Gene Structure Analysis

General

GenLang (finds introns, exons and other gene features)
NetPlantGene (predict splice sites)
RepeatMasker (repeat detection in genomic sequence)
ORF finder (search for open reading frames in DNA sequence)
WebGene (prediction of  gene structure, TATA boxes, poly-A sites and splice sites)
Internet Resources for UTR analysis (databases of UTR sequence and search tools for detecting UTR functional elements)
Restrict (Finds restriction enzyme cleavage sites)

Promoter Analysis

PLACE (search for known plant cis-acting elements)
PlantCARE (search for known plant cis-acting elements)
PROSCAN (detection of Eukaryotic promoter regions in genomic DNA)
Improbizer (novel motif detection using multiple sequences)
MEME (novel motif detection using multiple sequences)
MotifMatcher (find a known motif in a sequence)
MAST (search for a motif in a database, uses MEME output format)
Dnanalyze (TF mapping)
Dragon Promoter Finder 1.2 (TSS finder and promoter region analysis)
FunSiteP 2.1
HCtata (TATA signal prediction)
McPromoter Ver.3
MatInspector (Search for TF binding sites)
ModelGenerator and ModelInspector
NNPP2.1 (TSS finder)
PromoterInspector (Strand non-specific promoter region finder)
Promoter2.0 (TSS finder)
Promoter Scan II (Promoter region prediction)
RGSiteScan
Signal Scan (Search for Eukaryotic Transcriptional Elements)
TESS (Search for Transcription Elements)
TFSEARCH (Predicts TF binding sites based on TRANSFAC data)
TRANSFAC (TF database and a number of associated programs)
TSSG and TSSW

UTR Analysis

UTR Home Page
UTR Database ( A specialized sequence collection, deprived from redundancy, of 5' and 3' UTR sequences from eukaryotic mRNAs)
UTRSite (A collection of functional sequence patterns located in 5' or 3' UTR sequences)
UTR Scan (Looks for UTR functional elements by searching through user submitted query sequences for the patterns defined in the UTRsite collection)
UTR Blast (Searches for similarity between a query sequence and 5' or 3' UTR sequences in UTRdb collections)

ORF Analysis

ORF finder (search for open reading frames in DNA sequence)