Human Gene SCOC (uc011che.1) Description and Page Index
  Description: Homo sapiens short coiled-coil protein (SCOC), transcript variant 6, mRNA.
RefSeq Summary (NM_001153446): This gene encodes a short coiled-coiled domain-containing protein that localizes to the Golgi apparatus. The encoded protein interacts with ADP-ribosylation factor-like proteins. Pseudogenes of this gene are found on chromosomes 1 and 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009].
Transcript (Including UTRs)
   Position: hg19 chr4:141,264,597-141,303,710 Size: 39,114 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr4:141,264,793-141,302,258 Size: 37,466 Coding Exon Count: 4 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:141,264,597-141,303,710)mRNA (may differ from genome)Protein (122 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIPubMedReactome
Stanford SOURCETreefamUniProtKB

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SCOC
CDC HuGE Published Literature: SCOC

-  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: 34.31 RPKM in Brain - Hypothalamus
Total median expression: 587.98 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -1.9045-0.042 Picture PostScript Text
3' UTR -324.391452-0.223 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:
PF10224 - Predicted coiled-coil protein (DUF2205)

ModBase Predicted Comparative 3D Structure on Q9UIL1-2
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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK027797 - Homo sapiens cDNA FLJ14891 fis, clone PLACE1004256, weakly similar to Mus musculus short coiled coil protein SCOCO (Scoc) mRNA.
BC062684 - Homo sapiens short coiled-coil protein, mRNA (cDNA clone MGC:71935 IMAGE:4691440), complete cds.
CU687588 - Synthetic construct Homo sapiens gateway clone IMAGE:100022985 5' read SCOC mRNA.
HQ447592 - Synthetic construct Homo sapiens clone IMAGE:100070935; CCSB014816_02 short coiled-coil protein (SCOC) gene, encodes complete protein.
KJ894501 - Synthetic construct Homo sapiens clone ccsbBroadEn_03895 SCOC gene, encodes complete protein.
AF330205 - Homo sapiens short coiled-coil protein SCOCO mRNA, complete cds.
AF448857 - Homo sapiens short coiled coil protein mRNA, complete cds.
AB015335 - Homo sapiens HRIHFB2072 mRNA, partial cds.
BC016511 - Homo sapiens, Similar to short coiled-coil protein, clone IMAGE:3861477, mRNA, partial cds.
LF210838 - JP 2014500723-A/18341: Polycomb-Associated Non-Coding RNAs.
AL133580 - Homo sapiens mRNA; cDNA DKFZp434N2072 (from clone DKFZp434N2072).
LF341465 - JP 2014500723-A/148968: Polycomb-Associated Non-Coding RNAs.
AK092794 - Homo sapiens cDNA FLJ35475 fis, clone SMINT2007526, weakly similar to Mus musculus short coiled coil protein SCOCO (Scoc) mRNA.
LF341464 - JP 2014500723-A/148967: Polycomb-Associated Non-Coding RNAs.
JD312587 - Sequence 293611 from Patent EP1572962.
JD362921 - Sequence 343945 from Patent EP1572962.
JD019068 - Sequence 92 from Patent EP1572962.
JD028103 - Sequence 9127 from Patent EP1572962.
LF341463 - JP 2014500723-A/148966: Polycomb-Associated Non-Coding RNAs.
JD098445 - Sequence 79469 from Patent EP1572962.
JD136438 - Sequence 117462 from Patent EP1572962.
JD154002 - Sequence 135026 from Patent EP1572962.
JD290036 - Sequence 271060 from Patent EP1572962.
JD120273 - Sequence 101297 from Patent EP1572962.
JD213955 - Sequence 194979 from Patent EP1572962.
LF341462 - JP 2014500723-A/148965: Polycomb-Associated Non-Coding RNAs.
JD168095 - Sequence 149119 from Patent EP1572962.
JD348983 - Sequence 330007 from Patent EP1572962.
LF341461 - JP 2014500723-A/148964: Polycomb-Associated Non-Coding RNAs.
LF341460 - JP 2014500723-A/148963: Polycomb-Associated Non-Coding RNAs.
JD257277 - Sequence 238301 from Patent EP1572962.
JD055933 - Sequence 36957 from Patent EP1572962.
JD164500 - Sequence 145524 from Patent EP1572962.
LF341459 - JP 2014500723-A/148962: Polycomb-Associated Non-Coding RNAs.
JD491539 - Sequence 472563 from Patent EP1572962.
MA446415 - JP 2018138019-A/18341: Polycomb-Associated Non-Coding RNAs.
MA577042 - JP 2018138019-A/148968: Polycomb-Associated Non-Coding RNAs.
MA577041 - JP 2018138019-A/148967: Polycomb-Associated Non-Coding RNAs.
MA577040 - JP 2018138019-A/148966: Polycomb-Associated Non-Coding RNAs.
MA577039 - JP 2018138019-A/148965: Polycomb-Associated Non-Coding RNAs.
MA577038 - JP 2018138019-A/148964: Polycomb-Associated Non-Coding RNAs.
MA577037 - JP 2018138019-A/148963: Polycomb-Associated Non-Coding RNAs.
MA577036 - JP 2018138019-A/148962: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UIL1 (Reactome details) participates in the following event(s):

R-HSA-6814096 ARL1:GTP binds SCOC
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: HRIHFB2072, NM_001153446, NP_115936, Q9UIL1-2, SCOCO
UCSC ID: uc011che.1
RefSeq Accession: NM_001153446
Protein: Q9UIL1-2, splice isoform of Q9UIL1 CCDS: CCDS3750.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001153446.1
exon count: 5CDS single in 3' UTR: no RNA size: 1876
ORF size: 369CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 907.00frame shift in genome: no % Coverage: 99.47
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.