LOCUS       NM_001367314            6446 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens BEN domain containing 3 (BEND3), transcript variant 2,
            mRNA.
ACCESSION   NM_001367314 XM_005267079
VERSION     NM_001367314.1
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 6446)
  AUTHORS   Kurniawan,F., Chetlangia,N., Kamran,M., Redon,C.E., Pongor,L.,
            Sun,Q., Lin,Y.C., Mohan,V., Shaqildi,O., Asoudegi,D., Hao,Q.,
            Khan,A., Aladjem,M.I., Prasanth,K.V. and Prasanth,S.G.
  TITLE     BEND3 safeguards pluripotency by repressing
            differentiation-associated genes
  JOURNAL   Proc Natl Acad Sci U S A 119 (9) (2022)
   PUBMED   35217604
  REMARK    GeneRIF: BEND3 safeguards pluripotency by repressing
            differentiation-associated genes.
REFERENCE   2  (bases 1 to 6446)
  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 6446)
  AUTHORS   Pitchai,G.P., Kaulich,M., Bizard,A.H., Mesa,P., Yao,Q., Sarlos,K.,
            Streicher,W.W., Nigg,E.A., Montoya,G. and Hickson,I.D.
  TITLE     A novel TPR-BEN domain interaction mediates PICH-BEND3 association
  JOURNAL   Nucleic Acids Res 45 (19), 11413-11424 (2017)
   PUBMED   28977671
  REMARK    GeneRIF: Data indicate BEND3 as a new interaction partner for PICH
            in mitosis, and have defined the residues within a TPR-BEN domain
            interface that mediate this interaction.
REFERENCE   4  (bases 1 to 6446)
  AUTHORS   Pitchai,G.P., Hickson,I.D., Streicher,W., Montoya,G. and Mesa,P.
  TITLE     Characterization of the NTPR and BD1 interacting domains of the
            human PICH-BEND3 complex
  JOURNAL   Acta Crystallogr F Struct Biol Commun 72 (Pt 8), 646-651 (2016)
   PUBMED   27487930
  REMARK    GeneRIF: Characterization of the NTPR and BD1 interacting domains
            of the human PICH-BEND3 complex has been reported.
REFERENCE   5  (bases 1 to 6446)
  AUTHORS   Aghajanirefah,A., Nguyen,L.N. and Ohadi,M.
  TITLE     BEND3 is involved in the human-specific repression of calreticulin:
            Implication for the evolution of higher brain functions in human
  JOURNAL   Gene 576 (1 Pt 3), 577-580 (2016)
   PUBMED   26481236
  REMARK    GeneRIF: propose that there is a link between binding of BEND3 to
            the CALR rs138452745 C-allele and removal of NFI binding site from
            this nucleotide, and the evolution of human-specific higher brain
            functions
REFERENCE   6  (bases 1 to 6446)
  AUTHORS   Khan,A., Giri,S., Wang,Y., Chakraborty,A., Ghosh,A.K.,
            Anantharaman,A., Aggarwal,V., Sathyan,K.M., Ha,T., Prasanth,K.V.
            and Prasanth,S.G.
  TITLE     BEND3 represses rDNA transcription by stabilizing a NoRC component
            via USP21 deubiquitinase
  JOURNAL   Proc Natl Acad Sci U S A 112 (27), 8338-8343 (2015)
   PUBMED   26100909
  REMARK    GeneRIF: Data show that SUMOylated BANP, E5R, and Nac1 (BEN) domain
            3 (BEND3) stabilizes NoRC component TTF-1-interacting protein 5
            (Tip5)via association with ubiquitin specific protease 21 (USP21)
            debiquitinase.
REFERENCE   7  (bases 1 to 6446)
  AUTHORS   Shiheido,H. and Shimizu,J.
  TITLE     Basic amino acid residues located in the N-terminal region of BEND3
            are essential for its nuclear localization
  JOURNAL   Biochem Biophys Res Commun 457 (4), 589-594 (2015)
   PUBMED   25600804
  REMARK    GeneRIF: Three basic amino acid residues located in the N-terminal
            region of BEND3 (BEND356-58, KRK) are essential for its nuclear
            localization, suggesting that these residues play a role as a
            functional nuclear localization signals.
REFERENCE   8  (bases 1 to 6446)
  AUTHORS   Khan,A. and Prasanth,S.G.
