /translation="MSKEPLILWLMIEFWWLYLTPVTSETVVTEVLGHRVTLPCLYSS
                     WSHNSNSMCWGKDQCPYSGCKEALIRTDGMRVTSRKSAKYRLQGTIPRGDVSLTILNP
                     SESDSGVYCCRIEVPGWFNDVKINVRLNLQRASTTTHRTATTTTRRTTTTSPTTTRQM
                     TTTPAALPTTVVTTPDLTTGTPLQMTTIAVFTTANTCLSLTPSTLPEEATGLLTPEPS
                     KEGPILTAESETVLPSDSWSSVESTSADTVLLTSKESKVWDLPSTSHVSMWKTSDSVS
                     SPQPGASDTAVPEQNKTTKTGQMDGIPMSMKNEMPISQLLMIIAPSLGFVLFALFVAF
                     LLRGKLMETYCSQKHTRLDYIGDSKNVLNDVQHGREDEDGLFTL"
     exon            87..428
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /inference="alignment:Splign:2.1.0"
     exon            429..707
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /inference="alignment:Splign:2.1.0"
     exon            708..788
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /inference="alignment:Splign:2.1.0"
     exon            789..872
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /inference="alignment:Splign:2.1.0"
     exon            873..922
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /inference="alignment:Splign:2.1.0"
     exon            923..1040
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /inference="alignment:Splign:2.1.0"
     exon            1041..1080
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /inference="alignment:Splign:2.1.0"
     exon            1081..1330
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1245..1250
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /note="hexamer: CATAAA"
     polyA_site      1272
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /note="major polyA site"
     regulatory      1305..1310
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
                     /note="hexamer: AATGAA"
     polyA_site      1330
                     /gene="TIMD4"
                     /gene_synonym="SMUCKLER; TIM4"
ORIGIN      
        1 agactcctgg gtccggtcaa ccgtcaaaat gtccaaagaa cctctcattc tctggctgat
       61 gattgagttt tggtggcttt acctgacacc agtcacttca gagactgttg tgacggaggt
      121 tttgggtcac cgggtgactt tgccctgtct gtactcatcc tggtctcaca acagcaacag
      181 catgtgctgg gggaaagacc agtgccccta ctccggttgc aaggaggcgc tcatccgcac
      241 tgatggaatg agggtgacct caagaaagtc agcaaaatat agacttcagg ggactatccc
      301 gagaggtgat gtctccttga ccatcttaaa ccccagtgaa agtgacagcg gtgtgtactg
      361 ctgccgcata gaagtgcctg gctggttcaa cgatgtaaag ataaacgtgc gcctgaatct
      421 acagagagcc tcaacaacca cgcacagaac agcaaccacc accacacgca gaacaacaac
      481 aacaagcccc accaccaccc gacaaatgac aacaacccca gctgcacttc caacaacagt
      541 cgtgaccaca cccgatctca caaccggaac accactccag atgacaacca ttgccgtctt
      601 cacaacagca aacacgtgcc tttcactaac cccaagcacc cttccggagg aagccacagg
      661 tcttctgact cccgagcctt ctaaggaagg gcccatcctc actgcagaat cagaaactgt
      721 cctccccagt gattcctgga gtagtgttga gtctacttct gctgacactg tcctgctgac
      781 atccaaagag tccaaagttt gggatctccc atcaacatcc cacgtgtcaa tgtggaaaac
      841 gagtgattct gtgtcttctc ctcagcctgg agcatctgat acagcagttc ctgagcagaa
      901 caaaacaaca aaaacaggac agatggatgg aatacccatg tcaatgaaga atgaaatgcc
      961 catctcccaa ctactgatga tcatcgcccc ctccttggga tttgtgctct tcgcattgtt
     1021 tgtggcgttt ctcctgagag ggaaactcat ggaaacctat tgttcgcaga aacacacaag
     1081 gctagactac attggagata gtaaaaatgt cctcaatgac gtgcagcatg gaagggaaga
     1141 cgaagacggc ctttttaccc tctaacaacg cagtagcatg ttagattgag gatgggggca
     1201 tgacactcca gtgtcaaaat aagtcttagt agatttcctt gtttcataaa aaagactcac
     1261 ttattccatg gatgtcattg atccaggctt gctttagttt catgaatgaa gggtacttta
     1321 gagaccacaa
//
