Some websites for genomics, transcriptomes, and

transcription factor databases and tools

For gene descriptions, alternative annotation, isoforms, pathways, and expression data

NIH genetic sequence database:

Annotation of alternative RNA and gene isoforms & tissue-specific expression:

NCBI Gene Expression Omnibus:

General design of DNA primers:

GEO datasets for functional genomics:

DAVID functional annotation:

GeneCards (now has a fee for GO analysis):

GREAT functional annotation that also considers genes that are nearby even if they are not the
closest gene to DNA regions of interest:

Transcription factor (TF) binding sites:

In UCSC Genome Browser, rodent/human conserved TFBS, and ChIP-seq observed TFBS
(both are limited datasets but often useful):

CTCF searchable database: CTCFBSDB

Enhancers that were in vivo tested (and negative tested candidates):

CisFinder, identification of DNA overrepresented motifs:

CpG Island Searcher:

Finding restriction enzymes for a given recognition site or sequence:

Effects of CpG methylation on restriction enzyme cleavage:

Comparing cis elements between genes or within a conserved sequence:

Tm calculator:!/

miRBase, A searchable database of published miRNA sequences and annotation:

TarBase, The largest manually curated target database, indexing more than 65,000 miRNA-gene

TF binding and expression including diverse ncRNA genes: