This page contains a list of the genes, transposons and other repeats thus far identified from the annotation of sequenced BACs. The genes are placed in one of three groups: Putative genes with good to exact hits to sequences of known function, Predicted genes which are identical to an EST yet have no ascribed function, and Hypothetical genes which have no database match. The Gene Family heading in the first table below serves as a label for that group of sequences and may be linked to a type of review of those sequences. The entries under the BAC Identification heading provide links to the pages discussing that particular gene. If a gene is known to exhibit more than one function or is known to affect a second cellular process, that gene is listed under more than one Gene Family. As our annotation progresses, we will write and install more reviews of gene families and transposon groups and provide links to pages for each individual gene.
Follow this link to view a list of the annotation tools we use.
Gene Family |
Gene Name |
BAC Identification |
| Acetyl Transferase | similar to serine acetyl transferases | T17A5.1 |
| Acyl-carrier Proteins | similar to Brassica sp. acyl-carrier proteins, e.g., B. campestris ACP, Y00418 | T21B4.6 |
| Amino Acid Metabolism | ||
| putative chloroplast prephenate dehydratase (Phe) | T32N15.11 | |
| similar to prolyl 4-hydroxylase alpha (Pro) | T17A5.10 | |
| putative serine hydroxymethyltransferase (Ser) | F2P16.3 | |
| similar to Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase (Ser) | F2P16.25 | |
| putative tryptophan synthase alpha 1-like protein (Trp) | T10P11.11 | |
| AMP-binding protein | similar to other AMP-binding enzymes, possible fatty acyl-CoA synthetase | T17A5.12 |
| Aspartyl Protease | putative aspartyl protease | T17A5.8 |
| Calcium/calmodulin-binding | calmodulin-domain protein kinase isoform 6 | F5J6.5 |
| putative calmodulin-domain protein kinase | T13L16.9 | |
| putative calmodulin-binding protein | F2P16.9 | |
| Ca++ Pump | putative Ca++ ion pump/ATPase | T18A10.4 |
| Cell Cycle | similar to cullin family of cell cycle regulators | T10P11.14.1 |
| PROLIFERA | T10M13.7 | |
| Chaperone | similar to DnaJ proteins | T21B4.9 |
| putative DnaJ-like chaperonin | T13L16.10 | |
| Chloroplast Envelope | putative chloroplast outer envelope 86-like protein | T10P11.19 |
| Citric Acid Cycle | NAD+-dependent isocitrate dehydrogenase subunit 2 | F6P23.14 |
| Cold Shock | putative glycine-rich, zinc-finger DNA-binding protein | T13L16.11 |
| Cytochrome P450 | putative cytochrome P450 | F5I10.21 |
| Cytoskeleton | microfibrillar-associated protein | T3F12.11 |
| putative kinesin-like protein | T32N15.10 | |
| similar to A. thaliana kat family of kinesin-like, microtubule-binding proteins | F2P16.12 | |
| putative cyto- or nucleo-skeletal component, similar to S. cerevisae nuf1 and myosin heavy chain | T21B4.7 | |
| Disease Resistance | putative leucine-rich repeat disease resistance gene | F6P23.8 |
| putative leucine-rich repeat disease resistance gene | F6P23.9 | |
| similar to barley mlo | T10P11.12 | |
| putative mlo homolog | F5J6.19 | |
| putative mlo homolog | F5J6.23 | |
| DNA-binding proteins | (also see Transcription Factors) | |
| similar to A. thaliana AR411 DNA-binding protein | F2N1.6 | |
| G-box binding factor 2 | F2N1.12 | |
| similar to A. thaliana CCA1 DNA-binding protein | F2N1.20 | |
| putative zinc-finger protein | T18A10.2 | |
| putative G-box binding protein, similar to RAP1 | T18A10.7 | |
| putative zinc-finger protein | T10M13.1 | |
| putative zinc-finger protein | T10M13.22 | |
| putative zinc-finger protein | T10P11.4 | |
| putative bZIP-like DNA-binding protein | T10P11.9 | |
