LOCUS       NM_178232               1892 bp    mRNA    linear   PRI 08-JUN-2024
DEFINITION  Homo sapiens hyaluronan and proteoglycan link protein 3 (HAPLN3),
            transcript variant 2, mRNA.
ACCESSION   NM_178232
VERSION     NM_178232.4
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 1892)
  AUTHORS   Patel,P.G., Wessel,T., Kawashima,A., Okello,J.B.A.,
            Jamaspishvili,T., Guerard,K.P., Lee,L., Lee,A.Y., How,N.E.,
            Dion,D., Scarlata,E., Jackson,C.L., Boursalie,S., Sack,T., Dunn,R.,
            Moussa,M., Mackie/,K., Ellis,A., Marra,E., Chin,J., Siddiqui,K.,
            Hetou,K., Pickard,L.A., Arthur-Hayward,V., Bauman,G., Chevalier,S.,
            Brimo,F., Boutros,P.C., Lapointe PhD,J., Bartlett,J.M.S.,
            Gooding,R.J. and Berman,D.M.
  TITLE     A three-gene DNA methylation biomarker accurately classifies early
            stage prostate cancer
  JOURNAL   Prostate 79 (14), 1705-1714 (2019)
   PUBMED   31433512
  REMARK    GeneRIF: DNA methylation levels at GAS6(growth arrest specific
            6)/GSTP1(glutathione S-transferase pi 1)/HAPLN3(hyaluronan and
            proteoglycan link protein 3) genomic loci showed large differences
            between cancer and benign samples
REFERENCE   2  (bases 1 to 1892)
  AUTHORS   Kahler,A.K., Djurovic,S., Rimol,L.M., Brown,A.A., Athanasiu,L.,
            Jonsson,E.G., Hansen,T., Gustafsson,O., Hall,H., Giegling,I.,
            Muglia,P., Cichon,S., Rietschel,M., Pietilainen,O.P., Peltonen,L.,
            Bramon,E., Collier,D., St Clair,D., Sigurdsson,E., Petursson,H.,
            Rujescu,D., Melle,I., Werge,T., Steen,V.M., Dale,A.M.,
            Matthews,R.T., Agartz,I. and Andreassen,O.A.
  TITLE     Candidate gene analysis of the human natural killer-1 carbohydrate
            pathway and perineuronal nets in schizophrenia: B3GAT2 is
            associated with disease risk and cortical surface area
  JOURNAL   Biol Psychiatry 69 (1), 90-96 (2011)
   PUBMED   20950796
  REMARK    GeneRIF: Observational study and meta-analysis of gene-disease
            association. (HuGE Navigator)
REFERENCE   3  (bases 1 to 1892)
  AUTHORS   Kuo,S.J., Chien,S.Y., Lin,C., Chan,S.E., Tsai,H.T. and Chen,D.R.
  TITLE     Significant elevation of CLDN16 and HAPLN3 gene expression in human
            breast cancer
  JOURNAL   Oncol Rep 24 (3), 759-766 (2010)
   PUBMED   20664984
  REMARK    GeneRIF: Elevated CLDN16 gene expression was suggested to be
            involved in the development of breast cancer and to be a biomarker
            and target treatment for breast cancer.
REFERENCE   4  (bases 1 to 1892)
  AUTHORS   Palmer,D.J., Kelly,V.C., Smit,A.M., Kuy,S., Knight,C.G. and
            Cooper,G.J.
  TITLE     Human colostrum: identification of minor proteins in the aqueous
            phase by proteomics
  JOURNAL   Proteomics 6 (7), 2208-2216 (2006)
   PUBMED   16502470
REFERENCE   5  (bases 1 to 1892)
  AUTHORS   Clark,H.F., Gurney,A.L., Abaya,E., Baker,K., Baldwin,D., Brush,J.,
            Chen,J., Chow,B., Chui,C., Crowley,C., Currell,B., Deuel,B.,
            Dowd,P., Eaton,D., Foster,J., Grimaldi,C., Gu,Q., Hass,P.E.,
            Heldens,S., Huang,A., Kim,H.S., Klimowski,L., Jin,Y., Johnson,S.,
            Lee,J., Lewis,L., Liao,D., Mark,M., Robbie,E., Sanchez,C.,
            Schoenfeld,J., Seshagiri,S., Simmons,L., Singh,J., Smith,V.,
            Stinson,J., Vagts,A., Vandlen,R., Watanabe,C., Wieand,D., Woods,K.,
            Xie,M.H., Yansura,D., Yi,S., Yu,G., Yuan,J., Zhang,M., Zhang,Z.,
            Goddard,A., Wood,W.I., Godowski,P. and Gray,A.
