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Homo sapiens isolate CHM13 chromosome 10, alternate assembly T2T-CHM13v2.0

NCBI Reference Sequence: NC_060934.1

FASTA Graphics 

LOCUS       NC_060934               4440 bp    DNA     linear   CON 26-AUG-2024
DEFINITION  Homo sapiens isolate CHM13 chromosome 10, alternate assembly
            T2T-CHM13v2.0.
ACCESSION   NC_060934 REGION: 87903926..87908365
VERSION     NC_060934.1
DBLINK      BioProject: PRJNA807723
            BioSample: SAMN03255769
            Assembly: GCF_009914755.1
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            CP068268.2.
            Assembly name: T2T-CHM13v2.0
            The genomic sequence for this RefSeq record is from the
            whole-genome assembly released by the T2T Consortium on 2022/01/24.
            
            ##Genome-Assembly-Data-START##
            Assembly Date          :: 23-APR-2021
            Assembly Method        :: T2T assembly pipeline + rDNA (see
                                      manuscript for details) v. 04/23/2021
            Assembly Name          :: T2T-CHM13v2.0
            Genome Representation  :: Full
            Expected Final Version :: No
            Genome Coverage        :: 30.0x
            Sequencing Technology  :: PacBio Sequel II HiFi; Oxford Nanopore
                                      MinION; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Updated annotation
            Annotation Name             :: GCF_009914755.1-RS_2024_08
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.3
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           RefSeqFE; cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 08/23/2024
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..4440
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /isolate="CHM13"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /sex="female"
                     /cell_line="CHM13htert"
                     /tissue_type="hydatidiform mole"
                     /note="haploid cell line"
     misc_feature    <1..20
                     /standard_name="H3K4me1 hESC enhancer
                     GRCh37_chr10:88779570-88780070"
                     /note="Region: biological region; Derived by automated
                     computational analysis using gene prediction method:
                     RefSeqFE."
                     /db_xref="GeneID:127818708"
     regulatory      <1..20
                     /regulatory_class="enhancer"
                     /experiment="EXISTENCE:reporter gene assay evidence
                     [ECO:0000049][PMID:30033119]"
                     /note="H3K4me1 hESC enhancer chr10:88779570-88780070
                     (GRCh37/hg19 assembly coordinates)"
                     /function="activates a minimal SCP1, AML or CMV promoter
                     by ChIP-STARR-seq in naive H9 embryonic stem cells
                     {active_cell/tissue: H9 hESC(naive)}"
                     /db_xref="GeneID:127818708"
     gene            1..4440
                     /gene="FAM25A"
                     /gene_synonym="bA96C23.5"
                     /note="family with sequence similarity 25 member A;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefSeq."
                     /db_xref="GeneID:643161"
                     /db_xref="HGNC:HGNC:23436"
     mRNA            join(1..104,2021..2083,4251..4440)
                     /gene="FAM25A"
                     /gene_synonym="bA96C23.5"
                     /product="family with sequence similarity 25 member A"
                     /inference="similar to RNA sequence, mRNA (same
                     species):RefSeq:NM_001146157.3"
                     /exception="annotated by transcript or proteomic data"
                     /note="The RefSeq transcript has 1 substitution compared
                     to this genomic sequence; Derived by automated
                     computational analysis using gene prediction method:
                     BestRefSeq."
                     /transcript_id="NM_001146157.3"
                     /db_xref="GeneID:643161"
                     /db_xref="HGNC:HGNC:23436"
     misc_feature    21..521
                     /standard_name="H3K4me1 hESC enhancer
                     GRCh37_chr10:88780071-88780571"
                     /note="Region: biological region; Derived by automated
                     computational analysis using gene prediction method:
                     RefSeqFE."
                     /db_xref="GeneID:127818709"
     regulatory      21..521
                     /regulatory_class="enhancer"
                     /experiment="EXISTENCE:reporter gene assay evidence
                     [ECO:0000049][PMID:30033119]"
                     /note="H3K4me1 hESC enhancer chr10:88780071-88780571
                     (GRCh37/hg19 assembly coordinates)"
                     /function="activates a minimal SCP1, AML or CMV promoter
                     by ChIP-STARR-seq in naive H9 embryonic stem cells
                     {active_cell/tissue: H9 hESC(naive)}"
                     /db_xref="GeneID:127818709"
     CDS             join(32..104,2021..2083,4251..4384)
                     /gene="FAM25A"
                     /gene_synonym="bA96C23.5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefSeq."
                     /codon_start=1
                     /product="protein FAM25A"
                     /protein_id="NP_001139629.1"
                     /db_xref="GeneID:643161"
                     /db_xref="HGNC:HGNC:23436"
                     /translation="MLGGLGKLAAEGLAHRTEKATEGAIHAVEEVVKEVVGHAKETGE
                     KAIAEAIKKAQESGDKKMKEITETVTNTVTNAITHAAESLDKLGQ"
     misc_feature    4223..>4440
                     /standard_name="OCT4-NANOG-H3K27ac hESC enhancer
                     GRCh37_chr10:88784270-88785122"
                     /note="Region: biological region; Derived by automated
                     computational analysis using gene prediction method:
                     RefSeqFE."
                     /db_xref="GeneID:127818710"
     regulatory      4223..>4440
                     /regulatory_class="enhancer"
                     /experiment="EXISTENCE:reporter gene assay evidence
                     [ECO:0000049][PMID:30033119]"
                     /note="OCT4-NANOG-H3K27ac hESC enhancer
                     chr10:88784270-88785122 (GRCh37/hg19 assembly
                     coordinates)"
                     /function="activates a minimal SCP1, AML or CMV promoter
                     by ChIP-STARR-seq in naive H9 embryonic stem cells
                     {active_cell/tissue: H9 hESC(naive)}"
                     /db_xref="GeneID:127818710"
ORIGIN      
        1 atcctagttc accactgtct gctgccacac gatgctggga ggcctgggga agctggctgc
       61 cgaaggcctg gcccaccgca ccgagaaggc caccgaggga gccagtgagg acctggggct
      121 cctttctacc tgggctgggg ggatctgggg cagactgggt ctgtgggagg cggatctaag
      181 taggcaggtg aggacctggg aggaggcctt ggcccctcag gaaccctggt cccctgctct
      241 accaagtcag cacggagttg aggggtgcag acctggggag gtctcctggg ggcagggcat
      301 gagtcctggt gctgggtgaa cactggcagc ttggaccctt ccctctggaa atctggggag
      361 cctttcttgt caaaacagcc tattctgaat aacctatgca ggaaaaggaa gacggatttt
      421 tatttttacc ataactttaa agcttcaaag atttctaaac aagtcaccaa gtctgttcaa
      481 agtcaaaaag ggcattttca atttcatcca agtcccctga agcatgttta tttttatttt
      541 tatttgtatt tgaaatggag tcttgctctg gcacccaggc tggagtgtag tggtgcgatc
      601 tcggctcact gtaacctctg cctcctgggt tcaaagtgat tctcatgcct tagcctcctg
      661 agtgtctggg attacaggca cccaccacca tgcccaacta atttttatat ttttagcaga
      721 gacagggttt cgccatgttg gccaggctgg tctcaaactc ctgacctcaa gtgatccatt
      781 cctcttggcc tcccaaagtg ctgggattgc aggcgtgaac caccgcacct ggtcccgaag
      841 tgtatgttgt attcagaggt cagcagctat gtgtggggag gcccagccag gagccactca
      901 tgggtcatcg tgtgaaaaac agtcttgcct gagtttgtgt cctctttcta aatggcagca
      961 gacgcgtatt ttgtttttga ctctgcagct ggtgtggacc acctgcttta acctttcact
     1021 agcctctgag ttttgtatga ttcctgttgg gagaaaagct gagtattggg agagaagctg
     1081 aggcagggct tgctagattg gctggctcct tgcttctagc actcccattc tctcaagtag
     1141 ccgtatgttt ctcattcact tgatacaccg tttcctttca accgccacat cctcaccacc
     1201 tgtttctttg ttagatcacc aataaatagc atgggttccc agaactccgg gccttcgcag
     1261 cctccacact cgcgatggcg ccccgctccc attttctctc tcaaactgtc tctttctcat
     1321 tcctttgact cctctggact tgccgccccc gcgacctggt gttgggtctc atcaccccaa
     1381 cagattccca ttctaaagat gagggaacca agaggtggaa ggtagagtta gaataagaac
     1441 catttcttct gactctgaaa tccttcagtt ctagcatgct accacctaca ctttaaaaaa
     1501 ctctgaagta ggcagagaat tcccttttgt tggaggaatt gctttgagag acctggtttt
     1561 actggatgag gctttggaaa ccaacctgag gcaggcgcta gcacatcctg agaggggtgt
     1621 gacctggcac agaggcccag cctgggcttc atgtctcagc tggcaagatg gcctgctcat
     1681 tgccattcca ggccgggcag ggccaagggg cttcagggac ccatgccctc atggggctca
     1741 ctgagctcgt ctcccggcag ccaaggccct ggcgtctccg aaggaagcca gctgtggggg
     1801 aaggtccttc tcatgagcca gtctgtcctg gctgggggtg gcatcccaga gccccatcta
     1861 ggatgtccag ggatgtatag gtccattgtg aggataagcc agcactgagc cctcaccctg
     1921 gactgggagg gcagtgggcc tgctctgagc cctcaccctg gactgggagg gcagcggctc
     1981 tgctctgagc cctcaccctg gacttgtctc ctctgttcag ttcatgccgt ggaagaagtg
     2041 gtgaaggagg tggtgggaca tgccaaggag actggagaga aaggtacagc tggctgaggt
     2101 cgggcaggga aggagggagg gagcaaggga agctaggtgc tgggccaacc tgttctttga
     2161 ctaaccaggt caaactctgc ccccaatgtt gcagcctttc agagcctctt ggctggggca
     2221 gttatctatg ctcatcagag gccacagact gtactgcgtt agggcactgt ctagatggtt
     2281 ctgtctgtgg aataagaaga caaagtcaca caagactatg tgacagcaca ctgggacaaa
     2341 acatttaaca tggcagggcg cggtggctca cgcctgtaat cccagccctt tgggaggctg
     2401 aggagggtgg atcacgaggt caggagattg agaccatcct ggctaacacg gtgaaacccc
     2461 atctctacta aaaatacata aaaattagcc gggcatggtg gtgggtgcct atagtcccag
     2521 ctacttggga ggctgaggca ggagaatggt gtgtacctgg gaggcagagc ttgcagtgag
     2581 cctagatcat gccactgcac tccagcctgg gctacagagt gagactcggt ctcaaaaaaa
     2641 aaaaaagaaa aaaaaaattg ctgggtgtgg tggctcacgc ctgtgatccc agcactttgg
     2701 gagcctgagg tgggcggatc acgaggtcag gagatccaga ccacggtgaa accccatctc
     2761 tactaaaaat acaaaaaatt agctgggcac ggtggcgggt gcctgtagtc ccagctactc
     2821 gggaggctga ggcaggagaa tggcgtgaac ccggaaggcg gagcttgcag tgagccgaga
     2881 tcgtgccact gcactccagc ctgggcgaca gtgtgatact ccgtctcaaa aaaaaaaaaa
     2941 aatttaacat gtaaaattct atgttaaatg ttaaattgat gtgtgtgagc tatgagtaga
     3001 actatgtaca aagcatatgt atatctcatt ccttttcaac aaaatagatt ccaggtagat
     3061 gaaggactta aatttacata aatgaattta ttaacttact aggagataac catcttagct
     3121 caggctgcta ttataaaata ccataggcca ggtgcagtgg ctcacgcctg taatcctagc
     3181 ccttcgggag gccaaggtgg gtgggccacc tgaggtcagg agttcaagac cagcctgacc
     3241 aatatggtga aaccccgttg ctactaaaaa tacgaaaacc agctgggcgt ggtggcacat
     3301 gcctgtaatc ccagctactc aggagtctga ggcaggatac tcccttgaac ctgggaggcg
     3361 gaggttgcag tgagctgaga ttgcaccact gcaccccagc cttggtgaca gagcaagact
     3421 ctgtctcaaa aacaaaaaca aaccataaac tgggcgactt agaaacaaca gaaatttatt
     3481 tctcacactc ctggaggatg ggaagtccaa gatcaaggaa ggcactggca gatttggcat
     3541 ctggtgaggg agtctttctg gttcgtggat gggcccagct ctgtcctcac atggtggaag
     3601 gagctagctc tctgtggtct cttttatgtg ggtgctaatt tcaacctccc aaaggcccca
     3661 cctcttaata tcattacatt aagactgagg atttcaacgt atgagttttg agggggaaga
     3721 catcataaac atttagacat agtaataaca taaaagactt tggcctaatc ttggagaggg
     3781 gagaatcttt agaaccatga caaaaaaatc agcgccataa aggaaatatt aagtaaattt
     3841 gacaatccaa aactgaaatt ttctatagcc aaaaaaaaaa aactataaac caagccaaaa
     3901 gaaaaattac acactgatga aaaatatttg tcataaaaat gataatccaa tataacaacc
     3961 caatataaaa atggtcaaaa gacataagca ggcattttcc agaaaaaagg ataagcaggc
     4021 aatgtaccca tgagtagatg ctcagtctca ctcacagttg aagaaatgca agttgttggg
     4081 gaaattaaaa ccaaattcaa attcattctg cagtaatcct gctgcccttg gtcccatcgg
     4141 gccactccag agactaatcc attaagatgg ccacatccca caggccactc aaggggacac
     4201 aagttcagcg ggtggatcac taggacattc ttcctctttc tttccaacag ccattgctga
     4261 agccataaag aaagcccaag agtcagggga caaaaagatg aaggaaatca ctgagacagt
     4321 gaccaacaca gtcacaaatg ccatcaccca tgcagcagag agtctggaca aacttggaca
     4381 gtgagtgcac ctgctaccac ggcccttccc cagtctcaat aaaaagccat gacatgtgta
//
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