ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGAGCCGAGACGAACCATGAATGCAAGCGAGTGTGTTGCGCGGGGCTGTGCTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctcattttttttcttcctatgttgttttaagctatggcagggttagattattctagtgccggtctatatgatagactgtcgtctatgctccgt...

Basic information

species	Zea mays
transcript	GRMZM2G063676_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G063676_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g08840.1 (Oryza sativa), 5'ss of exon 1

GGAGCCGAGACGAACCATGAATGCAAGCGAGTGTGTTGCGCGGGGCTGTGCTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctcattttttt-----tcttcctatgttgttttaagctatggcagggttagattattctagtgccggtctatatgatagactgtcgtctatgctccgt
||| |||||  | || ||||||||||| || |||||||| ||||| || ||||| ||||||||| |||| ||||||||||||||||| ||||||||  |||||     | || | |||     |||    | |||  |||  ||  | |      ||  || | ||  | |   | |   ||||    |||    ||  ||    
GGAACCGAGGAGGACTATGAATGCAAGTGAATGTGTTGCCCGGGGATGCGCTCTTCAGTGTGCTGTTCTTAGCCCCACTTTCAAAGTCCGGGAATTTGAGgtactgatttatctatttaagtttctgttgacgtttgtttctgccgtagtgtatctattttgt-ctgattctaatgttcttgatta--tgtaacgtaaactag--

upper sequence: GRMZM2G063676_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G01750.1 (Glycine max), 5'ss of exon 2

GGAGCCGAGACGAACCATGAATGCAAGCGAGTGTGTTGCGCGGGGCTGTGCTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctcattttttttcttcctatgttgttttaagctatggcagggttagattattctagtgccggtctatatgatagactgtcgtctatgctccgt----
|||||| || || || |||||||| || |||||||||||  ||||||||||  | |||||||| ||||||||||| ||||| ||||| ||||| || |||||| ||    |||||   |     |||  ||||||||  |    ||   |   | | |||   |     |    || || ||||   |  | |  |   |    
GGAGCCTAGGCGGACAATGAATGCTAGTGAGTGTGTTGCCAGGGGCTGTGCATTGCAGTGTGCAATTCTCAGCCCAACTTTTAAAGTACGGGAGTTTCAGgtaaaa----attttccctgccattataatgttttaaaattattcaatatggaactgttcagatctttttacgaatcatggacttcagcattttttattttttt

upper sequence: GRMZM2G063676_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA13G43630.2 (Glycine max), 5'ss of exon 2

GGAGCCGAGACGAACCATGAATGCAAGCGAGTGTGTTGCGCGGGGCTGTGCTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctcattttttt-tcttcctatgttgttttaag---ctatggcagggttagattattctagtgccggtctatatgatagactgtcgtctatgctccgt
|||||| || || || |||||||| || |||||||||||  |||| |||||  | |||||||| |||||||| || ||||| ||||| ||||| || |||||| | | ||       | | || || | | |||| ||    ||   |||  |||  || |||  || |    |  |  | |     |||  | | |  |    
GGAGCCTAGGCGGACAATGAATGCTAGTGAGTGTGTTGCCAGGGGTTGTGCATTGCAGTGTGCAATTCTCAGTCCAACTTTTAAAGTACGGGAGTTTCAGgtaaattttcccccggctgtattgctctctagtttgaaatgccttctgcaaagttttataattaaagggatcatggacttcagcagttgttttgt-tattt---

upper sequence: GRMZM2G063676_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 2

GGAGCCGAGACGAACCATGAATGCAAGCGAGTGTGTTGCGCGGGGCTGTGCTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatct-cattttttttcttc------ctatgttgttttaagcta-tggcagg--gttagattattctagtgc--cggtctatatgat-----agactgtcgtctatgctccgt--------
|||||| || || || ||||||||||| ||||||||  || |||| |||||  | |||||||| |||||||| || || || ||||| || ||||||||||||   | | ||| | | | |||           ||| ||||||  || | | | |    | ||  | | |  | |  | |  ||| |||      | | | |  | |||  |  ||        
GGAGCCCAGGCGTACAATGAATGCAAGTGAGTGTGTGTCGAGGGGATGTGCCTTGCAGTGTGCCATTCTCAGTCCGACCTTTAAAGTTCGCGAATTCCAGgtaatttgtgcatatctatgcttaagtaaatgtcgttattttaatgtacttgtaagcaactcgagaactgttatactccaggttatctgactagtcatattatgatttattttttgttctcttag

upper sequence: GRMZM2G063676_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1

GGAGCCGAGACGAACCATGAATGCAAGCGAGTGTGTTGCGCGGGGCTGTGCTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctcattttttttct-tcctatgttgttttaagctatggcagggttagattattctagtgccggtctatatgatagactgtcgtctatgctccgt-
||| || || || || ||||||||||| |||||||| ||   |||||||||||| || ||||| ||||| ||||| || || |||||||| || || |||||| ||   | ||    ||   |  ||| || ||||      |    |   |  | |||  |  |||   | ||   | ||    ||    | | ||  || 
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcctttcaacttaggttgtatcttattttctttatttattgaagtgaaatatg-tgttgcttttttacg-gctattgagttaaatttccttggtt

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|21809991|gb|BQ668309.1|BQ668309

EST:     CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAG                         GTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG
genomic: CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctc ... tggtttgcagGTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG

EST: gi|18654537|gb|BM499342.1|BM499342

EST:     TTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAG                         GTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG
genomic: TTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctc ... tggtttgcagGTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG

EST: gi|18648899|gb|BM497718.1|BM497718

EST:     CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAG                         GTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG
genomic: CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctc ... tggtttgcagGTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG

EST: gi|211491245|gb|FK959660.1|FK959660

EST:     CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAG                         GTTAATGATGGGTTTCCT
genomic: CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctc ... tggtttgcagGTTAATGATGGGTTTCCT

EST: gi|18654531|gb|BM499336.1|BM499336

EST:     CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAG                         GTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAANCAAGACTCG
genomic: CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctc ... tggtttgcagGTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG

EST: gi|31355297|gb|CD439654.1|CD439654

EST:     CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAG                         GTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG
genomic: CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctc ... tggtttgcagGTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG

EST: gi|18654532|gb|BM499337.1|BM499337

EST:     CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAG                         GTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG
genomic: CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctc ... tggtttgcagGTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG

EST: gi|18654538|gb|BM499343.1|BM499343

EST:     CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAG                         GTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG
genomic: CTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctc ... tggtttgcagGTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCG

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: 49 (upstream exon), 49 (downstream exon)
Score: 251

GGAGCCGAGACGAACCATGAATGCAAGCGAGTGTGTTGCGCGGGGCTGTGCTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctc ... tggtttgcagGTTAATGATGGGTTTCCTTTCTCAATTGCATTGTCATGGAAACAAGACTCGCAGAACAGTGCACCCCAACAGACCCTTGTATTTCCAAAGGGGAATGTAA

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 77

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 116