LOCUS       NM_144693               7008 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens zinc finger protein 558 (ZNF558), transcript variant
            1, mRNA.
ACCESSION   NM_144693 XM_005259755
VERSION     NM_144693.3
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 7008)
  AUTHORS   Johansson,P.A., Brattas,P.L., Douse,C.H., Hsieh,P., Adami,A.,
            Pontis,J., Grassi,D., Garza,R., Sozzi,E., Cataldo,R., Jonsson,M.E.,
            Atacho,D.A.M., Pircs,K., Eren,F., Sharma,Y., Johansson,J.,
            Fiorenzano,A., Parmar,M., Fex,M., Trono,D., Eichler,E.E. and
            Jakobsson,J.
  TITLE     A cis-acting structural variation at the ZNF558 locus controls a
            gene regulatory network in human brain development
  JOURNAL   Cell Stem Cell 29 (1), 52-69 (2022)
   PUBMED   34624206
  REMARK    GeneRIF: A cis-acting structural variation at the ZNF558 locus
            controls a gene regulatory network in human brain development.
REFERENCE   2  (bases 1 to 7008)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   3  (bases 1 to 7008)
  AUTHORS   Lehner,B. and Sanderson,C.M.
  TITLE     A protein interaction framework for human mRNA degradation
  JOURNAL   Genome Res 14 (7), 1315-1323 (2004)
   PUBMED   15231747
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DB478966.1, AK291265.1, AC008734.7, AK307200.1, BC064356.1,
            AC012616.7 and DB547630.1.
            
            On Nov 23, 2018 this sequence version replaced NM_144693.2.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660809.127177.1,
                                           SRR1803616.18420.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000601372.6/ ENSP00000471277.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-45                DB478966.1         1-45
            46-128              AK291265.1         1-83
            129-129             AC008734.7         43957-43957         c
            130-473             AK291265.1         85-428
            474-549             AK307200.1         469-544
            550-552             AC008734.7         36741-36743         c
            553-1596            AK291265.1         508-1551
            1597-2820           BC064356.1         975-2198
            2821-2821           AC012616.7         5147-5147
            2822-3474           BC064356.1         2200-2852
            3475-3602           DB547630.1         314-441
            3603-7008           AC012616.7         5929-9334
FEATURES             Location/Qualifiers
     source          1..7008
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="19"
                     /map="19p13.2"
     gene            1..7008
                     /gene="ZNF558"
                     /note="zinc finger protein 558"
                     /db_xref="GeneID:148156"
                     /db_xref="HGNC:HGNC:26422"
     exon            1..96
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     exon            97..180
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     exon            181..287
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     exon            288..623
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     exon            624..719
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     CDS             689..1897
                     /gene="ZNF558"
                     /note="isoform 1 is encoded by transcript variant 1"
                     /codon_start=1
                     /product="zinc finger protein 558 isoform 1"
                     /protein_id="NP_653294.1"
