Human Gene RCC1 (uc001bqf.2)
  Description: Homo sapiens regulator of chromosome condensation 1 (RCC1), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:28,844,745-28,865,708 Size: 20,964 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr1:28,856,379-28,864,519 Size: 8,141 Coding Exon Count: 10 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:28,844,745-28,865,708)mRNA (may differ from genome)Protein (452 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: RCC1
Diseases sorted by gene-association score: renal-hepatic-pancreatic dysplasia (2), retinitis pigmentosa (1)

-  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: 29.43 RPKM in Testis
Total median expression: 303.13 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 -37.3085-0.439 Picture PostScript Text
3' UTR -397.391189-0.334 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
  Pfam Domains:
PF00415 - Regulator of chromosome condensation (RCC1) repeat
PF13540 - Regulator of chromosome condensation (RCC1) repeat

SCOP Domains:
50985 - RCC1/BLIP-II

ModBase Predicted Comparative 3D Structure on P18754-2
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 Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  X06130 - Human mRNA for cell cycle gene RCC1.
BC007300 - Homo sapiens SNHG3-RCC1 readthrough transcript, mRNA (cDNA clone MGC:15698 IMAGE:3351770), complete cds.
BC036903 - Homo sapiens SNHG3-RCC1 readthrough transcript, mRNA (cDNA clone MGC:46387 IMAGE:4536608), complete cds.
X12654 - Human mRNA for cell cycle gene RCC1.
BC069198 - Homo sapiens regulator of chromosome condensation 1, mRNA (cDNA clone MGC:78444 IMAGE:6586198), complete cds.
BC001589 - Homo sapiens regulator of chromosome condensation 1, mRNA (cDNA clone IMAGE:2966388).
BC010067 - Homo sapiens regulator of chromosome condensation 1, mRNA (cDNA clone MGC:19564 IMAGE:4122227), complete cds.
CU675603 - Synthetic construct Homo sapiens gateway clone IMAGE:100019325 5' read SNHG3-RCC1 mRNA.
AB527622 - Synthetic construct DNA, clone: pF1KB3382, Homo sapiens RCC1 gene for regulator of chromosome condensation 1, without stop codon, in Flexi system.
CR407693 - Homo sapiens full open reading frame cDNA clone RZPDo834E063D for gene CHC1, chromosome condensation 1 complete cds, without stopcodon.
KU177974 - Homo sapiens regulator of chromosome condensation 1 isoform 1 (RCC1) mRNA, partial cds.
KU177975 - Homo sapiens regulator of chromosome condensation 1 isoform 2 (RCC1) mRNA, partial cds.
KU177976 - Homo sapiens regulator of chromosome condensation 1 isoform 3 (RCC1) mRNA, partial cds.
DQ893153 - Synthetic construct clone IMAGE:100005783; FLH194394.01X; RZPDo839A1180D regulator of chromosome condensation 1 (RCC1) gene, encodes complete protein.
DQ896760 - Synthetic construct Homo sapiens clone IMAGE:100011220; FLH194390.01L; RZPDo839A1170D regulator of chromosome condensation 1 (RCC1) gene, encodes complete protein.
KJ890906 - Synthetic construct Homo sapiens clone ccsbBroadEn_00300 RCC1 gene, encodes complete protein.
AF498924 - Homo sapiens regulator of chromosome condensation 1 (CHC1) mRNA, complete cds.
S75708 - RCC1=RCC1-I {alternatively spliced, exon 6', insertion site} [human, mRNA Partial Mutant, 138 nt].
JD065364 - Sequence 46388 from Patent EP1572962.
JD419167 - Sequence 400191 from Patent EP1572962.
JD161404 - Sequence 142428 from Patent EP1572962.
JD321871 - Sequence 302895 from Patent EP1572962.
JD186608 - Sequence 167632 from Patent EP1572962.
JD418400 - Sequence 399424 from Patent EP1572962.
JD492830 - Sequence 473854 from Patent EP1572962.
JD068007 - Sequence 49031 from Patent EP1572962.
JD102906 - Sequence 83930 from Patent EP1572962.
JD171632 - Sequence 152656 from Patent EP1572962.
JD027226 - Sequence 8250 from Patent EP1572962.
JD433182 - Sequence 414206 from Patent EP1572962.
JD029773 - Sequence 10797 from Patent EP1572962.
JD154568 - Sequence 135592 from Patent EP1572962.
JD559956 - Sequence 540980 from Patent EP1572962.
JD038789 - Sequence 19813 from Patent EP1572962.
JD499222 - Sequence 480246 from Patent EP1572962.
JD251653 - Sequence 232677 from Patent EP1572962.
JD089299 - Sequence 70323 from Patent EP1572962.
JD232455 - Sequence 213479 from Patent EP1572962.
JD226324 - Sequence 207348 from Patent EP1572962.
JD220598 - Sequence 201622 from Patent EP1572962.
JD363043 - Sequence 344067 from Patent EP1572962.
JD091681 - Sequence 72705 from Patent EP1572962.
JD531610 - Sequence 512634 from Patent EP1572962.
JD354916 - Sequence 335940 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_ranPathway - Cycling of Ran in nucleocytoplasmic transport
h_npcPathway - Mechanism of Protein Import into the Nucleus
h_ranMSpathway - Role of Ran in mitotic spindle regulation

Reactome (by CSHL, EBI, and GO)

Protein P18754 (Reactome details) participates in the following event(s):

R-HSA-180687 Conversion of Ran-GDP to Ran-GTP
R-HSA-165054 Rev-mediated nuclear export of HIV RNA
R-HSA-180746 Nuclear import of Rev protein
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-177243 Interactions of Rev with host cellular proteins
R-HSA-162587 HIV Life Cycle
R-HSA-162909 Host Interactions of HIV factors
R-HSA-162906 HIV Infection
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: CHC1, NM_001048194, NP_001041659, P18754-2
UCSC ID: uc001bqf.2
RefSeq Accession: NM_001048194
Protein: P18754-2, splice isoform of P18754 CCDS: CCDS41295.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001048194.2
exon count: 11CDS single in 3' UTR: no RNA size: 2633
ORF size: 1359CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2178.00frame 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.