Human Gene NHP2 (uc003mir.2) Description and Page Index
  Description: Homo sapiens NHP2 ribonucleoprotein (NHP2), transcript variant 1, mRNA.
RefSeq Summary (NM_017838): This gene is a member of the H/ACA snoRNPs (small nucleolar ribonucleoproteins) gene family. snoRNPs are involved in various aspects of rRNA processing and modification and have been classified into two families: C/D and H/ACA. The H/ACA snoRNPs also include the DKC1, NOLA1 and NOLA3 proteins. These four H/ACA snoRNP proteins localize to the dense fibrillar components of nucleoli and to coiled (Cajal) bodies in the nucleus. Both 18S rRNA production and rRNA pseudouridylation are impaired if any one of the four proteins is depleted. The four H/ACA snoRNP proteins are also components of the telomerase complex. This gene encodes a protein related to Saccharomyces cerevisiae Nhp2p. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2008].
Transcript (Including UTRs)
   Position: hg19 chr5:177,576,465-177,580,961 Size: 4,497 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr5:177,576,714-177,580,818 Size: 4,105 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr5:177,576,465-177,580,961)mRNA (may differ from genome)Protein (153 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=H/ACA ribonucleoprotein complex subunit 2; AltName: Full=Nucleolar protein family A member 2; AltName: Full=snoRNP protein NHP2;
FUNCTION: Required for ribosome biogenesis and telomere maintenance. Part of the H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ("psi") residues, which may serve to stabilize the conformation of rRNAs. May also be required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme.
SUBUNIT: Part of the H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which contains NHP2/NOLA2, GAR1/NOLA1, NOP10/NOLA3, and DKC1/NOLA4, which is presumed to be the catalytic subunit. The complex contains a stable core formed by binding of one or two NOP10-DKC1 heterodimers to NHP2; GAR1 subsequently binds to this core via DKC1. The complex binds a box H/ACA small nucleolar RNA (snoRNA), which may target the specific site of modification within the RNA substrate. During assembly, the complex contains NAF1 instead of GAR1/NOLA1. The complex also interacts with TERC, which contains a 3'-terminal domain related to the box H/ACA snoRNAs. Specific interactions with snoRNAs or TERC are mediated by GAR1 and NHP2. Associates with NOLC1/NOPP140. H/ACA snoRNPs interact with the SMN complex, consisting of SMN1 or SMN2, GEMIN2/SIP1, DDX20/GEMIN3, and GEMIN4. This is mediated by interaction between GAR1 and SMN1 or SMN2. The SMN complex may be required for correct assembly of the H/ACA snoRNP complex. Component of the telomerase holoenzyme complex at least composed of TERT, DKC1, WRAP53/TCAB1, NOP10, NHP2, GAR1, TEP1, EST1A, POT1 and a telomerase RNA template component (TERC).
SUBCELLULAR LOCATION: Nucleus, nucleolus. Nucleus, Cajal body. Note=Also localized to Cajal bodies (coiled bodies).
TISSUE SPECIFICITY: Expressed in brain, colon, heart, kidney, ovary, pancreas, placenta, prostate, skeletal muscle, small intestine, spleen, testis and thymus. Also expressed at lower levels in the liver.
DEVELOPMENTAL STAGE: Transcript peaks at G1/S transition.
DISEASE: Defects in NHP2 are the cause of dyskeratosis congenita autosomal recessive type 2 (DKCB2) [MIM:613987]. A rare multisystem disorder caused by defective telomere maintenance. It is characterized by progressive bone marrow failure, and the clinical triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Common but variable features include premature graying, aplastic anemia, low platelets, osteoporosis, pulmonary fibrosis, and liver fibrosis among others. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy.
SIMILARITY: Belongs to the ribosomal protein L7Ae family.
SEQUENCE CAUTION: Sequence=AAF28964.1; Type=Frameshift; Positions=37, 119, 120;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NHP2
CDC HuGE Published Literature: NHP2
Positive Disease Associations: Glucose
Related Studies:
  1. Glucose
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: NHP2
Diseases sorted by gene-association score: dyskeratosis congenita, autosomal recessive 2* (1230), dyskeratosis congenita, autosomal recessive 1* (231), dyskeratosis congenita* (126), nhp2-related dyskeratosis congenita* (100), dyskeratosis congenita autosomal recessive (15), aplastic anemia (8)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 105.03 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2721.57 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 -53.60143-0.375 Picture PostScript Text
3' UTR -85.10249-0.342 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
IPR002415 - H/ACA_rnp_Nhp2_euk
IPR004038 - Ribosomal_L7Ae/L30e/S12e/Gad45
IPR018492 - Ribosomal_L7Ae/L8/Nhp2

