ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAAAGCACAATAAACTATTTGGAAGCTGGACAGCTCTCTTCATTTTTTAGAAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacataattcacgattaatgtttgcacatatgttatttttctttgtaagtggggaacttcaagggaatctttaattggttggtagttttatagtttgtaatgttacttttgcag

Basic information

species	Zea mays
transcript	GRMZM2G410515_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 5'ss of exon 3

GAAAGCACAATAAACTATTTGGAAGCTGGACAGCTCTCTTCATTTTTTAGAAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacataattcacgattaatgtttgcacatatgttatttttctttgtaagtggggaacttcaagggaatctttaattggttggtagttttatagtttgtaatgtta----cttttgcag
|||| ||||||||||| ||||||||||||||| || ||||||||||| |||||||| ||||  |||| ||| || || ||||||||| ||||||| |||||| ||| |||||||  |  |    ||  || ||   | ||||   | | ||  |    |||||  |  | |     |    | |  |||  || |||||| ||   ||      |||| |||
GAAAACACAATAAACTTTTTGGAAGCTGGACAACTATCTTCATTTTTCAGAAACAGTGAACAACCCACTAAACCATTACAGGTCGTGATTGCTGGAGCAGgtatgatataattctaggat----ttgacagatgaataatttacatatatatct----aactttgatagcagtcacatcgtggtcttagcattgtagtttttagctttgatttttttttcag

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|211005246|gb|FL018196.1|FL018196

EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGC

EST: gi|211002473|gb|FL018192.1|FL018192

EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GAATGGCTGGTCTATCAACAGCGAAGTAT
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTAT

EST: gi|211417844|gb|FL018174.1|FL018174

EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTTGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC

EST: gi|211417848|gb|FL018178.1|FL018178

EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC

EST: gi|211417840|gb|FL018170.1|FL018170

EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC

EST: gi|211417841|gb|FL018171.1|FL018171

EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC

EST: gi|74236167|gb|DT644081.1|DT644081

EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC

EST: gi|211002466|gb|FL018185.1|FL018185

EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC

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: 43 (upstream exon), 43 (downstream exon)
Score: 27

GAAAGCACAATAAACTATTTGGAAGCTGGACAGCTCTCTTCATTTTTTAGAAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 139

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 80