Protein:NT5C3A |
Protein Summary |
 Gene summary |
| Gene name: NT5C3A | ASpdb.0 ID: 51251 | Gene | Gene symbol | NT5C3A | Gene ID | 51251 |
| Gene name | 5'-nucleotidase, cytosolic IIIA |
| Synonyms | NT5C3|P5'N-1|P5N-1|PN-I|POMP|PSN1|UMPH|UMPH1|cN-III|hUMP1|p36 |
| Cytomap | 7p14.3 |
| Type of gene | protein-coding |
| Description | cytosolic 5'-nucleotidase 3A5'-nucleotidase, cytosolic III7-methylguanosine phosphate-specific 5'-nucleotidasecytosolic 5'-nucleotidase 3lupinpyrimidine 5'-nucleotidase 1uridine 5'-monophosphate hydrolase 1 |
| Modification date | 20240305 |
| UniProtAcc | Q9H0P0 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | NT5C3A | GO:0005654 | nucleoplasm | - |
| Gene | NT5C3A | GO:0005737 | cytoplasm | 8557639 |
| Gene | NT5C3A | GO:0005783 | endoplasmic reticulum | 8557639 |
| Gene | NT5C3A | GO:0005829 | cytosol | - |
| Gene | NT5C3A | GO:0008253 | 5'-nucleotidase activity | 10942414 |
| Gene | NT5C3A | GO:0016604 | nuclear body | - |
| Gene | NT5C3A | GO:0051607 | defense response to virus | 21478870 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| Q9H0P0-4 | Q9H0P0-4_2vkq_A.pdb | 2VKQ | X-ray | 2.5 | A | 64 | 336 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| Q9H0P0 | NT5C3A | Q9H0P0-4 | Q9H0P0-1 | 336 | 297 | 1 | 50 | Substitution | MRAPSMDRAAVARVGAVASASVCALVAGVVLAQYIFTLKRKTGRKTKIIE | MTNQESAVHVK | 1 | 11 |
| Q9H0P0 | NT5C3A | Q9H0P0-4 | Q9H0P0-2 | 336 | 286 | 1 | 50 | Deletion | none | none | 0 | 0 |
| Q9H0P0 | NT5C3A | Q9H0P0-4 | Q9H0P0-3 | 336 | 285 | 1 | 51 | Deletion | none | none | 0 | 0 |
| Multiple sequence alignment of our canonical and alternatively spliced NT5C3A |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of NT5C3A |
| UniProt-id | ENSG | ENST | ENSP |
| Q9H0P0-1 | ENSG00000122643.23 | ENST00000643244.1 | ENSP00000496364.1 |
| Q9H0P0-3 | ENSG00000122643.23 | ENST00000409467.6 | ENSP00000387166.1 |
| UniProt-id | NM ID | NP ID |
| Q9H0P0-1 | NM_001002009.2 | NP_001002009.1 |
| Q9H0P0-1 | NM_016489.12 | NP_057573.2 |
| Q9H0P0-3 | NM_001166118.2 | NP_001159590.1 |
| Amino acid sequences of our canonical and alternatively spliced NT5C3A |
| accession_id | Protein sequence |
| Q9H0P0-4 | MRAPSMDRAAVARVGAVASASVCALVAGVVLAQYIFTLKRKTGRKTKIIEMMPEFQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFD MTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVM LKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNFMDFDETGVLKGFKGELIHVFNKHDGALRNTEYFNQLKDNS |
| Q9H0P0-1 | MTNQESAVHVKMMPEFQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKE KYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGV YHPNVKVVSNFMDFDETGVLKGFKGELIHVFNKHDGALRNTEYFNQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLE |
| Q9H0P0-2 | MMPEFQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVL TVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNF MDFDETGVLKGFKGELIHVFNKHDGALRNTEYFNQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLV |
| Q9H0P0-3 | MPEFQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLT VEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNFM DFDETGVLKGFKGELIHVFNKHDGALRNTEYFNQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVQ |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| NT5C3A (go to UniProt):Q9H0P0 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
Gene Isoform Structures and Expression Levels for NT5C3A |
| Gene structures of our canonical and alternative spliced genes of NT5C3A * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of Q9H0P0-4 |
| 3D view using mol* of Q9H0P0-1 |
| 3D view using mol* of Q9H0P0-2 |
| 3D view using mol* of Q9H0P0-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of Q9H0P0-4 |
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| pLDDT distribution across the protein length of Q9H0P0-1 |
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| pLDDT distribution across the protein length of Q9H0P0-2 |
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| pLDDT distribution across the protein length of Q9H0P0-3 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of Q9H0P0-4 |
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| Ramachandran plot of Q9H0P0-3 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| Q9H0P0-4 | 1.044 | 379 | 0.999 | 866.075 | 0.459 | 0.764 | 1.005 | 0.5 | 1.224 | 0.409 | 0.644 | 88,90,91,96,101,102,103,104,105,107,108,109,111,11 2,113,114,118,121,122,124,125,127,128,132,135,136, 137,138,139,140,141,142,145,152,153,156,157,173,17 6,177,178,203,204,205,249,250,252,253,277,278,279, 280,281,283,299,300,301,302,303,306,307,310,311 |
| Q9H0P0-1 | 1.024 | 382 | 0.994 | 771.064 | 0.51 | 0.735 | 0.928 | 0.349 | 1.186 | 0.294 | 0.769 | 49,51,52,57,63,65,66,68,69,72,73,74,75,76,82,83,85 ,86,88,89,93,96,97,98,99,101,102,103,104,106,107,1 13,114,117,130,133,134,137,138,139,165,166,210,211 ,212,213,214,238,239,240,241,242,244,260,261,262,2 63,264,267,268,270,271,272 |