  TITLE     BEND3 mediates transcriptional repression and heterochromatin
            organization
  JOURNAL   Transcription 6 (5), 102-105 (2015)
   PUBMED   26507581
  REMARK    GeneRIF: Data shows that BEND3 associates with chromatin remodeling
            complexes to modulate gene expression and heterochromatin
            organization.
REFERENCE   9  (bases 1 to 6446)
  AUTHORS   Sathyan,K.M., Shen,Z., Tripathi,V., Prasanth,K.V. and Prasanth,S.G.
  TITLE     A BEN-domain-containing protein associates with heterochromatin and
            represses transcription
  JOURNAL   J Cell Sci 124 (Pt 18), 3149-3163 (2011)
   PUBMED   21914818
  REMARK    GeneRIF: associates with heterochromatin and represses
            transcription
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL355586.27.
            
            On Nov 21, 2018 this sequence version replaced XM_005267079.4.
            
            Transcript Variant: This variant (2) differs in the 5' UTR compared
            to variant 1. Variants 1 and 2 both encode the same protein.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR18074967.1952970.1,
                                           SRR14038194.3071566.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN03465403 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000369042.6/ ENSP00000358038.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-426               AL355586.27        124030-124455       c
            427-474             AL355586.27        108189-108236       c
            475-677             AL355586.27        107491-107693       c
            678-6446            AL355586.27        74122-79890         c
FEATURES             Location/Qualifiers
     source          1..6446
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6q21"
     gene            1..6446
                     /gene="BEND3"
                     /gene_synonym="KIAA1553"
                     /note="BEN domain containing 3"
                     /db_xref="GeneID:57673"
                     /db_xref="HGNC:HGNC:23040"
                     /db_xref="MIM:616374"
     exon            1..426
                     /gene="BEND3"
                     /gene_synonym="KIAA1553"
                     /inference="alignment:Splign:2.1.0"
     exon            427..474
                     /gene="BEND3"
                     /gene_synonym="KIAA1553"
                     /inference="alignment:Splign:2.1.0"
     CDS             438..2924
                     /gene="BEND3"
                     /gene_synonym="KIAA1553"
                     /note="BANP, E5R, and Nac1 (BEN) domain 3"
                     /codon_start=1
                     /product="BEN domain-containing protein 3"
                     /protein_id="NP_001354243.1"
                     /db_xref="CCDS:CCDS34507.1"
                     /db_xref="GeneID:57673"
                     /db_xref="HGNC:HGNC:23040"
                     /db_xref="MIM:616374"
                     /translation="MNSTEFTEDVEEVLKSITVKVETEAEDAALDCSVNSRTSEKHSV
                     DSVLTALQDSSKRKQLVSDGLLDSVPGVKRRRLIPEALLAGMRNRENSSPCQGNGEQA
                     GRGRSLGNVWPGEEEPCNDATTPSYKKPLYGISHKIMEKKNPPSGDLLNVYELFEKAN
                     ASNSPSSLRLLNEPQKRDCGSTGAGTDNDPNIYFLIQKMFYMLNTLTSNMSQLHSKVD