                     /db_xref="CCDS:CCDS12208.1"
                     /db_xref="GeneID:148156"
                     /db_xref="HGNC:HGNC:26422"
                     /translation="MAAVILPSTAAPSSLFPASQQKGHTQGGELVNELLTSWLRGLVT
                     FEDVAVEFTQEEWALLDPAQRTLYRDVMLENCRNLASLGCRVNKPSLISQLEQDKKVV
                     TEERGILPSTCPDLETLLKAKWLTPKKNVFRKEQSKGVKTERSHRGVKLNECNQCFKV
                     FSTKSNLTQHKRIHTGEKPYDCSQCGKSFSSRSYLTIHKRIHNGEKPYECNHCGKAFS
                     DPSSLRLHLRIHTGEKPYECNQCFHVFRTSCNLKSHKRIHTGENHHECNQCGKAFSTR
                     SSLTGHNSIHTGEKPYECHDCGKTFRKSSYLTQHVRTHTGEKPYECNECGKSFSSSFS
                     LTVHKRIHTGEKPYECSDCGKAFNNLSAVKKHLRTHTGEKPYECNHCGKSFTSNSYLS
                     VHKRIHNRWI"
     exon            720..808
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     exon            809..935
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     exon            936..1031
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     exon            1032..1114
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     exon            1115..7008
                     /gene="ZNF558"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3445..3450
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ZNF558"
                     /note="hexamer: AATAAA"
     polyA_site      3474
                     /gene="ZNF558"
                     /note="major polyA site"
     regulatory      4831..4836
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ZNF558"
                     /note="hexamer: AATAAA"
     polyA_site      4848
                     /gene="ZNF558"
     regulatory      6988..6993
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ZNF558"
                     /note="hexamer: AATAAA"
     polyA_site      7008
                     /gene="ZNF558"
ORIGIN      
        1 ggtaccgtgg gaggggccgc gcgtggggca gcggggagcg agtccctccg tccccgcgag
       61 tcggcgcttt tggccccgcg ggaggggccg ggctcgatga gaaaagcatc attcaagctc
      121 agattcgtgt tgaagcctgc cacaaggtcc acctgttgtt gtgggttttt gggtgaccag
      181 gggttacccc cagcagtgtg tgagaatgaa gagtgtgggc cactgtgtct ctgttgacct
      241 gccagatagg aaatagcgcc agagttgctg caatccacgt ctccctggaa ttcaggagca
      301 gcttggctgg aaggctctgg ctggaaactt gcagaaggct gtcagctggg tctgcatcat
      361 ctgaaggctc aacgggtacc gggggccact ccatggcctg cgagtcagag ctggccgtcg
      421 gtgggaggcc tcagttcctc tccacatagg cctctccaca gggccacttg agcgtcttcc
      481 caccatggca actggtgtcc tctagagcaa catccaggag accaaggcgg aagcagctgt
      541 agtgccttcc aagacctggt cctgaaagtc acccctgcac ccacccccgc tgtctcctca
      601 gccatattct gctggtcaca cagagcgctg cgggataaag gaggagcgtc ctgcttcccg
      661 gctgccctgt tgctgtcgga gtcacaggat ggcggctgtc atcctgccct cgactgctgc
      721 tccgtcttcc ctgttcccag cctctcagca aaaaggacac acacagggcg gagagctggt
      781 taatgagctc ctgacaagct ggctacgggg cttggtaacc ttcgaggatg tggccgtgga
      841 gttcacccag gaggagtggg cgttgctgga ccctgcccaa aggacactgt acagggatgt
      901 gatgctggag aactgcagga acctggcctc actagggtgt cgtgttaata aacccagtct
      961 gatatcccag ttggaacaag acaagaaggt ggtgacagag gaaagaggaa ttctaccaag
     1021 cacctgtcca gatttggaga ctctacttaa agccaaatgg ttaactccta agaagaatgt
     1081 tttcagaaaa gaacagtcta aaggtgtaaa aacggaaaga agtcatcgtg gagtgaaact
     1141 caatgaatgt aatcagtgtt ttaaagtctt cagcacgaaa tctaacctaa ctcagcacaa
     1201 gagaattcat actggagaaa aaccctatga ctgtagtcaa tgtgggaagt ccttcagtag
     1261 cagatcttac cttactattc ataagagaat ccataatggg gagaaaccct atgaatgcaa
     1321 tcactgtggg aaagcattta gtgatccctc atcccttaga ctgcatttga gaattcacac
