Non-Coding RNA Search

Here the various "field" names are explained:



FOLDALIGN INFO TRANSFRAG INFO MORE MAMMALS KNOWN GENES INFO REFSEQ GENES INFO EC GENES INFO ENSEMBL GENES INFO GENE ID GENES INFO
GENSCAN GENES INFO SGP GENES INFO TIGR GENES INFO TWINSCAN GENES INFO EST INFO FANTOM 3 ACEMBLY GENES INFO
CCDS GENES INFO VEGA GENES INFO YALE PSEUDOGENES INFO UNIGENE GENES INFO ADJACENT REFSEQ GENES KNOWN RNAs INFO SEQUENCE B PRIMERS

FOLDALIGN INFO

Name A : ID for the first sequence (in all human-mouse scans A = human)
Name B : ID for the second sequence (in al human-mouse scans B = mouse)
P-Score Number : The number of non-overlapping alignments which the P-Score is estimated from
Alignment Start A : The starting position of the actual alignment for sequence A
Alignment Stop A : The stopping position of the actual alignment for sequence A
Alignment Start B : The starting position of the actual alignment for sequence B
Alignment Stop B : The stopping position of the actual alignment for sequence B
Alignment Length : The length of the alignment
Sequence Identity : Sequence identity (%) of the alignment between the two sequences
Non-basepairs : The frequence(%) of non-basepairing bases
GC-Content A : The GC content (%) of the alignment in sequence A
GC-Content B : The GC content (%) of the alignment in sequence B
Sequence A : Sequence A (incl. gaps)
Structure : The foldalign structure prediction
Sequence B : Sequence B (incl. gaps)
Direction : If the alignment is on the forward or the reverse strand in sequence A
Adjacent Alignment : How many conserved sequence alignments, and on which strand, surround the prediction

TRANSFRAG INFO

Transfrag Overlap : If there is tranfrag overlap or not (TRANS/NOTRANS)
Antal Celllines : How many celllines the overlapping transfrags originate from
Cell Location : The cellular location of the overlapping transfrags (nuclear, cytosolic)
PolyA : If the tranfrag has polyA tail or not (polyA+, polyA-)
Transfrag Start : The starting positions of the transfrags
Transfrag Stop : The stopping positions of the transfrags
Transfrag Type : The type of the transfrag (0,1,2,3) - see Cheng et al, 2005 for details
Max Overlap : How much of the human candidate the biggest tranfrags overlaps

MORE MAMMALS

More mammals : If there is candidate in a third organism (YES/NO)

KNOWN GENES INFO

Known Overlap A/B : If the sequence A/B of the alignment overlaps a known gene or not (YES, NO)
KnownID A/B: The ID of the overlapping known gene
Known Strand A/B: The strand of the overlapping known gene
Known Start A/B: The starting position of the overlapping known gene
Known Stop A/B : The stopping position of the overlapping known gene
Known Gene Location A/B : Where the known gene is overlapped (INTRON, EXON, UTR5, UTR3)
Known Gene Location Start A/B : The starting position of f.ex. the intron
Known Gene Location Stop A/B : The stopping position of f.ex. the intron

REFSEQ GENES INFO

The same as for Known Genes

EC GENES INFO

The same as for Known Genes

ENSEMBL GENES INFO

The same as for Known Genes

GENE ID GENES INFO

The same as for Known Genes

GENSCAN GENES INFO

The same as for Known Genes

SGP GENES INFO

The same as for Known Genes

TIGR GENES INFO

The same as for Known Genes

TWINSCAN GENES INFO

The same as for Known Genes

ACEMBLY GENES INFO

The same as for Known Genes

CCDS GENES INFO

The same as for Known Genes

VEGA GENES INFO

The same as for Known Genes

UNIGENE GENES INFO

SEQUENCE B PRIMERS

Since we performed experiments on the mouse we predicted 3 primers for each of the mouse sequence
Primer Left : The first three left primers
Primer Right : The first three right primers
Primer Prodct : The product sizes of the PCR

EST INFO

EST Overlap A/B : If there is a EST overlap in sequence A/B
EST Max Overlap A/B : How much of the candidate is overlapped by an single EST
EST Strand A/B : The strand
EST Block Start A/B : The start position of the EST block
EST Block Stop A/B : The stop position of the EST block
EST Start A/B : The start position of a the whole EST (i.e. including all blocks)
EST Stop A/B : The stop position of the whole EST
EST Blocks nr. A/B : How many blocks the EST has
EST Block sizes A/B : How large thos blocks are
EST Target Starts A/B : Where each blocks starts inside the whole EST (local positions)
EST Query Starts A/B : Where each block starts in the genome (global positions)

FANTOM 3 INFO

Fantom Overlap : If the candidate overlaps transcript in the Fantom 3 (YES/NO)
data (only for mouse of course)
Fantom Start : The start position
Fantom Stop : The stop position
Fantom Size : The size of the Fantom transcript
Fantom Coding : If it's likely to be codeing or not (as annotated by the Fantom group)
Fantom Same Strand : If the transcript is on the same strand as the prediction (YES/NO)

ADJACENT REFSEQ INFO

The closest REFSEQ gene that does not overlap, the same as for Known Genes.

KNOWN RNAs INFO

If the candidate overlaps known ncRNAs (only the ncRNAs from UCSC are here), than information about these is to be found here