Human Gene RCCD1 (ENST00000394258.7) from GENCODE V44
  Description: Homo sapiens RCC1 domain containing 1 (RCCD1), transcript variant 1, mRNA. (from RefSeq NM_033544)
Gencode Transcript: ENST00000394258.7
Gencode Gene: ENSG00000166965.13
Transcript (Including UTRs)
   Position: hg38 chr15:90,954,884-90,963,125 Size: 8,242 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr15:90,956,735-90,961,769 Size: 5,035 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:90,954,884-90,963,125)mRNA (may differ from genome)Protein (376 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDMalacardsMGIneXtProtOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RCCD1_HUMAN
DESCRIPTION: RecName: Full=RCC1 domain-containing protein 1;
SIMILARITY: Contains 4 RCC1 repeats.

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.95 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 289.00 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 -86.00188-0.457 Picture PostScript Text
3' UTR -359.401356-0.265 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
IPR000408 - Reg_chr_condens
IPR009091 - Reg_csome_cond/b-lactamase_inh

Pfam Domains:
PF00415 - Regulator of chromosome condensation (RCC1) repeat

ModBase Predicted Comparative 3D Structure on A6NED2
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0006325 chromatin organization

Cellular Component:
GO:0005694 chromosome
GO:0005829 cytosol
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  AK054837 - Homo sapiens cDNA FLJ30275 fis, clone BRACE2002707.
BC140708 - Homo sapiens RCC1 domain containing 1, mRNA (cDNA clone MGC:176385 IMAGE:9021576), complete cds.
BC140709 - Homo sapiens RCC1 domain containing 1, mRNA (cDNA clone MGC:176386 IMAGE:9021577), complete cds.
BC094739 - Homo sapiens cDNA clone IMAGE:5269312.
BC008845 - Homo sapiens RCC1 domain containing 1, mRNA (cDNA clone IMAGE:4300738), with apparent retained intron.
JD232463 - Sequence 213487 from Patent EP1572962.
JD458226 - Sequence 439250 from Patent EP1572962.
KJ895150 - Synthetic construct Homo sapiens clone ccsbBroadEn_04544 RCCD1 gene, encodes complete protein.
BC113826 - Homo sapiens RCC1 domain containing 1, mRNA (cDNA clone IMAGE:40023565), partial cds.
BC064606 - Homo sapiens RCC1 domain containing 1, mRNA (cDNA clone IMAGE:5770298).
JD173474 - Sequence 154498 from Patent EP1572962.
JD139369 - Sequence 120393 from Patent EP1572962.
JD476364 - Sequence 457388 from Patent EP1572962.
JD461581 - Sequence 442605 from Patent EP1572962.
JD140868 - Sequence 121892 from Patent EP1572962.
JD209605 - Sequence 190629 from Patent EP1572962.
JD217715 - Sequence 198739 from Patent EP1572962.
JD466418 - Sequence 447442 from Patent EP1572962.
JD355849 - Sequence 336873 from Patent EP1572962.
AK092661 - Homo sapiens cDNA FLJ35342 fis, clone PROST2015900.
AL110105 - Homo sapiens EST from clone 121270, 5' end.
AL110104 - Homo sapiens EST from clone 44697, 5' end.
JD354800 - Sequence 335824 from Patent EP1572962.
JD565064 - Sequence 546088 from Patent EP1572962.
JD385742 - Sequence 366766 from Patent EP1572962.
JD204975 - Sequence 185999 from Patent EP1572962.
JD243702 - Sequence 224726 from Patent EP1572962.
JD486478 - Sequence 467502 from Patent EP1572962.
JD245895 - Sequence 226919 from Patent EP1572962.
JD092774 - Sequence 73798 from Patent EP1572962.
JD499253 - Sequence 480277 from Patent EP1572962.
JD171629 - Sequence 152653 from Patent EP1572962.
JD350225 - Sequence 331249 from Patent EP1572962.
JD233623 - Sequence 214647 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NED2, B2RTP9, ENST00000394258.1, ENST00000394258.2, ENST00000394258.3, ENST00000394258.4, ENST00000394258.5, ENST00000394258.6, NM_033544, Q29RX6, RCCD1_HUMAN, uc002bqk.1, uc002bqk.2, uc002bqk.3, uc002bqk.4, uc002bqk.5
UCSC ID: ENST00000394258.7
RefSeq Accession: NM_001017919
Protein: A6NED2 (aka RCCD1_HUMAN)

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