| putative RING zinc-finger protein | F5J6.21 | |
| putative NAM/no apical meristem protein | F6P23.7 | |
| putative zinc-finger protein | T3F12.10 | |
| putative WD-repeat-like/CDC20-like protein | F2P16.8 | |
| similar to C3HC4-type zinc fingers | T17A5.9 | |
| putative glycine-rich, zinc-finger DNA-binding protein | T13L16.11 | |
| DNA Repair | putative G/T mismatch repair enzyme | T10M13.8 |
| DNA Replication | PROLIFERA | T10M13.7 |
| Drought-induced | putative drought-induced-19-like 1 | T10M13.20 |
| putative drought-induced-19-like 2 | F2P16.10 | |
| Electron Transport | predicted NADH dehydrogenase 24 kDa subunit | T10P11.14 |
| NADPH thioredoxin reductase (Z23108) | F5J6.18 | |
| Flowering | LUMINIDEPENDENS | T10P11.15 |
| Glucosyl Transferase | putative UTP-glucose glucosyltransferase | F2N1.15 |
| Glutathione S Transferase | Atpm24.1 | T10P11.18 |
| Glycosyl Transferase | predicted glycosyl transferase | T10M13.14 |
| Glycosylation | predicted glycosyl hydrolase | F5J6.15 |
| GTP-binding Protein | ARAC1 GTP-binding protein | T17A5.6 |
| Histidine Kinase | putative histidine kinase | T13L16.16 |
| Histone Deacetylase | putative histone deacetylase | T32N15.8 |
| Hormone Respsonsive | putative auxin-induced mRNA | T18A10.6 |
| Isoprenoid Biosynthesis | 3-hydroxy-3-methylglutaryl-CoA reductase | F5J6.13 |
| Leucine-rich Protein | predicted leucine-rich protein | F6P23.14.1 |
| Ligand-gated Ion Channel | similar to ligand-gated channel proteins | F5J6.2 |
| similar to F5J6.2 (putative ligand-gated ion channel protein) | T21B4.3 | |
| Membrane Protein | (also see Chloroplast Envelope) | |
| similar to S. cerevisiae probable membrane protein YPR011c | F2N1.16 | |
| transmembrane protein, TMP-C | F5I10.2 | |
| putative membrane-associated protein | F5I10.20 | |
| putative receptor similar to receptor portion of receptor-linked protein kinases | F5I10.16 | |
| Nodule-specific Protein | putative early nodule-specific (ENOD8)-like protein | F2N1.17 |
| Nuclear Pore Component | putative nuclear pore complex protein | T13L16.1 |
| Nucleolar Proteins | similar to S. cerevisiae Sik1p and human hNop56 nucleolar protein | T21B4.12 |
| similar to S. cerevisiae Sik1p and human hNop56 nucleolar protein | T21B4.13 | |
| Nucleoskeleton | putative cyto- or nucleo-skeletal component, similar to S. cerevisiae nuf1 and myosin heavy chain | T21B4.7 |
| Nucleotide Biosynthesis | putative CTP synthase/UTP ammonia ligase | T10M13.13 |
| Pathogenesis | putative pathogenesis-related protein ATOZI1 | T18A10.21 |
| AtKAP alpha protein | T10M13.16 | |
| putative thaumatin-like pathogenesis-related protein | T13L16.12 | |
| Pattern Formation | putative curlyleaf-like 1 protein | T10M13.3 |
| LUMINIDEPENDENS | T10P11.15 | |
| putative NAM/no apical meristem protein | F6P23.7 | |
| Pectinesterase | putative pectinesterase-like protein | F2P16.5 |
| Phosphate Transport | putative Na+-dependent inorganic phosphate co-transporter | F5I10.21.1 |
| similar to mitochondrial phosphate translocator | F5J6.3 | |
| Phosphatidylinositol Kinase | putative phosphatidylinositol-4-phosphate-5-kinase a type I | F2N1.9 |
| Phosphoglyceride Transfer | putative phosphoglyceride transfer protein | T3F12.1 |
| Phospholipase | putative phospholipase D | F5I10.13 |
| Physical Impedence | putative physical impedence protein | T13L16.14 |
| Protease | putative zinc metalo-protease (STE24-like) | F2N1.21 |
| putative aspartyl protease | T17A5.8 | |
| mitochodrial LON protease | F2P16.23 | |
| putative serine protease | T13L16.2 | |
| Protein Kinase | MAP kinase | F2N1.2 |
| putative ser/thr protein kinase, most similar to T10P11.10 | F2N1.22 | |
