ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAGgtatatttatataaagtttatatacacaaatcattttatttatcctgctagttttgctccaaaaaatcaacaattggttctaactgcag

Basic information

species	Zea mays
transcript	GRMZM2G161728_T04
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G161728_T04 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g49070.1 (Oryza sativa), 5'ss of exon 7

TGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAGgtatatttatataaagtttatatacacaaatcattttatttatcctgctagttt--tgctccaaaaaatcaacaattggttctaactgcag
|||||||||| |||| || ||| |||| | ||| |   | |||||||| |||||||||||||| || ||||||||||||||| |||| || || | ||||||||  || |      || | || || ||| ||||||  ||    ||||| |||  | ||  ||| | ||||   ||||  |||| |||||
TGTTGGAGAGCTGAACATTACAGTGGTAAGAGGTATTCAGTTGGCCGTCAGAGACATGCTAACGAGCGATCCATATGTTGTTCTAACACTTGGGGAGCAGgtatgctttttctt--ttgaaattcataaaccattttgattgctatgctaatttgttcctttaaacattcaattgttggc-ctaattgcag

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|74234877|gb|DT642791.1|DT642791

EST:     GAGACATGCTAACAAGTGATCCATATGTTGTTTTTACGCTCGGAGGGCAG                         AAAGTTCAATCAACGGGTNNNNNNNGTGATCCTGAATCCGGTATGGAATGA
genomic: GAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAGgtatatttat ... ctaactgcagAAAGTTCAATCAACGGTTAAAAAAAGTGATC-TGAATCCGGTATGGAATGA

EST: gi|148982152|gb|EE028182.2|EE028182

EST:     GAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAG                         AAAGTTCAATCAACGGTTNNNNNNNGTGATCTGAATCCGGTATGGAATGAA
genomic: GAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAGgtatatttat ... ctaactgcagAAAGTTCAATCAACGGTTAAAAAAAGTGATCTGAATCCGGTATGGAATGAA

EST: gi|78079893|gb|DV508305.1|DV508305

EST:     GAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAG                         AAAGTTCAATCAACGGTT
genomic: GAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAGgtatatttat ... ctaactgcagAAAGTTCAATCAACGGTT

EST: gi|76287384|gb|DV026952.1|DV026952

EST:     GAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAG                         AAAGT-CAATCAACGGTTNNNNNNNGTGATCTGAATCCGGTATGGAATGAA
genomic: GAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAGgtatatttat ... ctaactgcagAAAGTTCAATCAACGGTTAAAAAAAGTGATCTGAATCCGGTATGGAATGAA

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: 266

TGTTGGAGAGTTGAATATCACACTGGTCAAAGGCACCAACTTGGCCGTTAGAGACATGCTAACAAGTGATCCATATGTTGTTTTAACGCTCGGAGGGCAGgtatatttat ... ctaactgcagAAAGTTCAATCAACGGTTAAAAAAAGTGATCTGAATCCGGTATGGAATGAAGTGCTTAAGATATCTGTTCCTCGAAATTATGGACCTCTAAAACTT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 376

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 420