  TITLE     The secreted protein discovery initiative (SPDI), a large-scale
            effort to identify novel human secreted and transmembrane proteins:
            a bioinformatics assessment
  JOURNAL   Genome Res 13 (10), 2265-2270 (2003)
   PUBMED   12975309
  REMARK    Erratum:[Genome Res. 2003 Dec;13(12):2759]
REFERENCE   6  (bases 1 to 1892)
  AUTHORS   Spicer,A.P., Joo,A. and Bowling,R.A. Jr.
  TITLE     A hyaluronan binding link protein gene family whose members are
            physically linked adjacent to chondroitin sulfate proteoglycan core
            protein genes: the missing links
  JOURNAL   J Biol Chem 278 (23), 21083-21091 (2003)
   PUBMED   12663660
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK292103.1 and AY262759.1.
            
            On Jun 2, 2019 this sequence version replaced NM_178232.3.
            
            Summary: This gene belongs to the hyaluronan and proteoglycan
            binding link protein gene family. The protein encoded by this gene
            may function in hyaluronic acid binding and cell adhesion.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (2) lacks an exon in the 5' UTR
            and coding region which results in the use of a dowstream start
            codon compared to variant 1. The encoded isoform (2) has a shorter
            N-terminus compared to isoform 1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AY358500.1, AY262759.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000359595.8/ ENSP00000352606.4
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-5                 AK292103.1         84-88
            6-1892              AY262759.1         1-1887
FEATURES             Location/Qualifiers
     source          1..1892
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="15"
                     /map="15q26.1"
     gene            1..1892
                     /gene="HAPLN3"
                     /gene_synonym="EXLD1; HsT19883"
                     /note="hyaluronan and proteoglycan link protein 3"
                     /db_xref="GeneID:145864"
                     /db_xref="HGNC:HGNC:21446"
     exon            1..86
                     /gene="HAPLN3"
                     /gene_synonym="EXLD1; HsT19883"
                     /inference="alignment:Splign:2.1.0"
     exon            87..257
                     /gene="HAPLN3"
                     /gene_synonym="EXLD1; HsT19883"
                     /inference="alignment:Splign:2.1.0"
     CDS             134..1216
                     /gene="HAPLN3"
                     /gene_synonym="EXLD1; HsT19883"
                     /EC_number="3.1.2.15"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; extracellular link domain containing, 1"
                     /codon_start=1
                     /product="hyaluronan and proteoglycan link protein 3
                     isoform 2 precursor"
                     /protein_id="NP_839946.1"
                     /db_xref="CCDS:CCDS10346.1"
                     /db_xref="GeneID:145864"
                     /db_xref="HGNC:HGNC:21446"
                     /translation="MGLLLLVPLLLLPGSYGLPFYNGFYYSNSANDQNLGNGHGKDLL
                     NGVKLVVETPEETLFTYQGASVILPCRYRYEPALVSPRRVRVKWWKLSENGAPEKDVL
                     VAIGLRHRSFGDYQGRVHLRQDKEHDVSLEIQDLRLEDYGRYRCEVIDGLEDESGLVE
                     LELRGVVFPYQSPNGRYQFNFHEGQQVCAEQAAVVASFEQLFRAWEEGLDWCNAGWLQ
                     DATVQYPIMLPRQPCGGPGLAPGVRSYGPRHRRLHRYDVFCFATALKGRVYYLEHPEK
