Human Gene P3H4 (uc002hxt.3)
  Description: Homo sapiens leprecan-like 4 (P3H4), mRNA.
RefSeq Summary (NM_006455): This nucleolar protein was first characterized because it was an autoantigen in cases on interstitial cystitis. The protein, with a predicted molecular weight of 50 kDa, appears to be localized in the particulate compartment of the interphase nucleolus, with a distribution distinct from that of nucleolar protein B23. During mitosis it is associated with chromosomes. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:39,958,205-39,968,451 Size: 10,247 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr17:39,959,209-39,968,167 Size: 8,959 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:39,958,205-39,968,451)mRNA (may differ from genome)Protein (437 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMalacardsMGIneXtProt
OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SC65_HUMAN
DESCRIPTION: RecName: Full=Synaptonemal complex protein SC65; AltName: Full=Leprecan-like protein 4; AltName: Full=Nucleolar autoantigen No55;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Chromosome. Note=Localized uniformly throughout the granular component of the nucleolus and on the surface of chromosomes during mitosis.
SIMILARITY: Belongs to the leprecan 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


-  MalaCards Disease Associations
  MalaCards Gene Search: P3H4
Diseases sorted by gene-association score: cystitis (3)

+  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: 17.26 RPKM in Cells - Cultured fibroblasts
Total median expression: 264.16 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 -138.30284-0.487 Picture PostScript Text
3' UTR -403.051004-0.401 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
IPR011990 - TPR-like_helical

SCOP Domains:
48439 - Protein prenylyltransferase
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on Q92791
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007130 synaptonemal complex assembly
GO:0017185 peptidyl-lysine hydroxylation
GO:0030199 collagen fibril organization
GO:0032964 collagen biosynthetic process
GO:0046849 bone remodeling

Cellular Component:
GO:0000794 condensed nuclear chromosome
GO:0000795 synaptonemal complex
GO:0005730 nucleolus
GO:0005783 endoplasmic reticulum
GO:1902494 catalytic complex


