ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaattggcatgtctactctttgtgttggttgtgttatgtttctctgtctgaattcctttatctactctatag

Basic information

species	Zea mays
transcript	GRMZM2G115757_T03
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G115757_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g32526.2 (Oryza sativa), 5'ss of exon 3

---------GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgat--taattggc-------atgtctactctttgtgttggttgtgttatgtttctctgtctgaat--tcctttatctactctatag--------------------
         |||||||||||||||||||| | ||||||||| |||||||||||||||||||| || |||||||| ||||||||||| ||||||||||||||| ||  |||| | |       ||  |||     |   ||  || |  |||  ||     | | |||  ||| || ||||    | |                     
CATTTACAGGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtag

upper sequence: GRMZM2G115757_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g32526.1 (Oryza sativa), 5'ss of exon 4

GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgat--taattggc-------atgtctactctttgtgttggttgtgttatgtttctctgtctgaat--tcctttatctactctatag--------------------
|||||||||||||||||||| | ||||||||| |||||||||||||||||||| || |||||||| ||||||||||| ||||||||||||||| ||  |||| | |       ||  |||     |   ||  || |  |||  ||     | | |||  ||| || ||||    | |                     
GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtag

upper sequence: GRMZM2G115757_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G10750.1 (Glycine max), 5'ss of exon 4

GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaattggcatgt--ctactctttgtgttggttgtgtta-tgtttctctgtctgaattcctttatctactctatag---------------------
|||||||| ||||||||||| ||||| ||||| |||| |||||||  | | || |||||||||||  | || ||||| |||||||||||||||   |  |    |     || ||  ||   ||   | |   | ||  |  ||| |||   |  ||||  || |   |                       
GGAAAACTCACTGATGGAACTGTTTTCGATTCTAGCTTTGAAAGAAATAATCCAATTGAATTTGAGCTTGGTACTGGTCAAGTGATCAAAGgtatgttgtgcataaacaacttctggtttcattacctataaaagtgactagctg-ctgtgcttgtttacttatttattgaaaatgaaagtaagtagataaa

upper sequence: GRMZM2G115757_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G21680.1 (Glycine max), 5'ss of exon 4

GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaattggcatgtctactctttgtgttggttgtgttatgtttctctgtctgaattcctttatctactctatag-----------------------
|||||||| ||||||||||| ||||| ||||| |||| |||||||  | | || |||||||||||  | || ||||| |||||||||||||||   |  |    |       ||  | ||||  || | |  | |   |   | | ||      || || || |                           
GGAAAACTCACTGATGGAACTGTTTTCGATTCTAGCTTTGAAAGAAATAATCCAATTGAATTTGAGCTTGGTACTGGTCAAGTGATCAAAGgtatgttgtgcataaacaacttcagtctgttaattttctggtttcattacctataaaagtgactagctgctgtgcttgtttgcttatttaatgaaaatga

upper sequence: GRMZM2G115757_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT3G25220.1 (Arabidopsis thaliana), 5'ss of exon 4

GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgt-----gattaattggcatgtctactctttgtgttggttgtgttatgttt---ctctgtctgaattcctttatctactctatag----------------------
|||||  | ||||||||||| || ||||||||||| | ||| ||||||||||| ||||| |||||  | || ||||| ||||| |||  ||||     | |   |   |   || ||||  | | ||   |  |||||  ||    | | | ||| |  |   ||  |   ||  |                      
GGAAAGTTAACTGATGGAACTGTCTTTGATTCAAGTTTTGAGAGAGGTGACCCTATTGAGTTTGAGCTTGGAACTGGTCAAGTCATCCCAGgtttgttgctatttcatcgcatcaactccatctttttccttcgttattgttaccttttttttgactgacaaaattgaaggtaatgcaattaattcgaaatgttgcag

upper sequence: GRMZM2G115757_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv00s0260g00060.t01 (Vitis vinifera), 5'ss of exon 4

GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaattggcatgtctactctttgtgttggttgtgttatgtttctctgtctgaattcctttatctactctatag-----------------------
|| ||||| || |||||||| ||||||||||| || | |||||| |||||||| ||||| |||||| | || | ||| ||||| || ||||||   |||    ||||      || | | |    ||| |||  | | ||| | | |   |  | |     |  | |                        
GGGAAACTCACAGATGGAACTGTTTTTGATTCCAGTTTTGAAAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaagaacatgaacttactgtttatacaatgttttacctatttcttttttaccccagtaaatggataaaaaagtgtatgagtattgcatgggtaa

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|32945395|gb|CF050214.1|CF050214

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|211343044|gb|FL472494.1|FL472494

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTTAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|213167545|gb|FM181750.1|FM181750

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|211214433|gb|FL151952.1|FL151952

EST:     CGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: CGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|32936362|gb|CF041181.1|CF041181

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|211343045|gb|FL472495.1|FL472495

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|32932853|gb|CF037665.1|CF037665

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|32868577|gb|CF008259.1|CF008259

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|211214432|gb|FL151951.1|FL151951

EST:     CGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: CGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|32933739|gb|CF038551.1|CF038551

EST:     ACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: ACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|37388080|gb|CF631245.1|CF631245

EST:     GGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: GGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|12968665|gb|BG265611.1|BG265611

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|166664120|gb|EG160415.1|EG160415

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTC
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTC

EST: gi|211322569|gb|FL457011.1|FL457011

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|33095696|gb|CF055690.1|CF055690

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|33095201|gb|CF055195.1|CF055195

EST:     AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

EST: gi|5762183|gb|AI967231.1|AI967231

EST:     AAGAGGTGNCCCGATTGAATTTGAATTGGGCNCTGGNCAAGTGATCAAAG                         GATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTAAAAAGCGGAAGTTAA
genomic: AAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGA

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), 47 (downstream exon)
Score: 284

GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaatt ... tactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGAAGATCCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 514

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 436

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 498

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaattggcatgtctactctttgtgttggttgtgttatgtttctctgtctgaattcctttatctactctatag

- - - - - - - - - - - - - - - - - - - -  AAGAGG