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    HFM1 helicase for meiosis 1 [ Homo sapiens (human) ]

    Gene ID: 164045, updated on 27-Nov-2024

    Summary

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    Official Symbol
    HFM1provided by HGNC
    Official Full Name
    helicase for meiosis 1provided by HGNC
    Primary source
    HGNC:HGNC:20193
    See related
    Ensembl:ENSG00000162669 MIM:615684; AllianceGenome:HGNC:20193
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MER3; POF9; Si-11; SEC63D1; Si-11-6; helicase
    Summary
    The protein encoded by this gene is thought to be an ATP-dependent DNA helicase and is expressed mainly in germ-line cells. Defects in this gene are a cause of premature ovarian failure 9 (POF9). [provided by RefSeq, Apr 2014]
    Expression
    Biased expression in testis (RPKM 6.6), ovary (RPKM 1.4) and 3 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HFM1 in Genome Data Viewer
    Location:
    1p22.2
    Exon count:
    44
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (91260766..91408007, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (91105413..91252636, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (91726323..91870394, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:91390503-91391117 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:91392347-91392959 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:91393061-91393667 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:91393668-91394273 Neighboring gene zinc finger protein 644 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:91439231-91440124 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:91486849-91487398 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:91487399-91487948 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:91487949-91488498 Neighboring gene ribosomal protein L5 pseudogene 6 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:91589111-91589852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:91654217-91654717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:91717359-91717859 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:91718677-91718849 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:91755191-91755405 Neighboring gene flap structure-specific endonuclease 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1066 Neighboring gene uncharacterized LOC124904661 Neighboring gene uncharacterized LOC107985417

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of a new splice-acceptor mutation in HFM1 and functional analysis through molecular docking in nonobstructive azoospermia. Saebnia N, et al. J Assist Reprod Genet, 2022 May. PMID 35486194, Free PMC Article
    2. Novel variants in helicase for meiosis 1 lead to male infertility due to non-obstructive azoospermia. Tang D, et al. Reprod Biol Endocrinol, 2021 Aug 24. PMID 34429122, Free PMC Article
    3. Mutations in HFM1 in recessive primary ovarian insufficiency. Wang J, et al. N Engl J Med, 2014 Mar 6. PMID 24597873
    4. A novel heterozygous splice-altering mutation in HFM1 may be a cause of premature ovarian insufficiency. Zhe J, et al. J Ovarian Res, 2019 Jul 6. PMID 31279343, Free PMC Article
    5. Association analysis between HFM1 variation and primary ovarian insufficiency in Chinese women. Pu D, et al. Clin Genet, 2016 May. PMID 26679638

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel pathogenic splicing variants in helicase for meiosis 1 (HFM1) are associated with diminished ovarian reserve and poor pregnancy outcomes.
      Title: Novel pathogenic splicing variants in helicase for meiosis 1 (HFM1) are associated with diminished ovarian reserve and poor pregnancy outcomes.
    2. Biallelic HFM1 variants cause non-obstructive azoospermia with meiotic arrest in humans by impairing crossover formation to varying degrees.
      Title: Biallelic HFM1 variants cause non-obstructive azoospermia with meiotic arrest in humans by impairing crossover formation to varying degrees.
    3. Identification of a new splice-acceptor mutation in HFM1 and functional analysis through molecular docking in nonobstructive azoospermia.
      Title: Identification of a new splice-acceptor mutation in HFM1 and functional analysis through molecular docking in nonobstructive azoospermia.
    4. Novel variants in helicase for meiosis 1 lead to male infertility due to non-obstructive azoospermia.
      Title: Novel variants in helicase for meiosis 1 lead to male infertility due to non-obstructive azoospermia.
    5. A novel heterozygous missense mutation in HFM1 (c.3470G > A) associated with premature ovarian insufficiency (POI) is in the affected family members and absent in the unaffected family members in China. Results of the minigene assay reveals that the mutation changes the mRNA splicing repertory.
      Title: A novel heterozygous splice-altering mutation in HFM1 may be a cause of premature ovarian insufficiency.
    6. Data suggest that HFM1 gene might be associated with primary ovarian insufficiency in Chinese population.
      Title: Association analysis between HFM1 variation and primary ovarian insufficiency in Chinese women.
    7. Exome sequencing of two Chinese sisters with primary ovarian insufficiency and their parents identified a shared compound heterozygous mutation in a meiotic gene, HFM1, which encodes a protein necessary for homologous recombination of chromosomes.
      Title: Mutations in HFM1 in recessive primary ovarian insufficiency.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
    9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    10. hHFM1 is the evolutionally conserved putative human DNA helicase, which may function as a modulator for genome integrity in germ-line tissues.
      Title: HFM1, the human homologue of yeast Mer3, encodes a putative DNA helicase expressed specifically in germ-line cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Premature ovarian failure 9
    MedGen: C3810376 OMIM: 615724 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ36760, FLJ39011, MGC163397

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables double-stranded DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables forked DNA-dependent helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables four-way junction helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in resolution of meiotic recombination intermediates IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    probable ATP-dependent DNA helicase HFM1
    Names
    HFM1, ATP dependent DNA helicase homolog
    SEC63 domain-containing protein 1
    helicase-like protein HFM1
    NP_001017975.5
    XP_011539151.1
    XP_011539152.1
    XP_011539153.1
    XP_011539154.1
    XP_011539157.1
    XP_011539159.1
    XP_011539161.1
    XP_016855979.1
    XP_016855980.1
    XP_016855981.1
    XP_016855982.1
    XP_016855983.1
    XP_016855984.1
    XP_016855985.1
    XP_024309476.1
    XP_047303894.1
    XP_047303896.1
    XP_047303911.1
    XP_047303912.1
    XP_054190738.1
    XP_054190739.1
    XP_054190740.1
    XP_054190741.1
    XP_054190742.1
    XP_054190743.1
    XP_054190744.1
    XP_054190745.1
    XP_054190746.1
    XP_054190747.1
    XP_054190748.1
    XP_054190749.1
    XP_054190750.1
    XP_054190751.1
    XP_054190752.1
    XP_054190753.1
    XP_054190754.1
    XP_054190755.1
    XP_054190756.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_034120.2 RefSeqGene

      Range
      8170..152241
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001017975.6 → NP_001017975.5  probable ATP-dependent DNA helicase HFM1

      Status: REVIEWED

      Source sequence(s)
      AC098691, BX323048
      Consensus CDS
      CCDS30769.2
      UniProtKB/Swiss-Prot
      A2PYH4, B1B0B6, Q8N9Q0
      Related
      ENSP00000359454.3, ENST00000370425.8
      Conserved Domains (2) summary
      COG1204
      Location:264 → 970
      BRR2; Replicative superfamily II helicase [Replication, recombination and repair]
      cd18023
      Location:280 → 488
      DEXHc_HFM1; DEXH-box helicase domain of ATP-dependent DNA helicase HFM1

    RNA

    1. NR_165455.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC098691, BX323048

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      91260766..91408007 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011540852.3 → XP_011539154.1  probable ATP-dependent DNA helicase HFM1 isoform X1

      See identical proteins and their annotated locations for XP_011539154.1

      UniProtKB/Swiss-Prot
      A2PYH4, B1B0B6, Q8N9Q0
      Conserved Domains (2) summary
      COG1204
      Location:264 → 970
      BRR2; Replicative superfamily II helicase [Replication, recombination and repair]
      cd18023
      Location:280 → 488
      DEXHc_HFM1; DEXH-box helicase domain of ATP-dependent DNA helicase HFM1

    2. XM_011540857.2 → XP_011539159.1  probable ATP-dependent DNA helicase HFM1 isoform X7

      Conserved Domains (3) summary
      cd00079
      Location:373 → 528
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00270
      Location:143 → 325
      DEAD; DEAD/DEAH box helicase
      pfam02889
      Location:636 → 949
      Sec63; Sec63 Brl domain

    3. XM_017000490.2 → XP_016855979.1  probable ATP-dependent DNA helicase HFM1 isoform X2

      Conserved Domains (3) summary
      cd00079
      Location:514 → 669
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00270
      Location:284 → 466
      DEAD; DEAD/DEAH box helicase
      pfam02889
      Location:752 → 1063
      Sec63; Sec63 Brl domain

    4. XM_017000491.2 → XP_016855980.1  probable ATP-dependent DNA helicase HFM1 isoform X3

      Conserved Domains (3) summary
      cd00079
      Location:514 → 669
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00270
      Location:284 → 466
      DEAD; DEAD/DEAH box helicase
      pfam02889
      Location:777 → 1046
      Sec63; Sec63 Brl domain

    5. XM_011540851.2 → XP_011539153.1  probable ATP-dependent DNA helicase HFM1 isoform X1

      See identical proteins and their annotated locations for XP_011539153.1

      UniProtKB/Swiss-Prot
      A2PYH4, B1B0B6, Q8N9Q0
      Conserved Domains (2) summary
      COG1204
      Location:264 → 970
      BRR2; Replicative superfamily II helicase [Replication, recombination and repair]
      cd18023
      Location:280 → 488
      DEXHc_HFM1; DEXH-box helicase domain of ATP-dependent DNA helicase HFM1

    6. XM_011540849.2 → XP_011539151.1  probable ATP-dependent DNA helicase HFM1 isoform X1

      See identical proteins and their annotated locations for XP_011539151.1

      UniProtKB/Swiss-Prot
      A2PYH4, B1B0B6, Q8N9Q0
      Conserved Domains (2) summary
      COG1204
      Location:264 → 970
      BRR2; Replicative superfamily II helicase [Replication, recombination and repair]
      cd18023
      Location:280 → 488
      DEXHc_HFM1; DEXH-box helicase domain of ATP-dependent DNA helicase HFM1

    7. XM_011540850.3 → XP_011539152.1  probable ATP-dependent DNA helicase HFM1 isoform X1

      See identical proteins and their annotated locations for XP_011539152.1

      UniProtKB/Swiss-Prot
      A2PYH4, B1B0B6, Q8N9Q0
      Conserved Domains (2) summary
      COG1204
      Location:264 → 970
      BRR2; Replicative superfamily II helicase [Replication, recombination and repair]
      cd18023
      Location:280 → 488
      DEXHc_HFM1; DEXH-box helicase domain of ATP-dependent DNA helicase HFM1

    8. XM_011540855.3 → XP_011539157.1  probable ATP-dependent DNA helicase HFM1 isoform X4

      Conserved Domains (3) summary
      cd00079
      Location:472 → 627
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00270
      Location:242 → 424
      DEAD; DEAD/DEAH box helicase
      pfam02889
      Location:735 → 1048
      Sec63; Sec63 Brl domain

    9. XM_017000492.1 → XP_016855981.1  probable ATP-dependent DNA helicase HFM1 isoform X8

      Conserved Domains (3) summary
      cd00079
      Location:193 → 348
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00270
      Location:10 → 145
      DEAD; DEAD/DEAH box helicase
      pfam02889
      Location:456 → 769
      Sec63; Sec63 Brl domain

    10. XM_011540859.3 → XP_011539161.1  probable ATP-dependent DNA helicase HFM1 isoform X9

      Conserved Domains (2) summary
      cd00079
      Location:123 → 278
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam02889
      Location:386 → 699
      Sec63; Sec63 Brl domain

    11. XM_017000493.1 → XP_016855982.1  probable ATP-dependent DNA helicase HFM1 isoform X12

      UniProtKB/TrEMBL
      B7ZM00
      Related
      ENST00000462405.5

    12. XM_047447938.1 → XP_047303894.1  probable ATP-dependent DNA helicase HFM1 isoform X5

    13. XM_047447940.1 → XP_047303896.1  probable ATP-dependent DNA helicase HFM1 isoform X6

    14. XM_047447956.1 → XP_047303912.1  probable ATP-dependent DNA helicase HFM1 isoform X11

    15. XM_047447955.1 → XP_047303911.1  probable ATP-dependent DNA helicase HFM1 isoform X10

    16. XM_017000494.2 → XP_016855983.1  probable ATP-dependent DNA helicase HFM1 isoform X13

      UniProtKB/TrEMBL
      D2KTB5

    17. XM_017000496.2 → XP_016855985.1  probable ATP-dependent DNA helicase HFM1 isoform X14

      UniProtKB/TrEMBL
      D2KTB5
      Conserved Domains (3) summary
      cd00079
      Location:514 → 669
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00270
      Location:284 → 466
      DEAD; DEAD/DEAH box helicase
      cl22482
      Location:777 → 810
      Sec63; Sec63 Brl domain

    18. XM_017000495.2 → XP_016855984.1  probable ATP-dependent DNA helicase HFM1 isoform X14

      UniProtKB/TrEMBL
      D2KTB5
      Conserved Domains (3) summary
      cd00079
      Location:514 → 669
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00270
      Location:284 → 466
      DEAD; DEAD/DEAH box helicase
      cl22482
      Location:777 → 810
      Sec63; Sec63 Brl domain

    19. XM_024453708.2 → XP_024309476.1  probable ATP-dependent DNA helicase HFM1 isoform X15

      UniProtKB/TrEMBL
      D2KTB5
      Conserved Domains (1) summary
      cl28231
      Location:264 → 753
      BRR2; Replicative superfamily II helicase [Replication, recombination and repair]

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      91105413..91252636 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334766.1 → XP_054190741.1  probable ATP-dependent DNA helicase HFM1 isoform X1

    2. XM_054334772.1 → XP_054190747.1  probable ATP-dependent DNA helicase HFM1 isoform X7

    3. XM_054334767.1 → XP_054190742.1  probable ATP-dependent DNA helicase HFM1 isoform X2

    4. XM_054334768.1 → XP_054190743.1  probable ATP-dependent DNA helicase HFM1 isoform X3

    5. XM_054334765.1 → XP_054190740.1  probable ATP-dependent DNA helicase HFM1 isoform X1

    6. XM_054334763.1 → XP_054190738.1  probable ATP-dependent DNA helicase HFM1 isoform X1

    7. XM_054334764.1 → XP_054190739.1  probable ATP-dependent DNA helicase HFM1 isoform X1

    8. XM_054334769.1 → XP_054190744.1  probable ATP-dependent DNA helicase HFM1 isoform X4

    9. XM_054334773.1 → XP_054190748.1  probable ATP-dependent DNA helicase HFM1 isoform X8

      UniProtKB/TrEMBL
      B4DYS5

    10. XM_054334774.1 → XP_054190749.1  probable ATP-dependent DNA helicase HFM1 isoform X9

    11. XM_054334777.1 → XP_054190752.1  probable ATP-dependent DNA helicase HFM1 isoform X12

    12. XM_054334770.1 → XP_054190745.1  probable ATP-dependent DNA helicase HFM1 isoform X5

    13. XM_054334771.1 → XP_054190746.1  probable ATP-dependent DNA helicase HFM1 isoform X6

    14. XM_054334776.1 → XP_054190751.1  probable ATP-dependent DNA helicase HFM1 isoform X11

    15. XM_054334775.1 → XP_054190750.1  probable ATP-dependent DNA helicase HFM1 isoform X10

    16. XM_054334778.1 → XP_054190753.1  probable ATP-dependent DNA helicase HFM1 isoform X13

    17. XM_054334780.1 → XP_054190755.1  probable ATP-dependent DNA helicase HFM1 isoform X14

    18. XM_054334779.1 → XP_054190754.1  probable ATP-dependent DNA helicase HFM1 isoform X14

    19. XM_054334781.1 → XP_054190756.1  probable ATP-dependent DNA helicase HFM1 isoform X15

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2PYH4.2 GenPept UniProtKB/Swiss-Prot:A2PYH4

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