LOCUS       NM_016176               1933 bp    mRNA    linear   PRI 07-APR-2024
DEFINITION  Homo sapiens stromal cell derived factor 4 (SDF4), transcript
            variant 2, mRNA.
ACCESSION   NM_016176
VERSION     NM_016176.6
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 1933)
  AUTHORS   He,S.W., Liang,Y.L., Zhang,Y., Liu,X., Gong,S., Ye,M.L.,
            Huang,S.Y., Tan,X.R., Zhou,S.Q., Zhao,Y., Liu,N. and Li,Y.Q.
  TITLE     LINC00173 facilitates tumor progression by stimulating
            RAB1B-mediated PA2G4 and SDF4 secretion in nasopharyngeal carcinoma
  JOURNAL   Mol Oncol 17 (3), 518-533 (2023)
   PUBMED   36606322
  REMARK    GeneRIF: LINC00173 facilitates tumor progression by stimulating
            RAB1B-mediated PA2G4 and SDF4 secretion in nasopharyngeal
            carcinoma.
REFERENCE   2  (bases 1 to 1933)
  AUTHORS   Tran,M.L., Tushaus,J., Kim,Y., Ramazanov,B.R., Devireddy,S.,
            Lichtenthaler,S.F., Ferguson,S.M. and von Blume,J.
  TITLE     Cab45 deficiency leads to the mistargeting of progranulin and
            prosaposin and aberrant lysosomal positioning
  JOURNAL   Traffic 24 (1), 4-19 (2023)
   PUBMED   36398980
  REMARK    GeneRIF: Cab45 deficiency leads to the mistargeting of progranulin
            and prosaposin and aberrant lysosomal positioning.
REFERENCE   3  (bases 1 to 1933)
  AUTHORS   Zhu,T., Su,Q., Wang,C., Shen,L., Chen,H., Feng,S., Peng,X.,
            Chen,S., Wang,Y., Jiang,H. and Chen,J.
  TITLE     SDF4 Is a Prognostic Factor for 28-Days Mortality in Patients With
            Sepsis via Negatively Regulating ER Stress
  JOURNAL   Front Immunol 12, 659193 (2021)
   PUBMED   34326834
  REMARK    GeneRIF: SDF4 Is a Prognostic Factor for 28-Days Mortality in
            Patients With Sepsis via Negatively Regulating ER Stress.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1933)
  AUTHORS   Sidisky,J.M., Weaver,D., Hussain,S., Okumus,M., Caratenuto,R. and
            Babcock,D.
  TITLE     Mayday sustains trans-synaptic BMP signaling required for synaptic
            maintenance with age
  JOURNAL   Elife 10, e54932 (2021)
   PUBMED   33667157
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1933)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   6  (bases 1 to 1933)
  AUTHORS   Zhu,Y., Wang,Q., Xu,W. and Li,S.
  TITLE     The ethanol response gene Cab45 can modulate the impairment
            elicited by ethanol and ultraviolet in PC12 cells
  JOURNAL   J Genet Genomics 35 (3), 153-161 (2008)
   PUBMED   18355758
REFERENCE   7  (bases 1 to 1933)
  AUTHORS   Lam,P.P., Hyvarinen,K., Kauppi,M., Cosen-Binker,L., Laitinen,S.,
            Keranen,S., Gaisano,H.Y. and Olkkonen,V.M.
  TITLE     A cytosolic splice variant of Cab45 interacts with Munc18b and
            impacts on amylase secretion by pancreatic acini
  JOURNAL   Mol Biol Cell 18 (7), 2473-2480 (2007)
   PUBMED   17442889
  REMARK    GeneRIF: In a yeast two-hybrid screen the EF-hand Ca(2+)-binding
            protein Cab45 was identified as an interaction partner of Munc18b.
REFERENCE   8  (bases 1 to 1933)
  AUTHORS   Honore,B. and Vorum,H.
  TITLE     The CREC family, a novel family of multiple EF-hand, low-affinity
            Ca(2+)-binding proteins localised to the secretory pathway of
            mammalian cells
  JOURNAL   FEBS Lett 466 (1), 11-18 (2000)
   PUBMED   10648803
  REMARK    Review article
REFERENCE   9  (bases 1 to 1933)
  AUTHORS   Koivu,T., Laitinen,S., Riento,K. and Olkkonen,V.M.
  TITLE     Sequence of a human cDNA encoding Cab45, a Ca2+-binding protein
            with six EF-hand motifs
  JOURNAL   DNA Seq 7 (3-4), 217-220 (1997)
   PUBMED   9254016
REFERENCE   10 (bases 1 to 1933)
  AUTHORS   Scherer,P.E., Lederkremer,G.Z., Williams,S., Fogliano,M.,
            Baldini,G. and Lodish,H.F.
  TITLE     Cab45, a novel (Ca2+)-binding protein localized to the Golgi lumen
  JOURNAL   J Cell Biol 133 (2), 257-268 (1996)
   PUBMED   8609160
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL162741.44.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Apr 22, 2020 this sequence version replaced NM_016176.5.
            
            Summary: This gene encodes a stromal cell derived factor that is a
            member of the CREC protein family. The encoded protein contains six
            EF-hand motifs and calcium-binding motifs. This protein localizes
            to the Golgi lumen and may be involved in regulating calcium
            dependent cellular activities. [provided by RefSeq, Sep 2011].
            
            Transcript Variant: This variant (2) uses a different splice site
            in the 3' coding region, compared to variant 1, that results in a
            frameshift. It encodes isoform 2, which has a shorter and distinct
            C-terminus compared to 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 :: BC022375.1, AK075352.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2153946, SAMEA2154405
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            CDS uses downstream in-frame AUG :: upstream AUG and CDS extension
                                                is not conserved
            MANE Ensembl match               :: ENST00000360001.12/
                                                ENSP00000353094.7
            RefSeq Select criteria           :: based on conservation,
                                                expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-110               AL162741.44        42004-42113         c
            111-589             AL162741.44        38580-39058         c
            590-726             AL162741.44        33944-34080         c
            727-840             AL162741.44        33356-33469         c
            841-999             AL162741.44        28881-29039         c
            1000-1175           AL162741.44        28570-28745         c
            1176-1933           AL162741.44        27043-27800         c
FEATURES             Location/Qualifiers
     source          1..1933
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p36.33"
     gene            1..1933
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /note="stromal cell derived factor 4"
                     /db_xref="GeneID:51150"
                     /db_xref="HGNC:HGNC:24188"
                     /db_xref="MIM:614282"
     exon            1..110
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /inference="alignment:Splign:2.1.0"
     exon            111..589
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /inference="alignment:Splign:2.1.0"
     CDS             285..1352
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; 45 kDa calcium-binding protein"
                     /codon_start=1
                     /product="45 kDa calcium-binding protein isoform 2
                     precursor"
                     /protein_id="NP_057260.3"
                     /db_xref="CCDS:CCDS30553.2"