     1381 tggagaaaaa ccctatgaat gtaaccagtg ttttcacgtt ttccgcacca gttgtaacct
     1441 caaaagccac aagaggattc acacggggga gaatcaccat gaatgtaatc agtgtggaaa
     1501 agctttcagc acaaggtcct ctctcactgg gcacaatagc attcatacag gggagaaacc
     1561 ttatgaatgt cacgattgtg ggaaaacctt caggaagagc tcctatctga cacagcacgt
     1621 aagaactcat actggagaaa aaccctatga atgtaacgag tgtgggaaat ccttcagcag
     1681 tagcttttct cttactgtgc acaagagaat acataccgga gagaaaccct acgagtgcag
     1741 tgactgtgga aaagccttta ataatctctc agctgtgaag aaacacttaa gaactcacac
     1801 tggagaaaaa ccctatgaat gtaatcattg tgggaaatcc ttcacaagta actcctatct
     1861 ttctgtgcac aagagaatac ataatagatg gatatgaatt actgcaggaa cttctggagg
     1921 aaagcactca ttgatctttc atccctaaga tagtttgaga gagctcacac tggatatata
     1981 agttatttgt tgcagcataa caaatgatcc ccgcaaattt tgtggcttca aacacgaaat
     2041 gtttattctc taacaatttc tacagatcag gaattcaaga acagcttatc tctgtagtta
     2101 cactgcagga tctctcatgc ctttacttac aatcaagatg tcagccaaag ctatagtcat
     2161 ctaacatctt tactgatgaa cagtccactt ccaagatgac ttattcacat gcctggaaag
     2221 ttgatgttgg ttgttgtcag gggaccttca gtcattacca tgtaggcctc tttacaaggc
     2281 ccagctcctt gacaatttgg caataagttc tcgccaaggt tagtgatcca agagaggacc
     2341 aatacagagg ccaaaatggc ttttatgacc tatcctcagg aggactgcta agctttcact
     2401 tatttcctat tgtgttggtc tcacaacaca ccaatcctga tacaatgtga gagactgcag
     2461 aaggtatgaa taccaggaaa cagataactc agaagcatct gggaaatttg ccatggaatt
     2521 aatgaagaaa agccctcagc acatcatcct tctactctaa tcaatatgaa atagcattca
     2581 gtaactccta ttaattcact ctgaagagaa accttttgag gacaatctgt atggtaaagc
     2641 tctcagctcg aattctcacc ttcatgggcc cagaagatta tgtactgaga gaatcctgaa
     2701 gaatggaaca gctgtagaaa gccttcagtg ctatcagcag ggattcatgt gacagctcac
     2761 actaagggag aaaacctgtg aaggtctcag aaggcttcag tgacagtcat cccttaagac
     2821 gcactggaaa tcacacaatg gaacaacact cagaaatgcg gaatacccta cagcaaaagt
     2881 gttcacatta ctgagcaaac tatagtgtgg tattctgcag tgactatggg aaagccttga
     2941 atgttctatc ggtttttaag ggacttgaga attaattctg gagagaatgc cccattgaac
     3001 atcatcaata ttggagagct ttctgttttt ctacatttgt taggaaactt gtgagcattc
     3061 acactacaga gaaacttgaa atataaagaa gaagagaaag ccttcagtga tgcctctgtg
     3121 ttagggaaaa tatggaactt ctccctggat gcaaaaccta tgagtatatt aatattggaa
     3181 aatttttcag tgattcttct ctttcttgta tatgagagaa cttatatgga gaaaccccta
     3241 ggaatgtaat cagtgttagg atgcctcagc ctgaactctt cactgagtgg ccacaatttt
     3301 cactgggaac aaaaagtata atcactgttt tgagtgtggg atatccttta tcagtgtctc
     3361 atctgtagat tggactgctg gctcattaat ttttttagtc tttttttctt ttaatataaa
     3421 catttgtgta tagctgttcc ctaaaataaa cattaacata tttcataatt ttaatgcaat
     3481 gtatttatta taattaattt gcttgttaaa gacatccaca cattgcatat tcaaaaagtt
     3541 atttccaaat accttctgag tgattcagtt tatcataatg gaaattagta tttataaaca
     3601 catttttcta atgtagtggt atttttggca gagtacatga gctttatgat actgattatt
     3661 ttctctctat cttggtatgc caaatactgt tggtttcttt cccagtgtcc gttctcttca
     3721 gtttattcgt ttaaagaaac aaacatgttg ttcaagttgt ctgtgaacaa tatcgaaagt
     3781 tctcaatctt atagtttttc ctgaagccca ggcgggtttt ttcgcactcc cctggcaatg
     3841 agaagtaagt cgaagtcact gtgtggaaca tctcctggct tgttctcctc acatattttc
     3901 cattcacctc acccattctg tctcttggaa agtggcctca aggtctagag tttgaagagc
     3961 ttctttttga ccacaatgac agaaaccaaa gtgcagccaa aaatcacaat gctttgggct
     4021 ctccaggagc ctccgattgg ctgcatctgc tctggactcc ttattcttat acttcttatg
     4081 tgactaaaag aaacccctag gctgggtgtg gtggctcacg cctttaatcc cagcactttt
     4141 gagaggctga ggtgggtgga tcatgaggtc aacagattga gaccatcctg gccaacgtgg
