Human Gene SURF6 (ENST00000372022.6_7) from GENCODE V47lift37
  Description: surfeit 6, transcript variant 3 (from RefSeq NR_103874.2)
Gencode Transcript: ENST00000372022.6_7
Gencode Gene: ENSG00000148296.7_9
Transcript (Including UTRs)
   Position: hg19 chr9:136,195,612-136,203,025 Size: 7,414 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr9:136,198,705-136,202,969 Size: 4,265 Coding Exon Count: 5 

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 (chr9:136,195,612-136,203,025)mRNA (may differ from genome)Protein (361 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SURF6_HUMAN
DESCRIPTION: RecName: Full=Surfeit locus protein 6;
FUNCTION: Binds to both DNA and RNA in vitro, with a stronger binding capacity for RNA. May represent a nucleolar constitutive protein involved in ribosomal biosynthesis or assembly (By similarity).
SUBCELLULAR LOCATION: Nucleus, nucleoplasm (By similarity). Nucleus, nucleolus (By similarity). Note=Granular component of the nucleolus (By similarity).
SIMILARITY: Belongs to the SURF6 family.

-  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           more ... click here to view the complete list

+  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: 17.77 RPKM in Colon - Transverse
Total median expression: 686.70 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 -16.4056-0.293 Picture PostScript Text
3' UTR -1099.403083-0.357 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
IPR007019 - Surf6

Pfam Domains:
PF04935 - Surfeit locus protein 6

ModBase Predicted Comparative 3D Structure on O75683
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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0042254 ribosome biogenesis
GO:0042273 ribosomal large subunit biogenesis
GO:0042274 ribosomal small subunit biogenesis

Cellular Component:
GO:0001652 granular component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0022625 cytosolic large ribosomal subunit


-  Descriptions from all associated GenBank mRNAs
  AF211978 - Homo sapiens LENG11 mRNA, partial sequence.
JD433632 - Sequence 414656 from Patent EP1572962.
JD321123 - Sequence 302147 from Patent EP1572962.
JD041376 - Sequence 22400 from Patent EP1572962.
JD169356 - Sequence 150380 from Patent EP1572962.
JD529229 - Sequence 510253 from Patent EP1572962.
JD557383 - Sequence 538407 from Patent EP1572962.
JD041375 - Sequence 22399 from Patent EP1572962.
JD041377 - Sequence 22401 from Patent EP1572962.
JD169355 - Sequence 150379 from Patent EP1572962.
JD169357 - Sequence 150381 from Patent EP1572962.
JD529228 - Sequence 510252 from Patent EP1572962.
JD529230 - Sequence 510254 from Patent EP1572962.
JD557382 - Sequence 538406 from Patent EP1572962.
JD557384 - Sequence 538408 from Patent EP1572962.
JD430203 - Sequence 411227 from Patent EP1572962.
JD118429 - Sequence 99453 from Patent EP1572962.
JD201299 - Sequence 182323 from Patent EP1572962.
JD326824 - Sequence 307848 from Patent EP1572962.
JD388315 - Sequence 369339 from Patent EP1572962.
JD523759 - Sequence 504783 from Patent EP1572962.
JD247780 - Sequence 228804 from Patent EP1572962.
JD388314 - Sequence 369338 from Patent EP1572962.
JD084367 - Sequence 65391 from Patent EP1572962.
JD169354 - Sequence 150378 from Patent EP1572962.
BC003001 - Homo sapiens surfeit 6, mRNA (cDNA clone IMAGE:2820773), partial cds.
BC006197 - Homo sapiens surfeit 6, mRNA (cDNA clone MGC:2367 IMAGE:2820773), complete cds.
JD381933 - Sequence 362957 from Patent EP1572962.
JD052852 - Sequence 33876 from Patent EP1572962.
JD040541 - Sequence 21565 from Patent EP1572962.
JD207249 - Sequence 188273 from Patent EP1572962.
JD260008 - Sequence 241032 from Patent EP1572962.
JD441081 - Sequence 422105 from Patent EP1572962.
JD496127 - Sequence 477151 from Patent EP1572962.
JD241699 - Sequence 222723 from Patent EP1572962.
JD192967 - Sequence 173991 from Patent EP1572962.
AK054884 - Homo sapiens cDNA FLJ30322 fis, clone BRACE2006703, highly similar to Surfeit locus protein 6.
JD305224 - Sequence 286248 from Patent EP1572962.
JD369228 - Sequence 350252 from Patent EP1572962.
JD302269 - Sequence 283293 from Patent EP1572962.
JD172820 - Sequence 153844 from Patent EP1572962.
BC014878 - Homo sapiens surfeit 6, mRNA (cDNA clone MGC:17229 IMAGE:4343122), complete cds.
JD423508 - Sequence 404532 from Patent EP1572962.
JD563289 - Sequence 544313 from Patent EP1572962.
JD060104 - Sequence 41128 from Patent EP1572962.
JD247584 - Sequence 228608 from Patent EP1572962.
JD492323 - Sequence 473347 from Patent EP1572962.
JD219496 - Sequence 200520 from Patent EP1572962.
JD109194 - Sequence 90218 from Patent EP1572962.
JD219495 - Sequence 200519 from Patent EP1572962.
JD167917 - Sequence 148941 from Patent EP1572962.
JD214275 - Sequence 195299 from Patent EP1572962.
JD173181 - Sequence 154205 from Patent EP1572962.
JD395337 - Sequence 376361 from Patent EP1572962.
JD086273 - Sequence 67297 from Patent EP1572962.
JD287902 - Sequence 268926 from Patent EP1572962.
JD064144 - Sequence 45168 from Patent EP1572962.
JD456867 - Sequence 437891 from Patent EP1572962.
JD533562 - Sequence 514586 from Patent EP1572962.
JD373480 - Sequence 354504 from Patent EP1572962.
JD339568 - Sequence 320592 from Patent EP1572962.
JD544078 - Sequence 525102 from Patent EP1572962.
EU831789 - Synthetic construct Homo sapiens clone HAIB:100066818; DKFZo008D0921 surfeit 6 protein (SURF6) gene, encodes complete protein.
KJ892233 - Synthetic construct Homo sapiens clone ccsbBroadEn_01627 SURF6 gene, encodes complete protein.
EU831867 - Synthetic construct Homo sapiens clone HAIB:100066896; DKFZo004D0922 surfeit 6 protein (SURF6) gene, encodes complete protein.
JD520330 - Sequence 501354 from Patent EP1572962.
JD483702 - Sequence 464726 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000372022.1, ENST00000372022.2, ENST00000372022.3, ENST00000372022.4, ENST00000372022.5, NR_103874, O75683, Q5T8U1, Q9BRK9, Q9BTZ5, Q9UK24, SURF-6, SURF6_HUMAN, uc318jow.1, uc318jow.2
UCSC ID: ENST00000372022.6_7
RefSeq Accession: NM_006753.6
Protein: O75683 (aka SURF6_HUMAN or SUR6_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.