[Gusdev-gusdev] RE: GUS features

[Matthew B. <mb...@sa...>]

Hi Chris=20
I'l do the same over here
Matt

-----Original Message-----
From: Chris Stoeckert [mailto:sto...@pc...]=20
Sent: 26 November 2002 19:37
To: Matthew Berryman
Cc: gusdev-gusdev
Subject: Re: GUS features


Hi Matt,
I've generated a list of the 26 subclass views of NAFeatureImp and=20
looked at the distinct names associated with. These are given below.=20
Will now start looking at the SO and SO lite for these.
Chris

On Friday, November 22, 2002, at 12:59  PM, Matt Berriman wrote:

> Hi Chris
> Do you have a list of GUS sequence features?  The SO group are
> preparing a "SO Lite" -- it would be good to check that everything is=20
> represented.
>
> cheers
> Matt

SUBCLASS_VIEW
<BindingSiteFeature: names of binding sites>
CentromereFeature:
	predicted centromere
DNARegulatory:
	-10_signal
	-35_signal
	CAAT_signal
	GC_signal
	TATA_signal
	attenuator
	enhancer
	promoter
	terminator
DNAStructure:
	D-loop
	primer_bind
	rep_origin
ExonFeature
	ExonFeature
GeneFeature
	CDS
	GeneFeature
	gene
	snRNA
	tRNA
HexamerFeature
	hexamer
Immunoglobulin
	C-region
	D_segment
	J_segment
	N_region
	S_region
	V_region
	V_segment
	iDNA
LowComplexityNAFeature
	low complexity sequence
Miscellaneous
	misc_binding
	misc_feature
	misc_signal
	protein_bind
	stem_loop
	unsure
PolyAFeature
	PolyAFeature
PromoterFeature
	PromoterFeature
	various promoter sets
ProteinFeature=09
	mat_peptide
	sig_peptide
	transit_peptide
RNAFeature
	PREDICTED REFSEQ
	PROVISIONAL REFSEQ
	REFSEQ
	REVIEWED REFSEQ
	RNAFeature
	assembly
	mRNA
RNAStructure
	RBS
	misc_RNA
RNAType
	rRNA
	scRNA
	snRNA
	tRNA
<Repeats: names of repeats>
RestrictionFragmentFeature
	RestrictionFragmentFeature
<SAGETagFeature: locations on chromosomes>
STS
	STS
ScaffoldGapFeature
	assembly gap
SeqVariation
	SNP
	allele
	conflict
	misc_difference
	misc_recomb
	modified_base
	mutation
	old_sequence
	variation
Source
	source
TandemRepeatFeature
	tandem repeat
TelomereFeature
	predicted telomere
Transcript
	3'UTR
	3'clip
	5'UTR
	5'clip
	CDS
	exon
	intron
	mRNA
	polyA_signal
	precursor_RNA
	prim_transcript