ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGTTGAGATCGACACCCTAACTGGGGATTTTTACACAAGGACAGCTGATATTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctctgcggaggaaatgttttgctaatttgcttcaacacgaaagagaggttccttctacatatttcctgtagtttaacgtactgtatttcag

Basic information

species	Zea mays
transcript	GRMZM2G050984_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G050984_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g31550.2 (Oryza sativa), 5'ss of exon 12

AGTTGAGATCGACACCCTAACTGGGGATTTTTACACAAGGACAGCTGATATTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctctgcggaggaaatgttttgctaatttgcttcaacacgaaagagaggttccttctacatatttcctgtagtttaacgtactgtatttcag-------------
|||||| || || |||||||||||||||||  ||||||||||||  ||||||||||||||||| || | |||||||||||| || ||||| ||||||||||||||           |||||||||| |||     |    || | ||  ||   ||| || | |  ||||| ||      |  | |  |  | ||||              
AGTTGAAATTGATACCCTAACTGGGGATTTCCACACAAGGACAGTAGATATTGTTATGGATCTTGGCTGTTCAATTAATCCGGCTATTGATATTGGCCAGgtatg---------atggaaatgtttggctgcccag----aataagatggacctgtttctcccatttatttacttcttcctgtcttctttaacttcaatggcttgtttcag

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|78023990|gb|DV492377.1|DV492377

EST:     ATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGGTA
genomic: ATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|60395383|gb|DN228252.1|DN228252

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|67016938|gb|CO445687.1|CO445687

EST:     ATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: ATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|14204330|gb|BG838007.1|BG838007

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATT-GGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|14204197|gb|BG837874.1|BG837874

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|45567638|gb|CK985669.1|CK985669

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|211338067|gb|FL010980.1|FL010980

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

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: 47 (upstream exon), 49 (downstream exon)
Score: 112

AGTTGAGATCGACACCCTAACTGGGGATTTTTACACAAGGACAGCTGATATTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTAAAATGGGGGGATGATAACCATAAGTGGATTCGACCTGGACACCTCTTCA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 320

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 363