                     LTLTEAREACQEDDATIAKVGQLFAAWKFHGLDRCDAGWLADGSVRYPVVHPHPNCGP
                     PEPGVRSFGFPDPQSRLYGVYCYRQH"
     exon            258..626
                     /gene="HAPLN3"
                     /gene_synonym="EXLD1; HsT19883"
                     /inference="alignment:Splign:2.1.0"
     exon            627..929
                     /gene="HAPLN3"
                     /gene_synonym="EXLD1; HsT19883"
                     /inference="alignment:Splign:2.1.0"
     exon            930..1892
                     /gene="HAPLN3"
                     /gene_synonym="EXLD1; HsT19883"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1863..1868
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HAPLN3"
                     /gene_synonym="EXLD1; HsT19883"
                     /note="hexamer: AATAAA"
     polyA_site      1892
                     /gene="HAPLN3"
                     /gene_synonym="EXLD1; HsT19883"
                     /note="major polyA site"
ORIGIN      
        1 atttccccga aatcagactg ctgccttgga ccgggacagc tcgcggcccc cgagagctct
       61 agccgtcgag gagctgcctg gggacgtttg ccctggggcc ccagcctggc ccgggtcacc
      121 ctggcatgag gagatgggcc tgttgctcct ggtcccgttg ctcctgctgc ccggctccta
      181 cggactgccc ttctacaacg gcttctacta ctccaacagc gccaacgacc agaacctagg
      241 caacggtcat ggcaaagacc tccttaatgg agtgaagctg gtggtggaga cacccgagga
      301 gaccctgttc acctaccaag gggccagtgt gatcctgccc tgccgctacc gctacgagcc
      361 ggccctggtc tccccgcggc gtgtgcgtgt caaatggtgg aagctgtcgg agaacggggc
      421 cccagagaag gacgtgctgg tggccatcgg gctgaggcac cgctcctttg gggactacca
      481 aggccgcgtg cacctgcggc aggacaaaga gcatgacgtc tcgctggaga tccaggatct
      541 gcggctggag gactatgggc gttaccgctg tgaggtcatt gacgggctgg aggatgaaag
      601 cggtctggtg gagctggagc tgcggggtgt ggtctttcct taccagtccc ccaacgggcg
      661 ctaccagttc aacttccacg agggccagca ggtctgtgca gagcaggctg cggtggtggc
      721 ctcctttgag cagctcttcc gggcctggga ggagggcctg gactggtgca acgcgggctg
      781 gctgcaggat gccacggtgc agtaccccat catgttgccc cggcagccct gcggtggccc
      841 gggcctggca cctggcgtgc gaagctacgg cccccgccac cgccgcctgc accgctatga
      901 tgtattctgc ttcgctactg ccctcaaggg gcgggtgtac tacctggagc accctgagaa
      961 gctgacgctg acagaggcaa gggaggcctg ccaggaagat gatgccacga tcgccaaggt
     1021 gggacagctc tttgccgcct ggaagttcca tggcctggac cgctgcgacg ctggctggct
     1081 ggcagatggt agcgtccgct accctgtggt tcacccgcat cctaactgtg ggcccccaga
     1141 gcctggggtc cgaagctttg gcttccccga cccgcagagc cgcttgtacg gtgtttactg
     1201 ctaccgccag cactaggacc tggggccctc ccctgccgca ttccctcact ggctgtgtat
     1261 ttattgagtg gttcgttttc ccttgtgggt tggagccatt ttaactgttt ttatacttct
     1321 caatttaaat tttctttaaa cattttttta ctattttttg taaagcaaac agaacccaat
     1381 gcctcccttt gctcctggat gccccactcc aggaatcatg cttgctcccc tgggccattt
     1441 gcggttttgt gggcttctgg agggttcccc gccatccagg ctggtctccc tcccttaagg
     1501 aggttggtgc ccagagtggg cggtggcctg tctagaatgc cgccgggagt ccgggcatgg
     1561 tgggcacagt tctccctgcc cctcagcctg ggggaagaag agggcctcgg gggcctccgg
     1621 agctgggctt tgggcctctc ctgcccacct ctacttctct gtgaagccgc tgaccccagt
     1681 ctgcccactg aggggctagg gctggaagcc agttctaggc ttccaggcga aagctgaggg
     1741 aaggaagaaa ctcccctccc cgttcccctt cccctctcgg ttccaaagaa tctgttttgt
     1801 tgtcatttgt ttctcctgtt tccctgtgtg gggaggggcc ctcaggtgtg tgtactttgg
     1861 acaataaatg gtgctatgac tgccttccgc ca
//
