Human Gene RALY (ENST00000246194.8_9) from GENCODE V47lift37
  Description: RALY heterogeneous nuclear ribonucleoprotein, transcript variant 1 (from RefSeq NM_016732.3)
Gencode Transcript: ENST00000246194.8_9
Gencode Gene: ENSG00000125970.12_14
Transcript (Including UTRs)
   Position: hg19 chr20:32,581,717-32,672,690 Size: 90,974 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr20:32,659,881-32,666,355 Size: 6,475 Coding Exon Count: 7 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:32,581,717-32,672,690)mRNA (may differ from genome)Protein (306 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RALY_HUMAN
DESCRIPTION: RecName: Full=RNA-binding protein Raly; AltName: Full=Autoantigen p542; AltName: Full=Heterogeneous nuclear ribonucleoprotein C-like 2; Short=hnRNP core protein C-like 2; AltName: Full=hnRNP associated with lethal yellow protein homolog;
FUNCTION: Probable-RNA binding protein. Could be a heterogeneous nuclear ribonucleoprotein (hnRNP). May be involved in pre-mRNA splicing (By similarity).
SUBUNIT: Identified in the spliceosome C complex.
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Expressed in heart, brain, lung, liver, skeletal muscle, kidney and pancreas. Weakly expressed in placenta.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
MISCELLANEOUS: Autoantigen found in infectious mononucleosis caused by Epstein-Barr virus. An epitope recognized by B-cells, which cross-react with the BKRF1 protein (EBNA-1 nuclear protein) of Epstein-Barr virus has been identified.
SIMILARITY: Belongs to the RRM HNRPC family. RALY subfamily.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  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: 86.62 RPKM in Testis
Total median expression: 2302.89 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 -136.60313-0.436 Picture PostScript Text
3' UTR -1728.034979-0.347 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
IPR017347 - hnRNP_C_Raly
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WF1 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9UKM9
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 DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003712 transcription cofactor activity
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0042632 cholesterol homeostasis
GO:1903506 regulation of nucleic acid-templated transcription

Cellular Component:
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AK226085 - Homo sapiens mRNA for RNA binding protein (autoantigenic, hnRNP-associated with lethal yellow) short isoform variant, clone: bm02760.
BC103753 - Homo sapiens RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse)), mRNA (cDNA clone MGC:117312 IMAGE:6182358), complete cds.
AK299766 - Homo sapiens cDNA FLJ56677 complete cds, highly similar to RNA-binding protein Raly.
AF148457 - Homo sapiens heterogeneous nuclear ribonucleoprotein, alternate transcript (RALY) mRNA, complete cds.
AK222915 - Homo sapiens mRNA for RNA binding protein (autoantigenic, hnRNP-associated with lethal yellow) long isoform variant, clone: HRC04171.
L38696 - Homo sapiens autoantigen p542 mRNA, complete cds.
BC105018 - Homo sapiens RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse)), mRNA (cDNA clone MGC:132678 IMAGE:8144021), complete cds.
AK291079 - Homo sapiens cDNA FLJ77422 complete cds, highly similar to Homo sapiens RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse)), transcript variant 1, mRNA.
AK291054 - Homo sapiens cDNA FLJ77421 complete cds, highly similar to Homo sapiens autoantigen p542 mRNA.
JD257191 - Sequence 238215 from Patent EP1572962.
JD187433 - Sequence 168457 from Patent EP1572962.
JD129255 - Sequence 110279 from Patent EP1572962.
JD406873 - Sequence 387897 from Patent EP1572962.
JD126617 - Sequence 107641 from Patent EP1572962.
JD272287 - Sequence 253311 from Patent EP1572962.
JD073367 - Sequence 54391 from Patent EP1572962.
JD277733 - Sequence 258757 from Patent EP1572962.
KJ902255 - Synthetic construct Homo sapiens clone ccsbBroadEn_11649 RALY gene, encodes complete protein.
AB528002 - Synthetic construct DNA, clone: pF1KE0723, Homo sapiens RALY gene for RNA binding protein, autoantigenic, without stop codon, in Flexi system.
AY635580 - Homo sapiens breast cancer antigen 10829 mRNA, partial sequence.
JD170546 - Sequence 151570 from Patent EP1572962.
LF350209 - JP 2014500723-A/157712: Polycomb-Associated Non-Coding RNAs.
JD253210 - Sequence 234234 from Patent EP1572962.
JD454628 - Sequence 435652 from Patent EP1572962.
JD398130 - Sequence 379154 from Patent EP1572962.
JD060004 - Sequence 41028 from Patent EP1572962.
JD457270 - Sequence 438294 from Patent EP1572962.
JD411643 - Sequence 392667 from Patent EP1572962.
JD253539 - Sequence 234563 from Patent EP1572962.
LF350210 - JP 2014500723-A/157713: Polycomb-Associated Non-Coding RNAs.
JD019640 - Sequence 664 from Patent EP1572962.
JD031495 - Sequence 12519 from Patent EP1572962.
JD035203 - Sequence 16227 from Patent EP1572962.
MA585786 - JP 2018138019-A/157712: Polycomb-Associated Non-Coding RNAs.
MA585787 - JP 2018138019-A/157713: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000246194.1, ENST00000246194.2, ENST00000246194.3, ENST00000246194.4, ENST00000246194.5, ENST00000246194.6, ENST00000246194.7, HNRPCL2, NM_016732, P542, Q14621, Q2M365, Q5QPL8, Q9BQX6, Q9UJE3, Q9UKM9, RALY_HUMAN, uc317ete.1, uc317ete.2
UCSC ID: ENST00000246194.8_9
RefSeq Accession: NM_016732.3
Protein: Q9UKM9 (aka RALY_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.