ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGCATCCCTCGACAAAATATTGGAAGAAAGTTTTGCCAAGAACGAGGCTTTCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAGgtgcctgattttttattttctacttgactggtgtttcagttttacagtattgtcattttattgatgtcaatgtaattctttttatagatgtcattctgtc...

Basic information

species	Zea mays
transcript	AC155496.2_FGT009
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC155496.2_FGT009 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 5'ss of exon 6

GGCATCCCTCGACAAAATATTGGAAGAAAGTTTTGCCAAGAACGAGGCTTTCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAGgtgcctgattttttattttctacttgac--tggtgtttcagttttacagtattgtcattttattgatgtcaatgtaattctttttatagatgtcattctgtc
|||||| || || | ||||||||| |||||||||||||| || ||||||||||||||||| |||||||| ||||| || || ||||||||| |||| |||||     || |||    |||| ||||||  |  | |||    |||   || |  | | || ||   |   |    |||  ||| || |  ||   | ||   
GGCATCGCTTGATAGAATATTGGAGGAAAGTTTTGCCAAAAATGAGGCTTTCTCCAATACAATAAAAGAGTCATTCGAACATCTTATCAATTTACGCCAGgtaggccatatttatgattctgcttgacaatattttttttcctttcttgtgtactgagttcatatcttatatcacaatattttgta-atttgctttcctac-

upper sequence: AC155496.2_FGT009 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G10030.1 (Glycine max), 5'ss of exon 6

GGCATCCCTCGACAAAATATTGGAAGAAAGTTTTGCCAAGAACGAGGCTTTCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAGgtgcctg--attttttattttctacttgactggtgtttcagttttacagtattgtcattttattgatgtcaatgtaattctttttatagatgtcattctgtc
||| || || |||| || || ||||||||| ||| ||||||| || || ||||  || ||||| ||||||||||||||||| || |||||||| || ||||| | |   ||||||| ||   || ||   || |  |  | ||| | |   || |||   ||   |  || |   |||  | |  | | || |||  ||   
GGCTTCTCTTGACACAACATGGGAAGAAAGCTTTTCCAAGAATGAAGCATTCTGTAACACCATTAAAGATTCATTTGAGCATCTCATCAATCTTCGTCAGgtacttcccattttttgttggttagtt--ttgatactgaaatttaataaatttctcaagatagaaagctccaaccaatcttctggaaatatctcaacctaat

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|32803931|gb|CD956167.1|CD956167

EST:     TCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAG                         AACCGACCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAACA
genomic: TCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAGgtgcctgatt ... cttacaacagAACCGACCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCT

EST: gi|32935166|gb|CF039978.1|CF039978

EST:     TCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAG                         AACCGACCTGCGGAATTGATTGCAACGTTTCTTGATGAGAAACTTCGAGCT
genomic: TCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAGgtgcctgatt ... cttacaacagAACCGACCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCT

EST: gi|61119354|gb|DN560315.1|DN560315

EST:     TCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAG                         AACCGACCTGCGGAATTGATTGCAAAGTTTCTTGACGAGAAACTTCGAGCT
genomic: TCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAGgtgcctgatt ... cttacaacagAACCGACCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCT

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 232

GGCATCCCTCGACAAAATATTGGAAGAAAGTTTTGCCAAGAACGAGGCTTTCTCCAATACCATAAAAGATTCATTTGAGCACCTTATCAATCTACGACAGgtgcctgatt ... cttacaacagAACCGACCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCTGGCAATAAAGGGACATCGGAAGAAGAGCTGGAGGGTATACTTGATAAAG

Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 118

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 118