ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAATGAGAAATTGCAATGGTTTTTGGACTCTATCAAGTCATACCCGAATGAAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAGgtaatgtcttgttctccttatagtattattttaatatcactatagttttatgtgcataatttgttgaactgagcttgcccacaattgttcttctttcttc...

Basic information

species	Zea mays
transcript	GRMZM2G020446_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G020446_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 5'ss of exon 3

CAATGAGAAATTGCAATGGTTTTTGGACTCTATCAAGTCATACCCGAATGAAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAGgtaa--------tgtcttgttctccttatagtattatt-ttaatatcactatagttttatgtgcata-atttgttgaactgagcttgcccacaattgttcttctttcttc
 ||||||||| | |||||||| || |||||||||||||||||| | ||||| |||| ||| || ||||||||||| |||||||||||||| |||||||||||||        ||   |  | | |||    ||| ||| ||   | |  |    | | ||  | |   |||||||    ||||||||  |    | ||            
TAATGAGAAACTACAATGGTTCTTAGACTCTATCAAGTCATACTCAAATGATATCACACTGGTGGGTGTTCATTGTCATCTGGGATCTACCATTACAAAGgtaaatgaattatgatgtactattctttggttataattgttggaaactttgagttgtaataagtaggtatttgttatggtgagcttgttcgtggtggtgt----------

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|20208183|gb|BQ134272.1|BQ134272

EST:     AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAG                         GTTGATATATTCAGAGATGCTGCAGTTCTTATGGTGAATTATGTCGATGAA
genomic: AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAGgtaatgtctt ... tcatttttagGTTGATATATTCAGAGATGCTGCAGTTCTTATGCTGAATTATGTCGATGAA

EST: gi|211042194|gb|FL157904.1|FL157904

EST:     AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAG                         GTTGATATATTCAGAGATGCTGCAGTTCTTATGGTGAATTATGTCGATGAA
genomic: AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAGgtaatgtctt ... tcatttttagGTTGATATATTCAGAGATGCTGCAGTTCTTATGCTGAATTATGTCGATGAA

EST: gi|9825116|gb|BE575318.1|BE575318

EST:     AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAG                         GTTGATATATTCAGAGATGCTGCAGTTCTTATGGTGAATTATGTCGATGAA
genomic: AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAGgtaatgtctt ... tcatttttagGTTGATATATTCAGAGATGCTGCAGTTCTTATGCTGAATTATGTCGATGAA

EST: gi|26456264|gb|CA827847.1|CA827847

EST:     AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAG                         GTTGATATATTCAGAGATGCTGCAGTTCTTATGGTGAATTATGTCGATGAA
genomic: AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAGgtaatgtctt ... tcatttttagGTTGATATATTCAGAGATGCTGCAGTTCTTATGCTGAATTATGTCGATGAA

EST: gi|211452559|gb|FL415488.1|FL415488

EST:     AAATCAAACTTGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAG                         GTTGATATATTCAGAGATGCTGCAGTTCTTATGGTGAATTATGTCGATGAA
genomic: AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAGgtaatgtctt ... tcatttttagGTTGATATATTCAGAGATGCTGCAGTTCTTATGCTGAATTATGTCGATGAA

EST: gi|211108459|gb|FL406876.1|FL406876

EST:     AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAG                         GTTGATATATTCAGAGACGCTGCAGTTCTTATGGTGAATTATGTCGATGAA
genomic: AAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAGgtaatgtctt ... tcatttttagGTTGATATATTCAGAGATGCTGCAGTTCTTATGCTGAATTATGTCGATGAA

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), 47 (downstream exon)
Score: 121

CAATGAGAAATTGCAATGGTTTTTGGACTCTATCAAGTCATACCCGAATGAAATCAAACTCGTTGGTGTTCATTGCCATCTGGGATCTACTATTACAAAGgtaatgtctt ... tcatttttagGTTGATATATTCAGAGATGCTGCAGTTCTTATGCTGAATTATGTCGATGAAATTCGAGCACAAGGTTTTAAGTTGGAGTACCTGAATATCGGAGGTGGTT

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 138

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 117