Table 3.

Protein-Coding Genes Corresponding to Small RNAs

AnnotationAccession
 NumberaChromosome
 (Small RNA Start Position)bSmall
 RNAcSmall RNA
 OrientationPosition
 in GenedESTse
Inorganic phosphate transporterAt1g20860I (7255467)23.1AntisenseIntron
Cytochrome P450At1g47630I (16956099)104.1SenseCR-intron
Hypothetical protein, no known similaritiesAt1g79970I (29737207)
 I (29737208)107.1
 14.1Antisense
 AntisenseIntron
 Intron+
Weak cathepsin L similarityAt2g39160II (16282272)40AntisenseCR
Zinc-finger/BTB domain–containing proteinAt2g40440II (16839165)17.2fAntisenseIntron
F-box–containing proteinAt3g21170III (7420343)97SenseCR
Scarecrow-likeAt4g00150IV (57411)39.1AntisenseCR+
Scarecrow-likeAt3g60630III (22420503)39.2AntisenseCR
Scarecrow-likeAt2g45160II (18567669)39.4AntisenseCR+
Hypothetical protein, similar to nuclear protein in riceAt4g18980IV (9360949)24.19SenseIntron
Hypothetical protein, no known similaritiesAt4g27930IV (12867464)55AntisenseCR
Ser carboxypeptidase–likeAt5g22960V (7660496)
 V (7659853)
 V (7659933)
 V (7660416)90.1
 90.2
 101.1
 101.2Sense
 Antisense
 Sense
 AntisenseIntron
 CR
 CR
 Intron
Hypothetical protein, no known similaritiesAt5g56070V (22423005)2.2AntisenseCR
Hypothetical protein, no known similaritiesAt5g49590V (19422956)105.2AntisenseIntron
Hypothetical protein, no known similaritiesAt4g34690IV (15520101)124AntisenseCR
SKI2-like RNA helicase proteinAt5g61140V (24315538)110.2SenseIntron+
  • a Determined by BLAST search with the small RNA sequence.

  • b First nucleotide position in the chromosome corresponding to the small RNA sequence.

  • c Unique code for each small RNA or small RNA locus.

  • d Location of the corresponding small RNA sequence in the gene. CR, coding region.

  • e +, EST in GenBank; −, no EST in GenBank.

  • f Small RNA 17 contained a single mismatch relative to the published Arabidopsis genome sequence.