Human - UCSC Genome Browser v167

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ncRNA Prediction and Mapping Tracks
Base Position	fRNAdb::RNAz	fRNAdb::EvoFold	fRNAdb::snoRNA	fRNAdb::rRNA
fRNAdb::tRNA	fRNAdb::piRNA	fRNAdb::Antisense	fRNAdb::Guide	fRNAdb::IRES
fRNAdb::Regulatory	fRNAdb::Ribozyme	fRNAdb::RNase-MRP	fRNAdb::RNase-P	fRNAdb::scRNA
fRNAdb::snRNA	fRNAdb::SRP	fRNAdb::Telomerase	fRNAdb::Vault	fRNAdb::Y
fRNAdb::uc-ncRNA	fRNAdb::uc-transcript	fRNAdb::Misc	fRNAdb::fly smallRNA	RNAz folds
ncRNAscan	ENOR	RNA Clusters	antisense ChenJ NAR2004	snoSeeker
tRNAscan-SE	QRNA predictions	Gersteins RNA	intronic ncRNAs	MFE
MFE [-]	Z score	Erdmann	H-inv 5 Noncoding	Sasaki and Hirose 150 ncRNA candidates
Jones and Eddy ncRNAs

Misc Genomic Element Tracks
Indel-conserved segments	Ultra Conserved Elements	Ultra Conserved Elements 17way	Transposon Free Region	Histone Enrichment
Fragile Sites	Enhancer Candidates	Tissue specific enhancer candidates	PReMod CRMs	Alu
H-inv 5 cDNA cluster

miRNA-related Tracks
Known miRNAs	Predicted miRNAs	Known targets	Predicted targets	miRNA Atlas
fRNAdb::pre-miRNA	fRNAdb::mature-miRNA

Affymetrix Transfrags
Human long RNA	Human short RNA

ncRNA Candidate Probe Tracks
Human Accelerated Region	Inverted Duplication	RNAmine	Rfam Seed mappable	Ultra Low Z score Region
miRRim	SelfChain RNAz EST	SelfChain RNAz Washietl	snoRNA	SynSeg
Ultra Conserved Region	Known Gene

Mapping and Sequencing Tracks
Chromosome Band	STS Markers	FISH Clones	Recomb Rate	Map Contigs
Assembly	Gap	Coverage	BAC End Pairs	Fosmid End Pairs
GC Percent	WSSD Duplication	Short Match	Restr Enzymes

Phenotype and Disease Associations
RGD QTL

Genes and Gene Prediction Tracks
Known Genes	CCDS	RefSeq Genes	Other RefSeq	MGC Genes
ORFeome Clones	Vega Genes	Vega Pseudogenes	Ensembl Genes	AceView Genes
ECgene Genes	N-SCAN	SGP Genes	Geneid Genes	Genscan Genes
Exoniphy	Augustus	Yale Pseudo	Superfamily	ACEScan
EvoFold	sno/miRNA	ExonWalk

mRNA and EST Tracks
Human mRNAs	Spliced ESTs	Human ESTs	Other mRNAs	Other ESTs
H-Inv 3	TIGR Gene Index	UniGene	Gene Bounds	Alt-Splicing
Poly(A)

Expression and Regulation
Affy All Exon	Affy HuEx 1.0	GNF Atlas 2	Allen Brain	GNF Ratio
Bertone Yale TAR	Affy U133	Affy GNF1H	Affy U133Plus2	Affy U95
CpG Islands	FirstEF	5x Reg Potential	SwitchGear TSS	Eponine TSS
Vista Enhancers	TFBS Conserved	Affy Tx lRNA Reg	Affy Tx lRNA Sig	Affy Tx sRNA Reg
Affy Tx sRNA Sig	Affy Txn Phase2	SGMO/EIO CD34 HS	NHGRI DNaseI-HS	7X Reg Potential

Comparative Genomics
Conservation	Human Accelerated	Fugu Blat	Fugu Chain	Fugu Net
Tetraodon Ecores	Tetraodon Chain	Tetraodon Net	Zebrafish Chain	Zebrafish Net
X. tropicalis Chain	X. tropicalis Net	Chicken Chain	Chicken Net	Opossum Chain
Opossum Net	Cow Chain	Cow Net	Cow BAC Ends	Cow Synteny
Rat Chain	Rat Net	Mouse Chain	Mouse Net	Rhesus Chain
Rhesus Net	Chimp Chain	Chimp Net	Dog Chain	Dog Net

Variation and Repeats
SNPs	SNP Arrays	HapMap SNPs	HapMap LD	Tajima's D SNPs
Tajima's D	SNP Recomb Rates	SNP Recomb Hots	Structural Var	Segmental Dups
RepeatMasker	Simple Repeats	Microsatellite	RIPs	Self Chain

ENCODE Regions and Genes
ENCODE Regions	Gencode Genes Mar07	Gencode Genes Oct05	Gencode Introns Oct05	Gencode RACEfrags
EGASP Full	EGASP Partial	EGASP Update	Pseudogenes	GIS PET RNA
Known+Pred RNA	UCSC EvoFold	Vienna RNAz

ENCODE Transcript Levels
Affy RNA Signal	Affy Transfrags	BU First Exon	Riken CAGE	Riken Cage 2007
Stanf Promoter	Stanf RTPCR	Yale MAS RNA	Yale MAS TAR	Yale RNA
Yale TAR

ENCODE Chromatin Immunoprecipitation
Affy pVal	Affy Sites	Affy Strict pVal	Affy Strict Sites	Affy Strict Sig
GIS ChIP-PET	LI ChIP Various	LI gIF ChIP	LI Ng gIF ChIP	LI Ng TAF1 IMR90
LI Ng Validation	Sanger ChIP	Sanger ChIP Hits	Stanf ChIP	Stanf ChIP Score
UCD Ng ChIP Hits	UCD Ng ChIP	UT-Austin ChIP	Uppsala ChIP	Uppsala ChIP Butyrate
Yale STAT1 pVal	Yale STAT1 Sig	Yale STAT1 Sites	Yale ChIP pVal	Yale ChIP Signal
Yale ChIP Sites	Yale ChIP RFBR

ENCODE Chromosome, Chromatin and DNA Structure
BU ORChID	Duke/NHGRI DNase	Stanf Meth	Stanf Meth Score	UNC FAIRE
UT-Austin STAGE	UVa DNA Rep	UVa DNA Rep Seg	UVa DNA Rep Ori	UVa DNA Rep TR50
UW QCP DNaseI Sens	UW DNase-array

ENCODE Comparative Genomics
Consens Elements	TBA Alignment	TBA Cons	TBA Elements	MLAGAN Alignment
MLAGAN Cons	MLAGAN Elements	MAVID Alignment	MAVID Cons	MAVID Elements
Align Agree	Align Gaps	DLESS

ENCODE Variation
NHGRI DIPs	HapMap Coverage	SNP Recomb Rates	SNP Recomb Hots	Sanger Assoc
HapMap SNPs

UCSC Genome Browser Test Tracks (Excerpt)
Rfam seed folds

Experimental Tracks
Similar to Mitochondria	Rfam cons	miRanda	Nimblegen [+]	Nimblegen [-]
TARs (Nimblegen:40%,250)	TARs (Nimblegen:40%,500)	TARs (Nimblegen:30%,250)	TARs (Nimblegen:30%,500)	selected TARs (Nimblegen:10%,250)
TARs (Nimblegen:20%,250)	TARs (Nimblegen:10%,250)	TARs (Nimblegen:10%,500)	TARs (Nimblegen:20%,500)	entropy
entropy [-]	EST Clusters