LOCUS       NM_001166701            3359 bp    mRNA    linear   PRI 25-FEB-2025
DEFINITION  Homo sapiens VCP nuclear cofactor family member 2 (VCF2),
            transcript variant 4, mRNA.
ACCESSION   NM_001166701
VERSION     NM_001166701.4
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 3359)
  AUTHORS   Korner,M., Meyer,S.R., Marincola,G., Kern,M.J., Grimm,C.,
            Schuelein-Voelk,C., Fischer,U., Hofmann,K. and Buchberger,A.
  TITLE     The FAM104 proteins VCF1/2 promote the nuclear localization of
            p97/VCP
  JOURNAL   Elife 12, e92409 (2023)
   PUBMED   37713320
  REMARK    GeneRIF: The FAM104 proteins VCF1/2 promote the nuclear
            localization of p97/VCP.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3359)
  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   3  (bases 1 to 3359)
  AUTHORS   Ross,M.T., Grafham,D.V., Coffey,A.J., Scherer,S., McLay,K.,
            Muzny,D., Platzer,M., Howell,G.R., Burrows,C., Bird,C.P.,
            Frankish,A., Lovell,F.L., Howe,K.L., Ashurst,J.L., Fulton,R.S.,
            Sudbrak,R., Wen,G., Jones,M.C., Hurles,M.E., Andrews,T.D.,
            Scott,C.E., Searle,S., Ramser,J., Whittaker,A., Deadman,R.,
            Carter,N.P., Hunt,S.E., Chen,R., Cree,A., Gunaratne,P., Havlak,P.,
            Hodgson,A., Metzker,M.L., Richards,S., Scott,G., Steffen,D.,
            Sodergren,E., Wheeler,D.A., Worley,K.C., Ainscough,R.,
            Ambrose,K.D., Ansari-Lari,M.A., Aradhya,S., Ashwell,R.I.,
            Babbage,A.K., Bagguley,C.L., Ballabio,A., Banerjee,R., Barker,G.E.,
            Barlow,K.F., Barrett,I.P., Bates,K.N., Beare,D.M., Beasley,H.,
            Beasley,O., Beck,A., Bethel,G., Blechschmidt,K., Brady,N.,
            Bray-Allen,S., Bridgeman,A.M., Brown,A.J., Brown,M.J., Bonnin,D.,
            Bruford,E.A., Buhay,C., Burch,P., Burford,D., Burgess,J.,
            Burrill,W., Burton,J., Bye,J.M., Carder,C., Carrel,L., Chako,J.,
            Chapman,J.C., Chavez,D., Chen,E., Chen,G., Chen,Y., Chen,Z.,
            Chinault,C., Ciccodicola,A., Clark,S.Y., Clarke,G., Clee,C.M.,
            Clegg,S., Clerc-Blankenburg,K., Clifford,K., Cobley,V., Cole,C.G.,
            Conquer,J.S., Corby,N., Connor,R.E., David,R., Davies,J., Davis,C.,
            Davis,J., Delgado,O., Deshazo,D., Dhami,P., Ding,Y., Dinh,H.,
            Dodsworth,S., Draper,H., Dugan-Rocha,S., Dunham,A., Dunn,M.,
            Durbin,K.J., Dutta,I., Eades,T., Ellwood,M., Emery-Cohen,A.,
            Errington,H., Evans,K.L., Faulkner,L., Francis,F., Frankland,J.,
            Fraser,A.E., Galgoczy,P., Gilbert,J., Gill,R., Glockner,G.,
            Gregory,S.G., Gribble,S., Griffiths,C., Grocock,R., Gu,Y.,
            Gwilliam,R., Hamilton,C., Hart,E.A., Hawes,A., Heath,P.D.,
            Heitmann,K., Hennig,S., Hernandez,J., Hinzmann,B., Ho,S., Hoffs,M.,
            Howden,P.J., Huckle,E.J., Hume,J., Hunt,P.J., Hunt,A.R.,
            Isherwood,J., Jacob,L., Johnson,D., Jones,S., de Jong,P.J.,
            Joseph,S.S., Keenan,S., Kelly,S., Kershaw,J.K., Khan,Z.,
            Kioschis,P., Klages,S., Knights,A.J., Kosiura,A., Kovar-Smith,C.,
            Laird,G.K., Langford,C., Lawlor,S., Leversha,M., Lewis,L., Liu,W.,
            Lloyd,C., Lloyd,D.M., Loulseged,H., Loveland,J.E., Lovell,J.D.,
            Lozado,R., Lu,J., Lyne,R., Ma,J., Maheshwari,M., Matthews,L.H.,
            McDowall,J., McLaren,S., McMurray,A., Meidl,P., Meitinger,T.,
            Milne,S., Miner,G., Mistry,S.L., Morgan,M., Morris,S., Muller,I.,
            Mullikin,J.C., Nguyen,N., Nordsiek,G., Nyakatura,G., O'Dell,C.N.,
            Okwuonu,G., Palmer,S., Pandian,R., Parker,D., Parrish,J.,
            Pasternak,S., Patel,D., Pearce,A.V., Pearson,D.M., Pelan,S.E.,
            Perez,L., Porter,K.M., Ramsey,Y., Reichwald,K., Rhodes,S.,
            Ridler,K.A., Schlessinger,D., Schueler,M.G., Sehra,H.K.,
            Shaw-Smith,C., Shen,H., Sheridan,E.M., Shownkeen,R., Skuce,C.D.,
            Smith,M.L., Sotheran,E.C., Steingruber,H.E., Steward,C.A.,
            Storey,R., Swann,R.M., Swarbreck,D., Tabor,P.E., Taudien,S.,
            Taylor,T., Teague,B., Thomas,K., Thorpe,A., Timms,K., Tracey,A.,
            Trevanion,S., Tromans,A.C., d'Urso,M., Verduzco,D., Villasana,D.,
            Waldron,L., Wall,M., Wang,Q., Warren,J., Warry,G.L., Wei,X.,
            West,A., Whitehead,S.L., Whiteley,M.N., Wilkinson,J.E.,
            Willey,D.L., Williams,G., Williams,L., Williamson,A.,
            Williamson,H., Wilming,L., Woodmansey,R.L., Wray,P.W., Yen,J.,
            Zhang,J., Zhou,J., Zoghbi,H., Zorilla,S., Buck,D., Reinhardt,R.,
            Poustka,A., Rosenthal,A., Lehrach,H., Meindl,A., Minx,P.J.,
            Hillier,L.W., Willard,H.F., Wilson,R.K., Waterston,R.H., Rice,C.M.,
            Vaudin,M., Coulson,A., Nelson,D.L., Weinstock,G., Sulston,J.E.,
            Durbin,R., Hubbard,T., Gibbs,R.A., Beck,S., Rogers,J. and
            Bentley,D.R.
  TITLE     The DNA sequence of the human X chromosome
  JOURNAL   Nature 434 (7031), 325-337 (2005)
   PUBMED   15772651
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL590240.5.
            
            On May 21, 2021 this sequence version replaced NM_001166701.3.
            
            Transcript Variant: This variant (4) differs in the 3' coding
            region and 3' UTR, compared to variant 1. The encoded isoform (4)
            has a distinct C-terminus and is the same length as isoform 1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR11853560.30055.1,
                                           SRR11853563.35214.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2158569, SAMEA2158800
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000685693.1/ ENSP00000509111.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-49                AL590240.5         112072-112120       c
            50-149              AL590240.5         110064-110163       c
            150-3359            AL590240.5         94037-97246         c
FEATURES             Location/Qualifiers
     source          1..3359
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xp11.21"
     gene            1..3359
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /note="VCP nuclear cofactor family member 2"
                     /db_xref="GeneID:90736"
                     /db_xref="HGNC:HGNC:25085"
                     /db_xref="MIM:301141"
     exon            1..49
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /inference="alignment:Splign:2.1.0"
     CDS             30..377
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /note="isoform 4 is encoded by transcript variant 4;
                     protein FAM104B; family with sequence similarity 104
                     member B; protein VCF2"
                     /codon_start=1
                     /product="protein VCF2 isoform 4"
                     /protein_id="NP_001160173.1"
                     /db_xref="CCDS:CCDS94615.1"
                     /db_xref="GeneID:90736"
                     /db_xref="HGNC:HGNC:25085"
                     /db_xref="MIM:301141"
                     /translation="MGGCPVRKRRRNGSKEGNHHSTQPKRNKRNPIFQDSQDTEFSWS
                     DNERSSSRINIPERASGPEGNLNQIVTEPDANFPQFLHEGYVPCQGLYSHINQTLKEA
                     HFNSLQQRGQAPT"
     exon            50..149
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /inference="alignment:Splign:2.1.0"
     exon            150..3359
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /inference="alignment:Splign:2.1.0"
     regulatory      415..420
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /note="hexamer: TATAAA"
     polyA_site      445
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
     regulatory      543..548
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /note="hexamer: AATAAA"
     polyA_site      563
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /note="major polyA site"
     regulatory      3333..3338
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /note="hexamer: AATAAA"
     polyA_site      3359
                     /gene="VCF2"
                     /gene_synonym="CXorf44; FAM104B"
                     /note="major polyA site"
ORIGIN      
        1 gcggttgcta tggttccgag ggcaggacta tgggaggctg ccctgtacgg aaaagaagaa
       61 gaaatggcag taaagagggc aaccatcatt ccacccagcc caaaaggaat aagagaaacc
      121 ctatctttca ggattctcaa gatacagagt tttcatggag tgataatgaa aggagcagca
      181 gccgcattaa tatcccagag agagcaagtg gaccagaagg caacttaaac cagattgtta
      241 ctgaacccga tgcaaacttt ccccagttct tgcatgaggg gtatgtacca tgccaaggtc
      301 tttactccca tatcaaccag accttgaagg aggctcactt caacagcctg cagcagcgag
      361 ggcaagctcc aacatgatga attaggactt ccttattcca acctaaactg tgtttataaa
      421 agcaattgca tacacaccaa aaaaagtcta ttggttttta agtctacatt ttaagtaaca
      481 agttaatggg cagttgttta attggggttt tacttcactg ttgtactttt aaaggggctg
      541 tgaataaatg tttatgaaat ttttattttt atttttattt tactctttct acatagagtt
      601 ttcaagttga gtgtcaattt catgttaagg tagcaatatg aggaaacttc tcctgtgcat
      661 tgaagccata tgtccaattc agattgattt ccagatctgt cagttagaaa ctctatgtta
      721 aacatctttt taaaatacaa gtaagtcttc atttttaaaa atacagtagc ctagtaaaga
      781 ggtatgtagc tttcatttaa aaaacaaaca aaaaatccac actcaaaaaa ccataagtta
      841 gtattcccaa atatgcaaag ccagattcag tcttgcactg aaatgaactg ccatactccc
      901 ctcagaaggt agatgttctg ttgaaattgc tctctagttg taatggcaac aatcagaccc
      961 agtttagact atgaacatga aaatctctct ctaataactg tctctacact ttgtatttcc
     1021 agggagaatg tttctaaggc tcttgtatac ttagatacct tctgtatcat ttatcctcta
     1081 gagtgtgcac ttcagactta gtaggaaaca ctgcacaatt ctgtcagata agaaatatgt
     1141 aatattttgt cttaaacaaa aatttattac gttagcacat tatgtgatct cataattcca
     1201 tctattatgt atagagttaa tgttaataca gtgtaagcta ctaaactgat gtttaaagta
     1261 acaagaatta tggaagtggg ttggacaact gtccacttta tgctacatag accctttccc
     1321 agagattagg gggctagctt ccattattaa aattgcaaag attcacatgg cttagaaaca
     1381 ataagctgag atgccattag aagaaacagg cagtactatt tatttagaga tgggggggtc
     1441 cccatgtttt agtcatacta aagagccaac caaatttgaa tggggaattc atagatgtgc
     1501 ttcctcagtg gtgagctgtg tgaacaaagg accaggatgc atcaggttat ctgccctgga
     1561 ctatgcaaag ggtacaacct gttgctagat ttaaacaaaa atgcgttaga gtctaacaat
     1621 cctctcctcc ctggtcacat tatcttttcc actatatttg gaggtccaca gagtgtaaac
     1681 tagcagatct gagaactatg gatagctcta caaagaggtg tttgccaatt ggcaaggttt
     1741 ggaaaagacg taaggttaca gttttactga aagaagaatg agattttatt aaatgacaga
     1801 attaacatat gaaaatgaac actatcttag gaaaagaata catacctaca cacacacaca
     1861 cacacacaca ttttcatggt tgtttccttg aatatgggta ggattttaag gaagatactt
     1921 gcagtagaat tttagtgtta tggggaaaaa attacagcac cacattggcc tcaaacttag
     1981 ggagtaggca tgagtcaatt atttcttaat tagatggttt gagtaagaac attttttcta
     2041 tggccagtgc ttccaaagtc aataccagat gtatggtgag aagaaattta aattctaaaa
     2101 ggttttatgg cagaaaatag agaaaggata cctagccacc agtttctcta acaataaagt
     2161 gagcaactaa gtactaaaga agatgagata tttgaatttt caacccacat gtacacaaca
     2221 ggattcagaa atacccagga agaattctgc atgcttaaat acatagcatc ctactgaaag
     2281 aaagtgtcta ttaaaaacac agtgtagttg aacagctgag aaagcaaatt tccattcatt
     2341 ccccctattt aaagatatca aagataaaac tgtcaccatg acaaagcatt attttttcaa
     2401 agtaaaataa taataataat aataaagcaa ttacatacac acagaaaaag tgttggcttt
     2461 tcagtctctg taagactttt cagtacttag ttgaactaag taagcacagt cttattccag
     2521 agtggtcagt gtaaatctct tgtcctagta aatacaatat gcaatctctg tcctgtcttt
     2581 tgcagattgt ctaaacctgt ttatgtcata aactggttta tgtcctttgg tcctgaaata
     2641 aaactcaata cttcacagca gggaaggaac caagctgttt aaaactactt atctccgcta
     2701 tgaaggagaa gtattttcaa ggaatatcag aagaaagtag aaagtgagag gaggttccag
     2761 ctgggcttcc tgggtcaagt aggggctcag aaagctgtga aactcactca tttcctgcat
     2821 gcggacttac tttggtcctg gatgaataat attgaagata tgtgcttaaa acattcctaa
     2881 catcagaatt tgcgcctgtg ttttcttccc caagaaagct ataaacagcg aaaattttgt
     2941 tgtaagcttc cctgtgtcct ctctccctct ctcccttccc cctcccctga aactaaaagg
     3001 aatgttaaaa gcccactttt ctgtgaccag cagaccttat ctatggtccc aattccaatt
     3061 ccttgtaaac acaatttgta aaatcccgtg agatcctgtc tcctttgcca tcccgctgca
     3121 aggttataag tagagaaaac ttaagttaca attccagttt tcctcaagat ctgagacatg
     3181 ttaattgtct ttgtttctcc ctctggtaac atcttcccac cacacatatt tcctgcctta
     3241 gagagtttaa aaggtgataa aaaaatctaa cactggctac cccgctcggg accccttcca
     3301 cgctgtgaaa gctttgtact gtcactctgc ttaataaagc ctacagcttt tttactctc
//
