Human Gene BEND3 (uc003prs.2) Description and Page Index
  Description: Homo sapiens BEN domain containing 3 (BEND3), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr6:107,386,385-107,435,636 Size: 49,252 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr6:107,389,908-107,420,489 Size: 30,582 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr6:107,386,385-107,435,636)mRNA (may differ from genome)Protein (828 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedStanford SOURCEUniProtKB

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

-  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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -237.40650-0.365 Picture PostScript Text
3' UTR -1158.483523-0.329 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

ModBase Predicted Comparative 3D Structure on Q5T5X7
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Protein Sequence   

-  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, KIAA1553, NM_001080450, NP_001073919, Q5T5X7, Q9HCL9
UCSC ID: uc003prs.2
RefSeq Accession: NM_001080450
Protein: Q5T5X7 (aka BEND3_HUMAN)
CCDS: CCDS34507.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001080450.2
exon count: 5CDS single in 3' UTR: no RNA size: 6660
ORF size: 2487CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4760.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.