Pfam Domains:
PF01248 - Ribosomal protein L7Ae/L30e/S12e/Gadd45 family

SCOP Domains:
55315 - L30e-like

ModBase Predicted Comparative 3D Structure on Q9NX24
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0034513 box H/ACA snoRNA binding
GO:0070034 telomerase RNA binding

Biological Process:
GO:0000469 cleavage involved in rRNA processing
GO:0000470 maturation of LSU-rRNA
GO:0006364 rRNA processing
GO:0006412 translation
GO:0007004 telomere maintenance via telomerase
GO:0031118 rRNA pseudouridine synthesis
GO:0031120 snRNA pseudouridine synthesis
GO:0042254 ribosome biogenesis
GO:1904874 positive regulation of telomerase RNA localization to Cajal body

Cellular Component:
GO:0000784 nuclear chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005697 telomerase holoenzyme complex
GO:0005730 nucleolus
GO:0005732 small nucleolar ribonucleoprotein complex
GO:0015030 Cajal body
GO:0031429 box H/ACA snoRNP complex
GO:0072589 box H/ACA scaRNP complex
GO:0090661 box H/ACA telomerase RNP complex
GO:0022625 cytosolic large ribosomal subunit

-  Descriptions from all associated GenBank mRNAs
  AF401217 - Homo sapiens NHP2-like protein mRNA, partial cds.
AK000486 - Homo sapiens cDNA FLJ20479 fis, clone KAT07382.
BC000009 - Homo sapiens NHP2 ribonucleoprotein homolog (yeast), mRNA (cDNA clone MGC:1038 IMAGE:3505294), complete cds.
AF161404 - Homo sapiens HSPC286 mRNA, partial cds.
AJ293309 - Homo sapiens mRNA for NHP2 protein.
BC006387 - Homo sapiens NHP2 ribonucleoprotein homolog (yeast), mRNA (cDNA clone MGC:13306 IMAGE:4109843), complete cds.
JD314398 - Sequence 295422 from Patent EP1572962.
AF401219 - Homo sapiens small nucleolar RNA binding-like protein NHP2 mRNA, complete cds.
JD121582 - Sequence 102606 from Patent EP1572962.
DL492461 - Novel nucleic acids.
DL490938 - Novel nucleic acids.
KJ894227 - Synthetic construct Homo sapiens clone ccsbBroadEn_03621 NHP2 gene, encodes complete protein.
KR709795 - Synthetic construct Homo sapiens clone CCSBHm_00006143 NHP2 (NHP2) mRNA, encodes complete protein.
KR709796 - Synthetic construct Homo sapiens clone CCSBHm_00006144 NHP2 (NHP2) mRNA, encodes complete protein.
CR457238 - Homo sapiens full open reading frame cDNA clone RZPDo834A069D for gene NOLA2, nucleolar protein family A, member 2 (H/ACA small nucleolar RNPs); complete cds, incl. stopcodon.
DQ600392 - Homo sapiens piRNA piR-38458, complete sequence.
DQ596835 - Homo sapiens piRNA piR-34901, complete sequence.
JD020228 - Sequence 1252 from Patent EP1572962.
JD030499 - Sequence 11523 from Patent EP1572962.
JD025846 - Sequence 6870 from Patent EP1572962.
JD035005 - Sequence 16029 from Patent EP1572962.
JD467317 - Sequence 448341 from Patent EP1572962.

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

Protein Q9NX24 (Reactome details) participates in the following event(s):

R-HSA-6790905 Box H/ACA snoRNP transforms uridine to pseudouridine in pre-rRNA
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: A6NKY8, HSPC286, NHP2_HUMAN, NM_017838, NOLA2, NP_060308, Q9NX24, Q9P095
UCSC ID: uc003mir.2
RefSeq Accession: NM_017838
Protein: Q9NX24 (aka NHP2_HUMAN)
CCDS: CCDS4432.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene NHP2:
dkc (Dyskeratosis Congenita)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_017838.3
exon count: 4CDS single in 3' UTR: no RNA size: 867
ORF size: 462CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1072.00frame shift in genome: no % Coverage: 98.50
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.