-  Descriptions from all associated GenBank mRNAs
  LF209335 - JP 2014500723-A/16838: Polycomb-Associated Non-Coding RNAs.
LF327762 - JP 2014500723-A/135265: Polycomb-Associated Non-Coding RNAs.
U47621 - Homo sapiens nucleolar autoantigen No55 mRNA, complete cds.
AK056016 - Homo sapiens cDNA FLJ31454 fis, clone NT2NE2001142, moderately similar to NUCLEOLAR AUTOANTIGEN NO55.
JD446106 - Sequence 427130 from Patent EP1572962.
JD543792 - Sequence 524816 from Patent EP1572962.
JD469805 - Sequence 450829 from Patent EP1572962.
JD438403 - Sequence 419427 from Patent EP1572962.
JD199343 - Sequence 180367 from Patent EP1572962.
JD367871 - Sequence 348895 from Patent EP1572962.
JD405915 - Sequence 386939 from Patent EP1572962.
LF327763 - JP 2014500723-A/135266: Polycomb-Associated Non-Coding RNAs.
JD255082 - Sequence 236106 from Patent EP1572962.
JD086536 - Sequence 67560 from Patent EP1572962.
JD122580 - Sequence 103604 from Patent EP1572962.
BC007942 - Homo sapiens synaptonemal complex protein SC65, mRNA (cDNA clone MGC:14267 IMAGE:4130726), complete cds.
AJ250583 - Homo sapiens mRNA for nucleolar protein No55 (No55 gene).
AK056085 - Homo sapiens cDNA FLJ31523 fis, clone NT2RI2000282, highly similar to NUCLEOLAR AUTOANTIGEN NO55.
JD440772 - Sequence 421796 from Patent EP1572962.
AK222945 - Homo sapiens mRNA for synaptonemal complex protein SC65 variant, clone: HRC12667.
JD063161 - Sequence 44185 from Patent EP1572962.
JD204593 - Sequence 185617 from Patent EP1572962.
JD065927 - Sequence 46951 from Patent EP1572962.
JD142887 - Sequence 123911 from Patent EP1572962.
JD048035 - Sequence 29059 from Patent EP1572962.
JD280168 - Sequence 261192 from Patent EP1572962.
JD050347 - Sequence 31371 from Patent EP1572962.
BC001047 - Homo sapiens synaptonemal complex protein SC65, mRNA (cDNA clone MGC:1322 IMAGE:3510406), complete cds.
JD059317 - Sequence 40341 from Patent EP1572962.
JD367434 - Sequence 348458 from Patent EP1572962.
JD383012 - Sequence 364036 from Patent EP1572962.
JD246892 - Sequence 227916 from Patent EP1572962.
JD413369 - Sequence 394393 from Patent EP1572962.
JD212689 - Sequence 193713 from Patent EP1572962.
BC011701 - Homo sapiens synaptonemal complex protein SC65, mRNA (cDNA clone MGC:19699 IMAGE:3510378), complete cds.
JD537859 - Sequence 518883 from Patent EP1572962.
JD293925 - Sequence 274949 from Patent EP1572962.
JD092303 - Sequence 73327 from Patent EP1572962.
JD183941 - Sequence 164965 from Patent EP1572962.
JD066651 - Sequence 47675 from Patent EP1572962.
JD176453 - Sequence 157477 from Patent EP1572962.
JD531843 - Sequence 512867 from Patent EP1572962.
JD066650 - Sequence 47674 from Patent EP1572962.
JD176452 - Sequence 157476 from Patent EP1572962.
JD531842 - Sequence 512866 from Patent EP1572962.
JD435613 - Sequence 416637 from Patent EP1572962.
JD307030 - Sequence 288054 from Patent EP1572962.
JD425040 - Sequence 406064 from Patent EP1572962.
JD401565 - Sequence 382589 from Patent EP1572962.
JD430447 - Sequence 411471 from Patent EP1572962.
JD194344 - Sequence 175368 from Patent EP1572962.
JD401564 - Sequence 382588 from Patent EP1572962.
JD170164 - Sequence 151188 from Patent EP1572962.
JD170166 - Sequence 151190 from Patent EP1572962.
JD076274 - Sequence 57298 from Patent EP1572962.
JD475092 - Sequence 456116 from Patent EP1572962.
JD283300 - Sequence 264324 from Patent EP1572962.
JD208620 - Sequence 189644 from Patent EP1572962.
JD105565 - Sequence 86589 from Patent EP1572962.
JD319456 - Sequence 300480 from Patent EP1572962.
JD043115 - Sequence 24139 from Patent EP1572962.
AK301301 - Homo sapiens cDNA FLJ53481 complete cds, highly similar to Nucleolar autoantigen No55.
JD105912 - Sequence 86936 from Patent EP1572962.
JD413056 - Sequence 394080 from Patent EP1572962.
JD319629 - Sequence 300653 from Patent EP1572962.
JD210168 - Sequence 191192 from Patent EP1572962.
JD276181 - Sequence 257205 from Patent EP1572962.
JD355551 - Sequence 336575 from Patent EP1572962.
JD139468 - Sequence 120492 from Patent EP1572962.
JD128279 - Sequence 109303 from Patent EP1572962.
JD435533 - Sequence 416557 from Patent EP1572962.
EU831442 - Synthetic construct Homo sapiens clone HAIB:100066471; DKFZo008D0617 synaptonemal complex protein SC65 protein (SC65) gene, encodes complete protein.
EU831534 - Synthetic construct Homo sapiens clone HAIB:100066563; DKFZo004D0618 synaptonemal complex protein SC65 protein (SC65) gene, encodes complete protein.
KJ905396 - Synthetic construct Homo sapiens clone ccsbBroadEn_14968 LEPREL4 gene, encodes complete protein.
DQ893598 - Synthetic construct clone IMAGE:100006228; FLH180939.01X; RZPDo839H08134D synaptonemal complex protein SC65 (SC65) gene, encodes complete protein.
LF327764 - JP 2014500723-A/135267: Polycomb-Associated Non-Coding RNAs.
LF327765 - JP 2014500723-A/135268: Polycomb-Associated Non-Coding RNAs.
CU674526 - Synthetic construct Homo sapiens gateway clone IMAGE:100023419 5' read SC65 mRNA.
LF327767 - JP 2014500723-A/135270: Polycomb-Associated Non-Coding RNAs.
LF327768 - JP 2014500723-A/135271: Polycomb-Associated Non-Coding RNAs.
DQ572687 - Homo sapiens piRNA piR-40799, complete sequence.
AY295765 - Homo sapiens nucleolar autoantigen 55-like mRNA, partial sequence.
MA563339 - JP 2018138019-A/135265: Polycomb-Associated Non-Coding RNAs.
MA563340 - JP 2018138019-A/135266: Polycomb-Associated Non-Coding RNAs.
MA563341 - JP 2018138019-A/135267: Polycomb-Associated Non-Coding RNAs.
MA563342 - JP 2018138019-A/135268: Polycomb-Associated Non-Coding RNAs.
MA563344 - JP 2018138019-A/135270: Polycomb-Associated Non-Coding RNAs.
MA563345 - JP 2018138019-A/135271: Polycomb-Associated Non-Coding RNAs.
MA444912 - JP 2018138019-A/16838: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: LEPREL4, NM_006455, NOL55, NP_006446, Q53GI6, Q92791, Q9H4F6, SC65, SC65_HUMAN
UCSC ID: uc002hxt.3
RefSeq Accession: NM_006455
Protein: Q92791 (aka SC65_HUMAN)
CCDS: CCDS11408.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006455.2
exon count: 8CDS single in 3' UTR: no RNA size: 2619
ORF size: 1314CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2683.00frame shift in genome: no % Coverage: 99.35
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: 57# 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.