ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatctgtttctttaggtattcattttactttacagtataacacatctcggataaagcattaatctctcggttaaccctttgcaacctatatgct...

Basic information

species	Zea mays
transcript	GRMZM2G479744_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G479744_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g61050.1 (Oryza sativa), 5'ss of exon 11

TGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatctgtttctttaggtattcattttactttacagtataacacatctcggataaagcattaatctctcggttaaccctttgcaaccta-tatgct
|||||| || ||||||||||||||||| |||||||||||||| || ||||||||||| |||||||||||||||||||  || || |||||||| |||||||||   |   ||||| |||| ||    | ||||   || | || |  | | |   | ||  |  |  |  |  |    ||||    |     |   | |  
TGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCTCCGCACCATCCACTTAAGgtacatagcatgtttttttatgtcaataatttagagtaaattacacaaaaccataggtattgtgtccaagttacacaaaaccacaggagttttggcacgt-

upper sequence: GRMZM2G479744_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G14690.1 (Glycine max), 5'ss of exon 13

TGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatctgtttctttaggtattcattttactttacagtataacacatctcggataaagcattaatctctcggttaaccctttgcaacctatatgct
 || || || |||||||| ||||| |||||||| ||||| || || ||||||||||| |||||||||||||| || | ||| || || ||||| || |||| |||  || |||||     |  |||   |       |||   |      | |     || |  || ||   | | || |                    
AGACAATGTTGATGGTGGGGATGATCTTGATCTAATTGTCACAACAATGAATGGCAATGTCTTCTGCTTCTCAACCCCATCTCCTCATCATCCCCTAAAGgcagg--atatgttt-----gaaatttgatcattgaaacaacctcggttttgttactgaatggctttatacattgtttcag-------------------

upper sequence: GRMZM2G479744_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA01G27250.2 (Glycine max), 5'ss of exon 11

TGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatctgtttctttaggt-attcattttactttacagtataacacatctcggataaagcattaatctctcggttaaccctttgcaacctatatgct
 || ||||| |||||||| ||||| |||||||| ||||| || |||||||||||||| |||||||||||||| || |  || || || ||||| || |||| |||  || | | |  || | | ||| |    |||||    | | ||  |  | |  | |  | ||    | || |                        
AGACAACGTTGATGGTGGGGATGATCTTGATCTAATTGTCACAACTATGAATGGCAATGTCTTCTGCTTCTCAACCCCGTCTCCTCATCATCCCCTAAAGgcaggatatgtttgtaatttgatcattgaaacaactttg-gttgttactgaa-tggctttatacgttg---tttcag------------------------

upper sequence: GRMZM2G479744_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 11

TGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtagg--caatctg----tttctttaggtattcattttactttacag---tataacacatctcggataaagcattaatctctcggttaaccctttgcaacctatatgct---
|||||| || || ||||||||||| || |||||||||||  | ||||||||||| |||||||| |||||||| || |  || || |||||||| ||||||| | |  ||| |      | | |||  |      || | ||  |||    | | |    | |   | |  |    |||  ||   || || ||| |   || |  |  |   
TGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag

upper sequence: GRMZM2G479744_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 5'ss of exon 11

TGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtagg-------caa--------tctgtttctttaggtattcattttactttacagtataacacatctcggataaagcattaatctctcggttaaccctttgcaacctatatgct
 || || || |||||||||||||| ||||||||||||||||| || ||||||||||| || || ||||| || ||||   | ||||| ||||| || |||| |||       |||        | | ||| |||  ||||  |||||| || | ||  |        ||  | |      |||| ||    || || |||| | |          
GGACAATGTTGATGGTGGAGATGATCTTGATCTTATTGTTACAACCATGAATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAGgcaggatagacccaaaactgaattttatttttttgtgtataaattttatttcataggtt--tgtgattcataaaggtttctaatatcatattttacacttttccag---------

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|211499292|gb|FL279211.1|FL279211

EST:     ATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAG                         GAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC
genomic: ATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatc ... ttgatggcagGAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC

EST: gi|32860179|gb|CD999860.1|CD999860

EST:     ATGGTTTCGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAG                         GAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC
genomic: ATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatc ... ttgatggcagGAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC

EST: gi|213183278|gb|FM192491.1|FM192491

EST:     ATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAG                         GAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC
genomic: ATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatc ... ttgatggcagGAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC

EST: gi|211461237|gb|FL278650.1|FL278650

EST:     ATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAG                         GAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC
genomic: ATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatc ... ttgatggcagGAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC

EST: gi|6431890|gb|AW172094.1|AW172094

EST:     ATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAG                         GAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC
genomic: ATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatc ... ttgatggcagGAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAAC

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), 49 (downstream exon)
Score: 120

TGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtaggcaatc ... ttgatggcagGAATGGAGGTCATCAAACCAAGGAAGGAATAATGCTGCATATCAGTACAACCGTGAAGGTATCTATGTTAAGCATGGTTCCAGGACCTTCCGTGACGAAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 110