Human Gene RRP7A (ENST00000323013.7_8) from GENCODE V47lift37
  Description: ribosomal RNA processing 7 homolog A (from RefSeq NM_015703.5)
Gencode Transcript: ENST00000323013.7_8
Gencode Gene: ENSG00000189306.12_10
Transcript (Including UTRs)
   Position: hg19 chr22:42,904,350-42,915,802 Size: 11,453 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr22:42,908,916-42,915,792 Size: 6,877 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:42,904,350-42,915,802)mRNA (may differ from genome)Protein (280 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RRP7A_HUMAN
DESCRIPTION: RecName: Full=Ribosomal RNA-processing protein 7 homolog A; AltName: Full=Gastric cancer antigen Zg14;
SIMILARITY: Belongs to the RRP7 family.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SEQUENCE CAUTION: Sequence=AAH31838.1; Type=Erroneous initiation;

-  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: 19.93 RPKM in Prostate
Total median expression: 562.93 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
3' UTR -1858.904566-0.407 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom
IPR024326 - RRP7

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF12923 - Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain
PF17799 - Rrp7 RRM-like N-terminal domain

SCOP Domains:
46894 - C-terminal effector domain of the bipartite response regulators
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q9Y3A4
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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 orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000028 ribosomal small subunit assembly
GO:0001825 blastocyst formation
GO:0006364 rRNA processing

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0032545 CURI complex
GO:0034456 UTP-C complex


-  Descriptions from all associated GenBank mRNAs
  JD479154 - Sequence 460178 from Patent EP1572962.
JD479155 - Sequence 460179 from Patent EP1572962.
JD543587 - Sequence 524611 from Patent EP1572962.
JD543588 - Sequence 524612 from Patent EP1572962.
JD497899 - Sequence 478923 from Patent EP1572962.
JD222944 - Sequence 203968 from Patent EP1572962.
JD142584 - Sequence 123608 from Patent EP1572962.
BC073834 - Homo sapiens ribosomal RNA processing 7 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:90162 IMAGE:5533064), complete cds.
JD517678 - Sequence 498702 from Patent EP1572962.
JD366504 - Sequence 347528 from Patent EP1572962.
JD517679 - Sequence 498703 from Patent EP1572962.
JD366505 - Sequence 347529 from Patent EP1572962.
JD366503 - Sequence 347527 from Patent EP1572962.
JD366506 - Sequence 347530 from Patent EP1572962.
JD145067 - Sequence 126091 from Patent EP1572962.
JD079520 - Sequence 60544 from Patent EP1572962.
JD243194 - Sequence 224218 from Patent EP1572962.
JD136154 - Sequence 117178 from Patent EP1572962.
BC031838 - Homo sapiens ribosomal RNA processing 7 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:4394667), partial cds.
JD534727 - Sequence 515751 from Patent EP1572962.
JD155777 - Sequence 136801 from Patent EP1572962.
JD105400 - Sequence 86424 from Patent EP1572962.
JD517259 - Sequence 498283 from Patent EP1572962.
JD287835 - Sequence 268859 from Patent EP1572962.
JD554140 - Sequence 535164 from Patent EP1572962.
JD461275 - Sequence 442299 from Patent EP1572962.
JD366208 - Sequence 347232 from Patent EP1572962.
JD452606 - Sequence 433630 from Patent EP1572962.
JD537883 - Sequence 518907 from Patent EP1572962.
JD381232 - Sequence 362256 from Patent EP1572962.
JD344195 - Sequence 325219 from Patent EP1572962.
JD381231 - Sequence 362255 from Patent EP1572962.
DQ570348 - Homo sapiens piRNA piR-30460, complete sequence.
JD387042 - Sequence 368066 from Patent EP1572962.
JD435300 - Sequence 416324 from Patent EP1572962.
JD382353 - Sequence 363377 from Patent EP1572962.
JD083365 - Sequence 64389 from Patent EP1572962.
AY039240 - Homo sapiens gastric cancer antigen Zg14 mRNA, partial cds.
BC041639 - Homo sapiens ribosomal RNA processing 7 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:5094598), partial cds.
BC064560 - Homo sapiens ribosomal RNA processing 7 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:5548615), containing frame-shift errors.
BC035992 - Homo sapiens ribosomal RNA processing 7 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:4657614).
BC063537 - Homo sapiens ribosomal RNA processing 7 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:4442745), partial cds.
AK092492 - Homo sapiens cDNA FLJ35173 fis, clone PLACE6013288.
AX747570 - Sequence 1095 from Patent EP1308459.
BC042335 - Homo sapiens ribosomal RNA processing 7 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:5744277), partial cds.
DQ583078 - Homo sapiens piRNA piR-50190, complete sequence.
JD391844 - Sequence 372868 from Patent EP1572962.
JD201220 - Sequence 182244 from Patent EP1572962.
BC121118 - Homo sapiens ribosomal RNA processing 7 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:150422 IMAGE:40120513), complete cds.
BC121119 - Homo sapiens ribosomal RNA processing 7 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:150423 IMAGE:40120514), complete cds.
JD251215 - Sequence 232239 from Patent EP1572962.
JD384833 - Sequence 365857 from Patent EP1572962.
JD472066 - Sequence 453090 from Patent EP1572962.
JD472065 - Sequence 453089 from Patent EP1572962.
JD495182 - Sequence 476206 from Patent EP1572962.
JD060589 - Sequence 41613 from Patent EP1572962.
AK314650 - Homo sapiens cDNA, FLJ95494, highly similar to Homo sapiens CGI-96 protein (CGI-96), mRNA.
KJ893640 - Synthetic construct Homo sapiens clone ccsbBroadEn_03034 RRP7A gene, encodes complete protein.
AB527998 - Synthetic construct DNA, clone: pF1KE0685, Homo sapiens RRP7A gene for ribosomal RNA processing 7 homolog A, without stop codon, in Flexi system.
JD409754 - Sequence 390778 from Patent EP1572962.
JD134256 - Sequence 115280 from Patent EP1572962.
JD439831 - Sequence 420855 from Patent EP1572962.
JD094429 - Sequence 75453 from Patent EP1572962.
DQ574488 - Homo sapiens piRNA piR-42600, complete sequence.
JD364088 - Sequence 345112 from Patent EP1572962.
JD473654 - Sequence 454678 from Patent EP1572962.
JD154616 - Sequence 135640 from Patent EP1572962.

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

Protein Q9Y3A4 (Reactome details) participates in the following event(s):

R-HSA-6790906 EMG1 of the SSU processome methylates pseudouridine-1248 of 18S rRNA yielding N(1)-methylpseudouridine-1248
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A4FTX2, B2RBG4, CGI-96, ENST00000323013.1, ENST00000323013.2, ENST00000323013.3, ENST00000323013.4, ENST00000323013.5, ENST00000323013.6, NM_015703, Q0VAD0, Q5JZ94, Q6P4B5, Q8IVR9, Q8IVY0, Q8N5Q3, Q8NEY6, Q9Y3A4, Q9Y3H5, RRP7A , RRP7A_HUMAN, uc317rjo.1, uc317rjo.2
UCSC ID: ENST00000323013.7_8
RefSeq Accession: NM_015703.5
Protein: Q9Y3A4 (aka RRP7A_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.