ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtctgccccatctcatcatatgcgtagcactatgagatttgaaactgtttttttgcttatctatcctcttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGCAAGAGAGCCATCCGCGCCGCAACCTATGATCTAGCTAAGAACGATCCAT

Basic information

species	Zea mays
transcript	GRMZM2G000660_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G000660_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g02120.2 (Oryza sativa), 3'ss of exon 5

gtaagtctgccccatctcatcatatgcgtagcactatgagatt-tgaaactgtttttttgcttatc--tatcctcttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGCAAGAGAGCCATCCGCGCCGCAACCTATGATCTAGCTAAGAACGATCCAT
    ||  |   |||||  |   || | || |       | || | |  | |      | |||| |  |   || || |  ||||||||| || |||||| |||| ||||| || | |||||||||||||||||  |||||||| ||||| || ||||| |||||||| |||||||| |||||| 
----gtaggtttcatcttcttgaattcttaacttgtcagggttataagccaggccacattcttagcatttatcttttgcttgcagCTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAATAAGAGAGCGATCCGTGCTGCAACTTATGATCTTGCTAAGAATGATCCAC

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|60341755|gb|DN208728.1|DN208728

EST:     AGCACCTGCGGTTGCAATCGCTTACATGTTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: AGCACCTGCGGTTGCAATCGCTTACATG-TTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|76290166|gb|DV029734.1|DV029734

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|76920052|gb|DV167984.1|DV167984

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|84969993|gb|DV171122.2|DV171122

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|78075797|gb|DV504231.1|DV504231

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|93283003|gb|EB675267.1|EB675267

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|71302330|gb|DR787283.1|DR787283

EST:     GAGCACTTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|28984682|gb|BQ539185.2|BQ539185

EST:     GCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|71302332|gb|DR787284.1|DR787284

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAA
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAA

EST: gi|71311577|gb|DR792164.1|DR792164

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTAT
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTAT

EST: gi|71312902|gb|DR792973.1|DR792973

EST:     AGCACCTGCGGTTGTCA-TCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGT
genomic: AGCACCTGCGGTTG-CAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAG-

EST: gi|16378243|gb|BI992345.1|BI992345

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|78105235|gb|DV523653.1|DV523653

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|83279413|gb|DV943421.1|DV943421

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|78105236|gb|DV523654.1|DV523654

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|76920051|gb|DV167983.1|DV167983

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|71426637|gb|DR807687.1|DR807687

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATC

EST: gi|76290165|gb|DV029733.1|DV029733

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|78075798|gb|DV504232.1|DV504232

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|101383569|gb|EB813840.1|EB813840

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|76927038|gb|DV171123.1|DV171123

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

EST: gi|71311576|gb|DR792163.1|DR792163

EST:     GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGAT                         CTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC
genomic: GAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGC

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: 40 (upstream exon), 48 (downstream exon)
Score: 51

GTCGCAGCGCAAAGGGCGGGTTTATGTCCACTGCACCGCTGGGCTTGGGAGAGCACCTGCGGTTGCAATCGCTTACATGTTTTGGTTTGAGAACATGGATgtaagtctgc ... ttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGCAAGAGAGCCATCCGCGCCGCAACCTATGATCTAGCTAAGAACGATCCAT

Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 25

Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 10

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 50

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtagcactatgagatttgaaactgtttttttgcttatctatcctcttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGCAAGAGAGCCATCCGCGCCGCAACCTATGATCTAGCTAAGAACGATCCAT

                                          ctcttac  putative branch site (score: 50)
                        tttttttgcttatcta  CT-rich tract
                      tgttttttt  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctgccccatctcatcatatgcgtagcactatgagatttgaaactgtttttttgcttatctatcctcttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGCAAGAGAGCCATCCGCGCCGCAACCTATGATCTAGCTAAGAACGATCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC