Human Gene BEND3 (ENST00000369042.6_6) from GENCODE V47lift37
  Description: BEN domain containing 3, transcript variant 2 (from RefSeq NM_001367314.1)
Gencode Transcript: ENST00000369042.6_6
Gencode Gene: ENSG00000178409.14_7
Transcript (Including UTRs)
   Position: hg19 chr6:107,386,386-107,436,719 Size: 50,334 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr6:107,389,908-107,420,489 Size: 30,582 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:107,386,386-107,436,719)mRNA (may differ from genome)Protein (828 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BEND3_HUMAN
DESCRIPTION: RecName: Full=BEN domain-containing protein 3;
SIMILARITY: Contains 4 BEN domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.04 RPKM in Testis
Total median expression: 27.56 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -237.20437-0.543 Picture PostScript Text
3' UTR -1102.503522-0.313 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR018379 - BEN_domain

Pfam Domains:
PF10523 - BEN domain

SCOP Domains:
48201 - Uteroglobin-like

ModBase Predicted Comparative 3D Structure on Q5T5X7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000182 rDNA binding
GO:0003677 DNA binding
GO:0005515 protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000183 chromatin silencing at rDNA
GO:0006306 DNA methylation
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0034773 histone H4-K20 trimethylation
GO:0036124 histone H3-K9 trimethylation
GO:0043967 histone H4 acetylation
GO:0051260 protein homooligomerization
GO:0080182 histone H3-K4 trimethylation
GO:0098532 histone H3-K27 trimethylation
GO:1903580 positive regulation of ATP metabolic process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005720 nuclear heterochromatin
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  AB046773 - Homo sapiens mRNA for KIAA1553 protein, partial cds.
AK026996 - Homo sapiens cDNA: FLJ23343 fis, clone HEP13562.
JD429495 - Sequence 410519 from Patent EP1572962.
JD188456 - Sequence 169480 from Patent EP1572962.
JD548332 - Sequence 529356 from Patent EP1572962.
JD454585 - Sequence 435609 from Patent EP1572962.
JD312369 - Sequence 293393 from Patent EP1572962.
JD111071 - Sequence 92095 from Patent EP1572962.
DQ588206 - Homo sapiens piRNA piR-55318, complete sequence.
JD089843 - Sequence 70867 from Patent EP1572962.
JD137577 - Sequence 118601 from Patent EP1572962.
JD530191 - Sequence 511215 from Patent EP1572962.
JD564814 - Sequence 545838 from Patent EP1572962.
JD333566 - Sequence 314590 from Patent EP1572962.
JD525250 - Sequence 506274 from Patent EP1572962.
DQ591238 - Homo sapiens piRNA piR-58350, complete sequence.
JD453565 - Sequence 434589 from Patent EP1572962.
JD053024 - Sequence 34048 from Patent EP1572962.
JD565935 - Sequence 546959 from Patent EP1572962.
JD307404 - Sequence 288428 from Patent EP1572962.
JD179999 - Sequence 161023 from Patent EP1572962.
JD235122 - Sequence 216146 from Patent EP1572962.
JD427410 - Sequence 408434 from Patent EP1572962.
JD450784 - Sequence 431808 from Patent EP1572962.
JD451287 - Sequence 432311 from Patent EP1572962.
JD149144 - Sequence 130168 from Patent EP1572962.
JD243423 - Sequence 224447 from Patent EP1572962.
JD193076 - Sequence 174100 from Patent EP1572962.
JD340296 - Sequence 321320 from Patent EP1572962.
JD167796 - Sequence 148820 from Patent EP1572962.
JD537102 - Sequence 518126 from Patent EP1572962.
JD059166 - Sequence 40190 from Patent EP1572962.
JD455169 - Sequence 436193 from Patent EP1572962.
JD515235 - Sequence 496259 from Patent EP1572962.
JD060624 - Sequence 41648 from Patent EP1572962.
JD482922 - Sequence 463946 from Patent EP1572962.
JD403424 - Sequence 384448 from Patent EP1572962.
JD384397 - Sequence 365421 from Patent EP1572962.
JD051712 - Sequence 32736 from Patent EP1572962.
JD129842 - Sequence 110866 from Patent EP1572962.
JD144844 - Sequence 125868 from Patent EP1572962.
JD228392 - Sequence 209416 from Patent EP1572962.
JD450451 - Sequence 431475 from Patent EP1572962.
DQ577114 - Homo sapiens piRNA piR-45226, complete sequence.
JD382913 - Sequence 363937 from Patent EP1572962.
JD135599 - Sequence 116623 from Patent EP1572962.
JD077635 - Sequence 58659 from Patent EP1572962.
JD266937 - Sequence 247961 from Patent EP1572962.
JD134402 - Sequence 115426 from Patent EP1572962.
JD408794 - Sequence 389818 from Patent EP1572962.
DQ570506 - Homo sapiens piRNA piR-30618, complete sequence.
DQ570505 - Homo sapiens piRNA piR-30617, complete sequence.
JD097766 - Sequence 78790 from Patent EP1572962.
BC131628 - Homo sapiens BEN domain containing 3, mRNA (cDNA clone MGC:149812 IMAGE:40118705), complete cds.
KJ899361 - Synthetic construct Homo sapiens clone ccsbBroadEn_08755 BEND3 gene, encodes complete protein.
DQ583300 - Homo sapiens piRNA piR-50412, complete sequence.
DQ576823 - Homo sapiens piRNA piR-44935, complete sequence.
DQ571563 - Homo sapiens piRNA piR-31675, complete sequence.
DQ580664 - Homo sapiens piRNA piR-48776, complete sequence.
DQ581075 - Homo sapiens piRNA piR-49187, complete sequence.
DQ574487 - Homo sapiens piRNA piR-42599, complete sequence.
JD532083 - Sequence 513107 from Patent EP1572962.
JD133775 - Sequence 114799 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A2RRH2, BEND3_HUMAN, ENST00000369042.1, ENST00000369042.2, ENST00000369042.3, ENST00000369042.4, ENST00000369042.5, KIAA1553, NM_001367314, Q5T5X7, Q9HCL9, uc318hha.1, uc318hha.2
UCSC ID: ENST00000369042.6_6
RefSeq Accession: NM_001367314.1
Protein: Q5T5X7 (aka BEND3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.