                     /db_xref="GeneID:51150"
                     /db_xref="HGNC:HGNC:24188"
                     /db_xref="MIM:614282"
                     /translation="MASRWGPLIGLAPCCLWLLGAVLLMDASARPANHSSTRERVANR
                     EENEILPPDHLNGVKLEMDGHLNRGFHQEVFLGKDLGGFDEDAEPRRSRRKLMVIFSK
                     VDVNTDRKISAKEMQRWIMEKTAEHFQEAMEESKTHFRAVDPDGDGHVSWDEYKVKFL
                     ASKGHSEKEVADAIRLNEELKVDEETQEVLENLKDRWYQADSPPADLLLTEEEFLSFL
                     HPEHSRGMLRFMVKEIVRDLDQDGDKQLSVPEFISLPVGTVENQQGQDIDDNWVKDRK
                     KEFEELIDSNHDGIVTAEELESYMDPMNEYNALNEAKQMIAVADENQNHHLEPEEVLK
                     YSEFFTGSKLVDYARSVHEEF"
     exon            590..726
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /inference="alignment:Splign:2.1.0"
     exon            727..840
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /inference="alignment:Splign:2.1.0"
     exon            841..999
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1000..1175
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1176..1933
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1928..1933
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /note="hexamer: AATATA"
     polyA_site      1933
                     /gene="SDF4"
                     /gene_synonym="Cab45; SDF-4"
                     /note="major polyA site"
ORIGIN      
        1 gcaccgcccc cgcccgcaag aaagatggca gtggcctgat ccgggcccgt tggcggcgtc
       61 actgacgctt cgctccggtc ctcggatccc gagcgcgggg aggcagaccg actgtgagct
      121 gcttgtcccc atcctgcggc cgtcctgggg acacagagcc ctccgtggtg cccggggatt
      181 ggattggagc caggacctca cttcctcctc tgcccctgcc cctgcccctc ccagcacctg
      241 gcccacaccc tgcagcccgc cccatggtct ggccctgggt ggcgatggcg tccaggtggg
      301 gtcccctcat tggcctggct ccgtgctgcc tctggctcct gggggcagtc cttctgatgg
      361 acgcgtctgc acggcctgcc aaccactcgt ccactcgaga gagagtagcc aacagggagg
      421 agaatgagat cctgccccca gaccacctga acggggtgaa gctggagatg gacgggcacc
      481 tcaatcgcgg cttccaccag gaggtcttcc taggcaagga cctgggtggc tttgatgagg
      541 acgcggagcc gcggcggagc cggaggaagc tgatggtcat cttttccaag gtggatgtga
      601 acactgaccg gaagatcagt gccaaggaga tgcagcgctg gatcatggag aagacggccg
      661 agcacttcca ggaggccatg gaggagagca agacacactt ccgcgccgtg gaccctgacg
      721 gggacggtca cgtgtcttgg gacgagtata aggtgaagtt tttggcgagt aaaggccata
      781 gcgagaagga ggttgccgac gccatcaggc tcaacgagga actcaaagtg gatgaggaaa
      841 cacaggaagt cctggagaac ctgaaggacc gctggtacca ggcggacagc ccccctgcag
      901 acctgctgct gacggaggag gagttcctgt cgttcctcca ccccgagcac agccggggaa
      961 tgctcaggtt catggtgaag gagatcgtcc gggacctgga ccaggacggt gacaagcagc
     1021 tctctgtgcc cgagttcatc tccctgcccg tgggcaccgt ggagaaccag cagggccagg
     1081 acattgacga caactgggtg aaagacagaa aaaaggagtt tgaggagctc attgactcca
     1141 accacgacgg catcgtgacc gccgaggagc tggagagcta catggacccc atgaacgagt
     1201 acaacgcgct gaacgaggcc aagcagatga tcgccgtcgc cgacgagaac cagaaccacc
     1261 acctggagcc cgaggaggtg ctcaagtaca gcgagttctt cacgggcagc aagctggtgg
     1321 actacgcgcg cagcgtgcac gaggagtttt gagcgcccgg ccgcgccccg cgccgccccc
     1381 cacgcaccac cggggcggcc tcgcgggtga ctccgggctc cgtggctgtc ccggacccca
     1441 cctcttccct gccgcccgcc accggccgac cgaccgcggc tgccccagtt gatgagcggc
     1501 gtgtcccctc tgcagcgcgc accccggcgg ggctttggct gtgacgcggt cggggcgcgg
     1561 ggctgggctg tggccccgcg gcgccgcctc ctccctggtc cctcgaaatc gtggcatctc
     1621 acttctgaga acgaaatctc gcttcagtca ctctgccgaa ggcgctgacg gcatcgcggc
     1681 cggaacctct gggcccggcc cctcccaggg ccgccgctcc gtgggaaaaa acagctcctc
     1741 catttccttg aaaactgaac gattattaaa aatagattaa acttcgctgg aaatgagtag
     1801 ccaggaagtt caggggaggg tgccgggtcc ttcccgggcc tggcgtgtcg gagccaccca
     1861 ggtcccgcag ctgccgctga gaaaatgcaa atatttgttg tgacaagaat cacatacatt
     1921 tactttaaat ata
//
