An Ensembl search (February 1, 2006). Category: Data mining
While working on a microarray experiement with a researcher, we had to find a bit of information about a gene with the gene symbol NCOA3. We went to the Ensembl web site (www.ensembl.org) and did a search which yielded the following information.
2. Ensembl Gene: ENSG00000124151
Ensembl gene ENSG00000124151 has 3 transcripts: ENST00000262979, ENST00000340189, ENST00000341724 and associated peptides: ENSP00000262979, ENSP00000342123, ENSP00000345671
Nuclear receptor coactivator 3 (EC 2.3.1.48) (NCoA-3) (Thyroid hormone receptor activator molecule 1) (TRAM-1) (ACTR) (Receptor-associated coactivator 3) (RAC-3) (Amplified in breast cancer-1 protein) (AIB-1) (Steroid receptor coactivator protein 3) (SRC- [Source:Uniprot/SWISSPROT;Acc:Q9Y6Q9]
The gene has the following external identifiers mapped to it:
Affymx Microarray U133: g2565049_3p_a_at, 207700_s_at, g2318005_3p_a_at, Hs.225977.1.A2_3p_a_at, g5729725_3p_a_at, 211352_s_at, 209062_x_at, 209060_x_at
CCDS: CCDS13406, CCDS13407.1, CCDS13407, CCDS13406.1
EMBL: AL034418, AF012108, AB209863, BC092516, AF010227, AF036892, AF016031
EntrezGene: 8202
GO: GO:0005634, GO:0046966, GO:0007165, GO:0004402, GO:0030528, GO:0030521, GO:0045893, GO:0008415, GO:0050681, GO:0005515, GO:0003713, GO:0016740, GO:0004871
HGNC Symbol: NCOA3, 7670
IPI: IPI00220081, IPI00069270.1, IPI00220079, IPI00220082.1, IPI00220079.1, IPI00220081.1, IPI00220082, IPI00220080.1, IPI00069270, IPI00220080
MIM: 601937
PDB: 1KBH
Predicted UniProt/TrEMBL: Q59EE8, Q59EE8_HUMAN, Q569F6, Q569F6_HUMAN
Protein ID: CAC17693.1, BAD93100, AAB92368, CAI42141.1, AAC51849, AAC51849.1, AAC51677, AAC51663, AAB92368.1, CAI42141, BAD93100.1, AAC51677.1, AAC51663.1, CAB40662, CAC17693, AAH92516, CAB40662.1, AAH92516.1
RefSeq DNA: NM_006534, NM_006534.2, NM_181659, NM_181659.1
RefSeq peptide: NP_858045.1, NP_006525.2, NP_006525, NP_858045
UniGene: Hs.382168
UniProt/Swiss-Prot: Q9Y6Q9, NCOA3_HUMAN
Geneview: http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000124151
ContigView: http://www.ensembl.org/Homo_sapiens/contigview?gene=ENSG00000124151
I want to use this example as an excuse to try to document the various naming conventions used in genetics. As you can see from my previous weblog entries, this is something I have tried to do in the past, but have just been too busy to follow-up on.
Previous weblog entries on this topic:
This webpage was written by Steve Simon and was last modified on 07/08/2008.