| Q9H0P0-2 | 1.025 | 384 | 1.021 | 796.446 | 0.482 | 0.735 | 0.948 | 0.57 | 1.104 | 0.517 | 0.855 | 38,40,41,46,51,52,53,54,55,57,58,59,61,62,63,64,65 ,71,74,75,77,78,82,85,86,87,88,89,90,91,92,93,95,9 6,102,103,106,119,122,123,126,127,128,153,154,155, 199,200,201,202,203,204,227,228,229,230,231,233,24 9,250,251,252,253,257,260,261 |
| Q9H0P0-3 | 1.05 | 359 | 1.001 | 722.015 | 0.441 | 0.772 | 0.999 | 0.39 | 1.235 | 0.316 | 0.688 | 37,39,40,45,50,51,52,53,54,56,57,58,60,61,62,63,64 ,70,73,74,76,77,81,84,85,86,87,89,90,91,94,101,102 ,105,118,121,122,125,126,127,153,154,198,199,201,2 26,227,228,229,230,248,249,250,251,252,255,256,258 ,259,260 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of Q9H0P0-4_Q9H0P0-4_2vkq_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9H0P0-4_2vkq_A_Q9H0P0-1.pdb |
| 3D view using mol* of Q9H0P0-4_2vkq_A_Q9H0P0-2.pdb |
| 3D view using mol* of Q9H0P0-4_2vkq_A_Q9H0P0-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9H0P0-4_Q9H0P0-1.pdb |
| 3D view using mol* of Q9H0P0-4_Q9H0P0-2.pdb |
| 3D view using mol* of Q9H0P0-4_Q9H0P0-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q9H0P0-4_vs_Q9H0P0-1.png |
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| ./stats/secondary_structure/figure/Q9H0P0-4_vs_Q9H0P0-2.png |
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| ./stats/secondary_structure/figure/Q9H0P0-4_vs_Q9H0P0-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q9H0P0-4_vs_Q9H0P0-1.png |
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| ./stats/relative_asa/Q9H0P0-4_vs_Q9H0P0-2.png |
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| ./stats/relative_asa/Q9H0P0-4_vs_Q9H0P0-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to NT5C3A |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to NT5C3A |
| Previous studies relating to the alternative splicing of NT5C3A and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| NT5C3A | 10984440 | Physical and genetic interaction of filamin with presenilin in Drosophila. | Presenilins were first identified as causative factors in early onset, familial Alzheimer's Disease (FAD). They are predicted to encode a highly conserved novel family of eight transmembrane domain proteins with a large hydrophilic loop between TM6 and TM7 that is the site of numerous FAD mutations. Here, we show that the loop region of Drosophila and human presenilins interacts with the C-terminal domain of Drosophila filamin. Furthermore, we show that Drosophila has at least two major filamin forms generated by alternative splicing from a gene that maps to position 89E10-89F4 on chromosome 3. The longest form is enriched in the central nervous system and ovaries, shares 41.7% overall amino acid identity with human filamin (ABP-280) and contains an N-terminal actin-binding domain. The shorter form is broadly expressed and encodes an alternatively spliced form of the protein lacking the actin-binding domain. Finally, we show that presenilin and filamin are expressed in overlapping patterns in Drosophila and that dominant adult phenotypes produced by overexpression of presenilin can be suppressed by overexpression of filamin in the same tissue. Taken together, these results suggest that presenilin and filamin functionally interact during development. | D000544 | Alzheimer Disease |
| NT5C3A | 11369620 | Genetic basis of hemolytic anemia caused by pyrimidine 5' nucleotidase deficiency. | Pyrimidine 5' nucleotidase (P5'N-1) deficiency is an autosomal recessive condition causing hemolytic anemia characterized by marked basophilic stippling and the accumulation of high concentrations of pyrimidine nucleotides within the erythrocyte. It is implicated in the anemia of lead poisoning and is possibly associated with learning difficulties. Recently, a protein with P5'N-1 activity was analyzed and a provisional complementary DNA (cDNA) sequence published. This sequence was used to study 3 families with P5'N-1 deficiency. This approach generated a genomic DNA sequence that was used to search GenBank and identify the gene for P5'N-1. It is found on chromosome 7, consists of 10 exons with alternative splicing of exon 2, and produces proteins 286 and 297 amino acids long. Three homozygous mutations were identified in this gene in 4 subjects with P5'N-1 deficiency: codon 98 GAT-->GTT, Asp-->Val (linked to a silent polymorphism codon 92, TAC-->TAT), codon 177, CAA-->TAA, Gln-->termination, and IVS9-1, G-->T. The latter mutation results in the loss of exon 9 (201 bp) from the cDNA. None of these mutations was found in 100 normal controls. The DNA analysis was complicated by P5'N-1 pseudogenes found on chromosomes 4 and 7. This study is the first description of the structure and location of the P5'N-1 gene, and 3 mutations have been identified in affected patients from separate kindreds. (Blood. 2001;97:3327-3332) | D000743 | Anemia, Hemolytic |
Clinically important variants in NT5C3A |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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