| putative receptor-linked ser/thr protein kinase | T18A10.18 | |
| putative receptor-linked ser/thr protein kinase | T18A10.19 | |
| putative ser/thr protein kinase | F5I10.8 | |
| putative light repressible protein kinase | F5I10.14 | |
| receptor-like protein kinase B | F5I10.19 | |
| putative serine/threonine protein kinase | T10M13.2 | |
| putative serine/threonine protien kinase | T10P11.10 | |
| calmodulin-domain protein kinase isoform 6 | F5J6.5 | |
| putative calmodulin-domain protein kinase | T13L16.9 | |
| ASK alpha shaggy-like ser/thr protein kinase | F2P16.21 | |
| similar to serine/threonine protein kinase | T17A5.2 | |
| Protein Transport | clathrin adaptor protein small subunit | F5J6.14 |
| Reverse Transcriptase | similar to Tal-1 reverse transcriptase | T13L16.7 |
| RNA-binding Protein | putative poly(A)-binding protein | T18A10.14 |
| Ribosomal Protein | putative L5 ribosomal protein | F2N1.3 |
| putative acidic ribosomal phosphoprotein P1 | T18A10.9 | |
| cytosolic ribosomal protein S4 | F5J6.12 | |
| Seed Imbibition | putative seed imbibition protein | F2N1.5 |
| Senescence | putatative senescence-associated rhodanese-like protein | T13L16.13 |
| Na+/H+ Pump | putative sodium/hydrogen exchanger | T21B4.4 |
| Na+/Pi Co-transport | putative Na+-dependent inorganic phosphate co-transporter | F5I10.21.1 |
| Steroid Biosynthesis | putative obtusifoliol 14-a demethylase | F5J6.9 |
| Sugar Transport | putative hexose transporter protein | T10M13.6 |
| Sulfate Transport | sulfate transporter | T10P11.3 |
| putative sulfate transporter | T3F12.7 | |
| Syntaxin | putative syntaxin-like | F2P16.16 |
| putative syntaxin-like | T10M13.19 | |
| Tetracycline Transporter-like | putative tetracycline transporter-like protein | F6P23.1 |
| putative tetracycline transporter-like protein | F6P23.2 | |
| Thaumatin | putative thaumatin-like pathogenesis-related protein | T13L16.12 |
| Transcription Factor | putative curlyleaf-like 1 protein | T10M13.3 |
| putative bZIP-like transcription factor | F6P23.12 | |
| putative NAM/no apical meristem protein | F6P23.7 | |
| tRNA Synthetase | similar to glycyl tRNA synthetase | T32N15.9 |
| putative threonyl-tRNA synthetase | F2P16.7 | |
| UTP | putative UTP-glucose glucosyltransferase | F2N1.15 |
| Vesicular Transport | SAR1/GTP-binding secretory factor | T10M13.9 |
| putative vacuolar trafficking component (similar to mouse beige protein product) | T10P11.7 | |
| similar to mouse MEM3 and S. cerevisiae vacuolar sorting protein 35 | T17A5.7 | |
| Zinc-Finger Protein | putative zinc-finger protein | T18A10.2 |
| putative zinc-finger protein | T10M13.1 | |
| putative zinc-finger protein | T10M13.22 | |
| putative zinc-finger protein | T10P11.4 | |
| putative RING zinc-finger protein | F5J6.21 | |
| putative bZIP-like transcription factor | F6P23.12 | |
| putative zinc-finger protein | T3F12.10 | |
| similar to C3HC4-type zinc fingers | T17A5.9 | |
| putative zinc-finger protein neighboring Tal-1-like reverse transcriptase | T13L16.6 | |
| putative Bop-like zinc-finger protein | T13L16.8 | |
| putative glycine-rich, zinc-finger DNA-binding protein | T13L16.11 |
PREDICTED PROTEINS
BAC Identification |
EST Identification |
|
| predicted protein of unknown function | F2N1.1 | EST AA395515 |
| predicted protein of unknown function | F2N1.31 | ESTs Z35621, T44720, T22670, & T41991 |
| predicted protein of unknown function | F2N1.4 | EST |
| predicted protein of unknown function similar to T18A10.12 | F2N1.25 | EST |
| predicted protein of unknown function, similar to hypothetical protein F5J6.22 | T18A10.3 | EST |
| predicted protein of unknown function, similar to F2N1.25 | T18A10.12 | EST |