     4201 tgaaacccta tctctactaa aagtataaag attagctggg tgtggtggtg cacacctgta
     4261 ttcccagcta ctcgggaaac tgagacagga gaattgcctg aacctgggag gtagaggttg
     4321 cagtgagcca agatggcgcc agtgcactcc agcctggcaa cagagcgaga ctccatctca
     4381 aaataaacaa ataaatattt ttaaaaaaag aaacccctaa ctgattgaag ccaacatgat
     4441 ctgttgtttg tttttgaggt ggtgttctgt taacttccag caggatgcag aatctaactg
     4501 gtaaacctat aaattggtca agttttaccc atgttgtttc tttgaaaaca atgtatattc
     4561 tctaatattt ggatataggg tatatgaaca ttaatgcaac ttaattgtat ttccaagtac
     4621 agtacgtatg ttcagatttc tttttctaac cttatttagt gatagaggtg tggtaaactc
     4681 ttccattatg tttatgtatt aacactgtaa ttttgtcatt tttatatatt ttgacattat
     4741 gtaactagat gcatacagga ttaggtattc tgtattcctt tttatgtgga gatgatattt
     4801 ttacatagca aagtattgta atgcattaat aataaatggt caaacattta tttatttatt
     4861 tatttatttt agatggagtt tcactcttgt catcaagggt ggagtgcaat ggtgcgatct
     4921 cggctcactg caaccttggc ctcccaggtt ccagcaattc tcctgcctca gcctcctgag
     4981 tagctgggat tacaggcacc tgccaccacg cccaggtaat ttttttatat ttttagtaga
     5041 gatggggttt caccatgttg gccaggctag tctcgaactc ctgatggtca gacatttata
     5101 ttgcacttcc catagatcag gcccccttct aaatgacata taagtattaa ctcagtatgc
     5161 attataaact taagtatgta atgttattat ccccagttta cagatgagaa aactggtatg
     5221 atacacttaa gttacttgcc tgcattcact gactggtaaa tggtagagcc aagatctgaa
     5281 cccagacagt ccatgcactt aaccactacc ctattaacgg agtatgttct gtgtgccagg
     5341 caaagttttg ccattgaaat acttcaccta atggaggagg aacagattat agaaaaatca
     5401 agaaaatatg gtattataga gttataggaa aaaaaagcat tttaggagag ttaagggggg
     5461 ttgggaataa taattttata taactaggaa aagaaagcct cttggtaagg agcatttgag
     5521 cggagatctc aacaagttgg gacagtgagt catatgaatt tgtcttgcaa gagtagtgtt
     5581 ggcatgcaaa ggcccacaac aaggaggcca atacagctgg agtggaacaa aggggtgatg
     5641 agggagcagt aaaagatgat gtggtcagag acatggtaga tcctgatctt gttgggtttt
     5701 ctgagacatt gttaggactt ttccttattt cagtgagttg gcacatcagt cagggtccca
     5761 gcaggaactc aggttgacac ccacagacta ggacaattca agtagagttt tcataaaggg
     5821 tctactcagt cctgtggaca ggatccaggg aaaccacaaa aagttgtaaa gcacccagca
     5881 gcttagcagg gcagagctct aacacctcac agcctgaagg gacgaaggga gggagcaact
     5941 gaatctggag acgagaggag agggctgcat tccaggagct gagagaggtc agtcagcgat
     6001 agcatccagc cccaggtcct cctgcaggaa atagccaggg tcagacctca ctctccttca
     6061 tccattgaga caggaaaata tccccattta tgaatatata aatcaatagc agatccagag
     6121 acaatttggg tattggagtt agcagacaaa gactttaaaa taaccaagaa taatatgtta
     6181 agggaaatgg aggaaacatg gacaaaccat agaaaatgag agacaaactg caaatctacc
     6241 aaacaaccaa agaagaagga cacattgctt tcaaagcagc atcagtaaga ctaatgatga
     6301 cttttcaaaa gaaactatgg aagcaagaag acaatgaatg acatctgaca tataaagggt
     6361 taaatgggtt ggaggagggg gaaattgtca atcaaaagtt ctgtaaccta agaaaatatt
     6421 cttcaaaact gaaggcaaca atgttttcca atgggaggga atattttttt tttttttttt
     6481 gagatggagt ctcactctgt cgccatgctg gagtgcagtg gcatgatctc ggctcactgc
     6541 aacctcctcc tcctgggttc aagtgattct cctgcctcag cctcctgagt agctgggact
     6601 acaggtgtgt gctaccacgc ccagctaatt tttgtatttt tagtggagac agggtttcac
     6661 catgttggcc aggatggtct cgatcctttg acctcacatg atttgcccac ctcggtctcc
     6721 caaagtgctg ggattacagg cgtgagccac cacgcccggc ctgggaggga tttttttaag
     6781 ctgagagaat taacagcata accgtatttt cagaaacact gaagagattt cttcaggctt
     6841 caggaaaatg attccataga gacatacata attccaggaa ttaagatcaa caggaaacat
     6901 aagatgcaag taaatataaa tcagtactga ctgtataaaa caaccctgta tagttttaca
     6961 acttttatgt atatctaaac tttccaaaat aaaatgcttt taaaaaca
//
