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: http://www.ncbi.nlm.nih.gov/genbank/

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

NCBI Gene Expression Omnibus: http://www.ncbi.nlm.nih.gov/geoprofiles/

General design of DNA primers: http://www.ncbi.nlm.nih.gov/tools/primer-blast/

GEO datasets for functional genomics: http://www.ncbi.nlm.nih.gov/geo/

DAVID functional annotation: http://david.abcc.ncifcrf.gov/

GeneCards (now has a fee for GO analysis): http://www.genecards.org/

GREAT functional annotation that also considers genes that are nearby even if they are not the
closest gene to DNA regions of interest: http://bejerano.stanford.edu/great/public/html/index.php

Transcription factor (TF) binding sites: http://www.gene-regulation.com/pub/databases.html

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

CTCF searchable database: CTCFBSDB http://insulatordb.uthsc.edu

Enhancers that were in vivo tested (and negative tested candidates): http://enhancer.lbl.gov/

CisFinder, identification of DNA overrepresented motifs: http://lgsun.grc.nia.nih.gov/CisFinder/

CpG Island Searcher: http://www.uscnorris.com/cpgislands2/cpg.aspx

Finding restriction enzymes for a given recognition site or sequence:
https://www.neb.com/tools-and-resources/interactive-tools/enzyme-finder

http://nc2.neb.com/NEBcutter2/

Effects of CpG methylation on restriction enzyme cleavage: https://www.neb.com/tools-andresources/usage-guidelines/effects-of-cpg-methylation-on-restriction-enzyme-cleavage

Comparing cis elements between genes or within a conserved sequence:
http://genometrafac.cchmc.org/genome-trafac/index.jsp

Tm calculator: http://tmcalculator.neb.com/#!/

miRBase, A searchable database of published miRNA sequences and annotation:
http://www.mirbase.org/

TarBase, The largest manually curated target database, indexing more than 65,000 miRNA-gene
interactions: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index

TF binding and expression including diverse ncRNA genes: http://deepbase.sysu.edu.cn/chipbase/