| predicted protein of unknown function | F5I10.4 | EST N96903 |
| predicted protein of unknown function | F5I10.17 | EST Z29119 |
| predicted protein of unknown function | T10M13.5 | EST N65123 |
| predicted protein of unknown function | T10M13.12 | rice EST D40083 |
| predicted protein of unknown function | T10M13.15 | similar to Z27280 & H76976 |
| predicted protein of unknown function | T10P11.1 | EST Z26196 |
| predicted protein of unknown function | T10P11.2 | EST T22660 & W43884 |
| predicted protein of unknown function | T10P11.16 | EST T41762 |
| predicted protein of unknown function | T10P11.17 | EST W43350 & T45153 |
| predicted protein of unknown function | T10P11.20 | EST N96444 |
| predicted protein of unknown function | F5J6.4 | EST |
| predicted protein similar to F5J6.10 | F5J6.8 | |
| predicted protein similar to F5J6.8 | F5J6.10 | |
| predicted protein of unknown function | F5J6.17 | EST |
| predicted protein of unknown function | F6P23.3 | gene F6P23.4 |
| predicted protein | F6P23.4 | EST T43411 |
| predicted protein of unknown function | F6P23.13 | ESTs H36005 and N65517 |
| predicted protein of unknown function | F2P16.4 | EST |
| predicted protein of unknown function | F2P16.22 | EST |
| predicted protein with similarity to hypothetical proteins of S. pombe and S. cerevisiae | T21B4.14 | EST |
HYPOTHETICAL PROTEINS
BAC Identification |
|
| hypothetical protein, similar to F20P5.5 | F2N1.14 |
| similar to A. thaliana hypothetical protein U19925 | F2N1.18 |
| hypothetical protein with homology to several A. thaliana proteins, best is T28M21.21 | F2N1.27 |
| hypothetical protein with similarity to T1B8.1 and T1B8.7 | F2N1.30 |
| hypothetical protein, similar to F5I10.6 and F5I10.12 | F2N1.32 |
| hypothetical protein, shows weak similarity to Z. mays extensin-like protein (Z34465) | T18A10.5 |
| hypothetical protein with similarity to mRNA expressed in mouse islet cells (Z47777) | T18A10.8 |
| hypothetical protein, similar to B. campestris EST L38241 | T18A10.13 |
| similar to human SYT, implicated in formation of synovial sarcoma | T18A10.22 |
| similar to castor bean EST T24242 | F5I10.1 |
| hypothetical protein similar to F5I10.12 | F5I10.6 |
| hypothetical protein similar to F5I10.6 | F5I10.12 |
| hypothetical protein similar to F19K23.19 | F5J6.7 |
| hypothetical protein similar to F6P23.10.1 | F6P23.10 |
| hypothetical protein similar to F6P23.10 | F6P23.10.1 |
| hypothetical protein with some protein kinase motifs | F6P23.11 |
| hypothetical protein with predicted heme-binding domain | T32N15.7 |
| similar to F2P16.19 and 89000 region of T21B4 | F2P16.17 |
| similar to F2P16.17 and 89000 region of T21B4 | F2P16.19 |
| similarity to orfs between putative ADP-glucose pyrophosphorylase subunit SH2 and putative NADPH-dependent reductase A1 genes in rice seq. U70541 | F2N1.10 |
| hypothetical protein with similarity to a S. bicolor hypothetical protein | F5I10.22 |
| similar to several other A. thaliana hypothetical proteins and to N. tabacum membrane-associated salt-inducible protein | T21B4.2 |
| similar to several other A. thaliana hypothetical proteins and to N. tabacum membrane-associated salt-inducible protein | T21B4.10 |
| contains similarity to Nicotiana tabacum membrane-associated salt-inducible protein | T17A5.11 |
| contains similarity to Synechococcus PCC7942 chromosomal region used as basis of neutral site II recombinational cloning vector, orf5 | T21B4.11 |
| hypothetical protein | F2N1.8 |
| hypothetical protein | F2N1.11 |
| hypothetical protein | F2N1.13 |
| hypothetical protein | F2N1.19 |
| hypothetical protein | F2N1.24 |
| hypothetical protein | F2N1.26 |
| hypothetical protein | F2N1.28 |
| hypothetical protein | T18A10.1 |
| hypothetical protein | T18A10.10 |
| hypothetical protein | T18A10.11 |
| hypothetical protein | T18A10.16 |
| hypothetical protein | T18A10.17 |
| hypothetical protein | T18A10.20 |
| hypothetical protein | T18A10.23 |
| hypothetical protein | T18A10.24 |
| hypothetical protein | F5I10.3 |
| hypothetical protein | F5I10.5 |
| hypothetical protein | F5I10.9 |
| hypothetical protein similar to a region of light repressible protein kinase | F5I10.10 |
| hypothetical protein | F5I10.11 |
| hypothetical protein | F5I10.15 |
| hypothetical protein | F5I10.18 |
| hypothetical protein | F5I10.23 |
| hypothetical protein | F5I10.24 |
| hypothetical protein | T10M13.4 |
| hypothetical protein | T10M13.10 |
| hypothetical protein | T10M13.11 |
| hypothetical protein | T10M13.17 |
| hypothetical protein | T10M13.18 |
| hypothetical protein | T10M13.21 |
| hypothetical protein | T10P11.5 |
| hypothetical protein | T10P11.6 |
| hypothetical protein | T10P11.8 |
| hypothetical protein | T10P11.13 |
| hypothetical protein | F5J6.1 |
| hypothetical protein | F5J6.6 |
| hypothetical protein | F5J6.11 |
| hypothetical protein | F5J6.16 |
| hypothetical protein | F5J6.20 |
| hypothetical protein | F5J6.22 |
| hypothetical protein | F6P23.6 |
| hypothetical protein | F6P23.15 |
| hypothetical protein | F6P23.16 |
| hypothetical protein | T3F12.2 |
| hypothetical protein | T3F12.3 |
| hypothetical protein | T3F12.4 |
| hypothetical protein | T3F12.5 |
| hypothetical protein | T3F12.6 |
| hypothetical protein containing a mudr-like transposon insertion | T3F12.8 |
| hypothetical protein | T3F12.9 |
| hypothetical protein | T32N15.1 |
| hypothetical protein | T32N15.2 |
| hypothetical protein | T32N15.3 |
| hypothetical protein | T32N15.4 |
| hypothetical protein | T32N15.5 |
| hypothetical protein | T32N15.6 |
| hypothetical protein | T32N15.12 |
| hypothetical protein with similarity to rice EST D47470 | F2P16.6 |
| hypothetical protein | F2P16.13 |
| hypothetical protein | F2P16.14 |
| hypothetical protein | F2P16.15 |
| hypothetical protein | F2P16.18 |
| hypothetical protein | F2P16.20 |
| hypothetical protein | F2P16.24 |
| hypothetical protein | T21B4.5 |
| hypothetical protein | T21B4.8 |
| hypothetical protein | T21B4.15 |
| hypothetical protein | T21B4.16 |
| hypothetical protein | T13L16.2 |
| hypothetical protein | T13L16.4 |
| hypothetical protein | T13L16.5 |
| hypothetical protein | T13L16.15 |
| hypothetical protein | T17A5.4 |
| hypothetical protein | T17A5.3 |
| hypothetical protein similar to hypothetical protein F6P23.6 | T17A5.2.1 |
| hypothetical protein similar to hypothetical proteins F6P23.10 and F6P23.10.1 | T17A5.2.2 |
| hypothetical protein | T17A5.7.1 |
TRANSPOSONS
Identification |
BAC |
| similar to maize Mu3 transposon | F2N1.7 |
| similar to BAC T32N15 | T10M13 |
| non-autonomous transposon | F6P23 |
| Copia-like transposable element | F6P23 |
| non-autonomous transposon similar to BAC F2N1 | T3F12 |
| putative transposon | T10M13 |
| non-autonomous transposon similar to BAC F2N1 and PAC MDJ22 | T3F12 |
| similar to mudr transposon of maize | T3F12 |
| similar to BAC F19P19 and ESSA chromosome IV contig-1 | T3F12 |
| putative non-autonomous transposon | Tn1 of T32N15 |
| del-like retrotransposon | T32N15 |
| Activator-like transposon | T32N15 |
| putative transposon | Tn2 of T32N15 |
| putative transposon | Tn3 of T32N15 |
| similar to zinc-finger protein of Tal1 retrotransposon | F2P16.1 |
| similar to maize mudrA protein and T6B20.1 | T21B4.1 |
| similar to Tal-1 retrotransposon | T13L16.6 and T13L16.7 |
tRNA Genes
tRNA |
BAC |
| His | T10M13 |
| Ile | T13L16 |
| Ile | T17A5 |