                     LLSLEVSRIKKQVSPTEMVAKFQPPPEYQLTAAELKQIVDQSLSGGDLACRLLVQLFP
                     ELFSDVDFSRGCSACGFAAKRKLESLHLQLIRNYVEVYYPSVKDTAVWQAECLPQLND
                     FFSRFWAQREMEDSQPSGQVASFFEAEQVDPGHFLDNKDQEEALSLDRSSTIASDHVV
                     DTQDLTEFLDEASSPGEFAVFLLHRLFPELFDHRKLGEQYSCYGDGGKQELDPQRLQI
                     IRNYTEIYFPDMQEEEAWLQQCAQRINDELEGLGLDAGSEGDPPRDDCYDSSSLPDDI
                     SVVKVEDSFEGERPGRRSKKIWLVPIDFDKLEIPQPDFEVPGADCLLSKEQLRSIYES
                     SLSIGNFASRLLVHLFPELFTHENLRKQYNCSGSLGKKQLDPSRIKLIRHYVQLLYPR
                     AKNDRVWTLEFVGKLDERCRRRDTEQRRSYQQQRKVHVPGPECRDLTSYAINPERFRE
                     EFEGPPLPPERSSKDFCKIPLDELVVPSPDFPVPSPYLLSDKEVREIVQQSLSVGNFA
                     ARLLVRLFPELFTAENLRLQYNHSGACNKKQLDPTRLRLIRHYVEAVYPVEKMEEVWH
                     YECIPSIDERCRRPNRKKCDILKKAKKVEK"
     exon            475..677
                     /gene="BEND3"
                     /gene_synonym="KIAA1553"
                     /inference="alignment:Splign:2.1.0"
     exon            678..6446
                     /gene="BEND3"
                     /gene_synonym="KIAA1553"
                     /inference="alignment:Splign:2.1.0"
     regulatory      6431..6436
                     /regulatory_class="polyA_signal_sequence"
                     /gene="BEND3"
                     /gene_synonym="KIAA1553"
                     /note="hexamer: TATAAA"
     polyA_site      6446
                     /gene="BEND3"
                     /gene_synonym="KIAA1553"
                     /note="major polyA site"
ORIGIN      
        1 actgcgctgg ccgagcgcgc cgggccgcct gggtcccggg agtgcgcgcc cgagctcccc
       61 gccgcggccg ttcacgcccg agcgccgccg ccgccggtcc cgcgtgtgcc ccgctgaggg
      121 ggaggggcgg gccgggggtg ggggcggagg ggttgtggtt ccactgcagc gggggctcct
      181 gtgtccttgt gcggaaatga cacacggagt cccgtcacgt cacgcgagag cgcagcgcac
      241 ggacacacac aaagagaggg gaaaatacac ggcgctcgcc cgcccgccgc ccccagcgcc
      301 tccccgggcc gccctggcca ggccctccgc gcgcggcccc cactccccgg ccccgcgccc
      361 tcccccccac gtggcgccca aactcggcgc gggcccgccc ggcaaagtac agaactcgcg
      421 tcccagcgga atagaagatg aactcaactg aattcaccga agatgtagaa gaagttctaa
      481 aaagtatcac tgtgaaagtg gagacagagg ctgaagatgc tgctctggac tgctccgtga
      541 attccaggac ttctgagaag cactctgtgg acagcgtcct cactgccctg caggactcca
      601 gcaaacgaaa gcagctggtc agcgatggcc tgctagactc tgtccccggc gtgaagagga
      661 ggcggctgat ccccgaggct ctcctagcag gcatgcggaa ccgtgagaac agctcgccct
      721 gccaaggcaa tggtgagcag gccggcaggg gcaggagcct gggcaatgtg tggcctggag
      781 aggaggagcc ctgcaacgat gccaccaccc cttcctacaa gaagcctctg tatggcatct
      841 cgcacaagat catggagaag aagaatcctc cctcggggga cctgctaaac gtgtacgagc
      901 tctttgagaa ggcaaacgcc agcaacagcc cctcgtcact gcggctcctg aatgagccac
      961 agaagcggga ctgtggcagc accggggcag gcactgacaa cgaccccaac atctacttcc
     1021 tgatccagaa gatgttctac atgctgaaca ccctcacgtc caacatgtcc cagctgcaca
     1081 gcaaggtgga cctgctctcc cttgaggtga gccgcatcaa gaagcaggtg agccccactg
     1141 agatggtggc caaattccag ccgccccctg agtaccagct cacagccgca gagctcaagc
     1201 agatcgtgga ccagagcctg tcaggggggg acctggcctg ccgcttgctg gtgcagctct
     1261 tccccgagct cttcagcgac gtggacttct cccggggctg cagtgcctgt ggctttgcgg
     1321 ccaagcgcaa gctggagtcg ctgcacctgc agctcatccg caactatgtg gaggtctact
     1381 acccctcggt gaaggacacg gctgtgtggc aggccgagtg cctgccccag ctgaacgact
     1441 tcttcagccg cttctgggcc cagcgggaaa tggaggacag ccagcccagc ggccaggtcg
     1501 ccagcttctt tgaggcagag caggtggacc ccggccactt cctggacaac aaagaccagg
     1561 aggaggccct gtctcttgac cggagcagca ccatcgcctc agaccacgtg gtggacacgc
     1621 aggacctcac tgagttcctg gacgaagcct cctcaccagg cgagtttgcc gtcttcctcc
     1681 tccaccggct cttccccgag ctcttcgacc accgcaagct gggtgaacag tacagctgct
     1741 acggggacgg tggaaagcag gagctggacc cgcagcggct gcagatcatc cgcaactaca
     1801 cggagatcta cttccctgac atgcaggagg aggaggcctg gctgcagcag tgtgcccagc
     1861 gcatcaacga cgagctcgag ggcctggggc tggacgcggg cagtgaaggc gaccccccgc
     1921 gtgatgactg ctacgactcc tccagtctgc ccgacgacat ctcagtggtc aaggtggagg
     1981 acagcttcga gggcgagcgg ccgggtcgcc gctccaagaa gatctggctg gtgcccatcg
     2041 acttcgacaa gttagagatc ccccagcctg acttcgaggt gcccggtgcc gactgcctgc
     2101 tcagcaagga gcagctacgc agcatctacg agagcagcct gtccatcggc aacttcgcct
     2161 cgcgcctgct ggtgcacctg ttccccgagc tcttcacgca cgagaacctg cgcaagcagt
     2221 acaactgcag cggctccctg ggcaagaagc agctggaccc ctcccgcatc aagctcatcc
     2281 gccactacgt gcagctgctc tacccacgcg ccaaaaacga ccgcgtctgg accctggagt
     2341 tcgtgggcaa actggatgag cgctgccggc gccgggacac ggagcaaagg cgctcctacc
     2401 agcagcagcg caaggtccac gtgccgggcc ctgagtgcag agacttgacc agctatgcaa
     2461 tcaaccccga gaggttccgg gaggagtttg aggggccccc actgcccccc gagaggagca
     2521 gcaaggactt ttgcaagatc cccttggacg agctggtggt cccctcgcct gacttcccgg
     2581 tgccttctcc ctacctgctg tctgacaagg aggtgcgtga gatcgtgcag cagagcctct
     2641 ccgtgggcaa ctttgccgcc cggctcctcg tccgcctgtt tcccgaactc ttcaccgccg
     2701 agaacctccg gctgcagtac aaccattccg gggcttgcaa caagaagcaa ctggacccca
     2761 cgcggctgcg gctcatccgc cactacgtgg aagccgtcta cccggtggag aagatggagg
     2821 aggtgtggca ctacgaatgt atccccagca tcgatgagag gtgccgccgc cccaacagga
     2881 aaaaatgcga catcctcaag aaagcaaaga aagtggagaa gtgaaggccc gtgacctgcc
     2941 cagagattcg gggtcaccag aggctgagcg atgggcaccc ttgggactga gcaatacttg
     3001 ggagcacgcc tatggcatcc acagacaggc accttatgtc cgtggggagt ggcttactac
     3061 atttgcacac gtaaacaccc acccaaccgc aagaaagaag ccttgagttt ggtctcttgt
     3121 acttacaact tctgtcctat gtgccccggc ggggcagcct gagtgtgggg agagcaagct
     3181 gtgagggcag ggaccagagg ttaggggtcc tctctccctg gttgtgccct ccccagcccc
     3241 tcacagctta taatgcaaac ccagcaactc tcttgcccct cttcccatat tttacatctt
     3301 ccattttgac ccattttttt ttaattaaaa agaaaccctt aaaaaaaatc attgggctct
     3361 ttgggggcca ttttacttag aaaaaaatct ctttaaaagt gccatgttcg tgcacagtgg
     3421 ctaatcatag cttcaggtgg catggatact gattttactg accttgtttt ttacatctga
     3481 ttttggaaga gtcaagatgc cccttggatg gcagtagagg ggatggaata gtgcgaagtc
     3541 ctttacgacc acatgcaagt tttcccttct gctctggtgc cagggaaggc ttccgttcag
     3601 cttggcctgt ccttcaggcg cgttggtaga atgttgtgtc actctttagg cgagaacact
     3661 ggatgatgat gatatgaatg tagacagccg tggaaacacg ttcgcagtgt ctccatctga
     3721 gccgtgtcct tccgctgccc ccattccttc tccatacatg gttgctggtt ggagggagtg
     3781 gacatgtttc cttggaaaac agtgcagggg cttttggctt cttgttagat ttaagggtgg
     3841 gcctctttga gctcaccatg aactgtttac ttttccgtgt gtgtatttgt acaaaatcca
     3901 ggttccggga gctttgtggt gacttcccca gacctcagtg ttagctactc caggcagtac
     3961 tacatcctca ttcctcaggg cgggcccagg tctgggcccc tcttggggat accatgcatt
     4021 ggaaggacac aggccatttt agatggggta cacatgtccc ttcccagggt ccactcagaa
     4081 ctttcctctt ggactctcta gaaggtcctg ctgtcctata cctggccacc ccctgccttg
     4141 gggggcacat gtcttcgttc cctcccgact gggaatgtca ggctcctgca ggccagctgc
     4201 atgctctcca ggagcaccaa ctgggaaatc ccctgacagg taaagtcctt taaaatgata
     4261 cttttaccta cctaactctg ggggccaaat gcttaagagg gaaaggaaac agtcgaatgc
     4321 aaacagtgtg tcataccaga gtcctggaaa atttattgaa tcacacaggg tagtcataga
     4381 acccctgtgg gatggcttaa tattttgcta ctttaaaatg cagagataac agaaacaatc
     4441 tggattttct tcattcagct gataagaact tcagttccag tggctgtatg acataatttt
     4501 gcctgtaccc aggagcattt tttaaaatac aggattttaa aagcaatgtt aagttgctga
     4561 tctaactagt aaatttgctc ctaagtgtca tttacagatt atttctgttg aaactgcaaa
     4621 cagatttaga aaggcacagg gactgaatga ctctctgtct tacacagcta ctcatgcaca
     4681 cacgcactgc ttactaaaag ctgaagtgag atgaaggggg cctacacgaa taacaagttc
     4741 aacttctttg tgcctggaaa ggagggactg gagcagccag gagactcact ttcccccctc
     4801 gcttgggccc ttctctatgc cttagtctct ccagcacatg cacacagcat gcacacacac
     4861 gcaccctacc caaagacagc tgtggccctc tcccaccacc tcccccttcc caccgctggt
     4921 tgttgggggc tggaggcggg aggtcccatg gaatttgttc tggtttctag gatgtaaacg
     4981 aggactccaa gccatgaatt gccctgcttt ctagagggtg gaatgttgac cctgcaactt
     5041 tagaagcaca atcatttatt aataattttt ttgaaactcc catctacccc tgttagagaa
     5101 atcaacaggt tctaggaatt aaatatgtct ctttgtaacc cagagcatgt tcaatttttg
     5161 gaaaccgtat ttcagtgatt ttcttaatac cttacatgtg tagggcatct tcccccagaa
     5221 tcttacagtc cctttctgtg aagagaagtg gacacacgtg ggaactctca ccatctctgg
     5281 actgtcgtca ggaaacgcct gcaggtcctt gccctgtctg tatggtgtcc tcacttctcc
     5341 atccatacag gtggctccag tgggcatttt tttattttaa attttttaca tgaagcaata
     5401 gaagtacaaa atacttattt tttcaaaatt taatgtgttc catgaaacct gttggcagtc
     5461 gctttccttc ccccacatct aaattctttg gtttttagtt gtttgttttt tggatttttt
     5521 tttttttttt tttggccttg tatcccaagg actaaaagat tagcacagac acgttttgat
     5581 gttgaatgaa ctagtaagtc acagtaggtg gtagtcttca ttgatttctc tgtaagtttt
     5641 taaagaatgt atgaagatag tcacgaatgt actgagtgtt cgcatccccc ttcagttcac
     5701 cttggctgtg tctacaggac aacaaatgtt tgacagggaa taaagtcgtg tctggtgtca
     5761 tttgcgctag cgtgcccctc ccctttcggt gttggctcca aaccttcctt tccttttatg
     5821 tttgtgggga gtggggaacc acatcagcag caatcatcaa ccaaccaacc aatgggatct
     5881 acttagtggt gaatagattg gctatttaat tggtaaaagt tgctggtctg accacaccac
     5941 agcatgacca ctgggttcat ttagagatgg cctccgtttc caacgttccc cacaaatgtt
     6001 tgcttctttc ccagtcaaga ggggatctcg agactcccga gtggaggtcg tgagcttgca
     6061 ccccgcctgg ctgtgtagat cgactgtata gatacatgaa gtgggggtga gggccaaggg
     6121 gctattactg ctgttgggaa atacttgcct ctcgtagatc cagccttaat gtttttctga
     6181 catcctagta atagcagacc ctgcacaaag tggatatcag acttaatact gtgaggagac
     6241 aaaataatga gaatagtttt accaaagata atgaaatctc gcatcatgtc tgcattttac
     6301 catagattgg agtgcatcct taggaaactg aatgtaacaa aaacccagga catttttgga
     6361 aattgtatgc tctctagcaa ctttgtgtga atttttatac aaacactgtt ttatgagtta
     6421 tataaaatgt tataaaaata gaaaaa
//
