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

...tgtatttctgttatgcaaataatagaaatgggggtatccttcctctcagcgagcataatctatttgctgtgatgatgtatatactttcttgcaggttcagAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAA

Basic information

species	Zea mays
transcript	GRMZM2G125556_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G125556_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 1

-tgtatttctgttatgcaaataatag-----aaatgggggtatccttcctctcagcgagcataatctatttgctgtgatgatgtatatactttcttgcaggttcagAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAA
 |      ||||| ||  |  | |        | ||      |      | |        |    | || || ||      |   | |  | | |||||| |  |||||||||  |||| |||||||| ||||| ||||| |  ||||||||||| ||| |||||| | | ||||| |||||||||||||| ||||||||      
attagaaactgttgtgggatcagtgtctctttagtgaattagtgtggatttttgtttgctacggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT------

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|211041276|gb|FL124823.1|FL124823

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         AGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCA
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... gcaggttcagAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCA

EST: gi|211466766|gb|FL298411.1|FL298411

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211041277|gb|FL124824.1|FL124824

EST:     GGNAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         AGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCA
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... gcaggttcagAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCA

EST: gi|211466762|gb|FL298407.1|FL298407

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211466772|gb|FL298417.1|FL298417

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211475757|gb|FL124814.1|FL124814

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|71421128|gb|DR805308.1|DR805308

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211464236|gb|FL298400.1|FL298400

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|76285485|gb|DV025053.1|DV025053

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211464239|gb|FL298403.1|FL298403

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211475756|gb|FL124813.1|FL124813

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211466761|gb|FL298406.1|FL298406

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211475759|gb|FL124816.1|FL124816

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211464237|gb|FL298401.1|FL298401

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211466767|gb|FL298412.1|FL298412

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211466770|gb|FL298415.1|FL298415

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211041272|gb|FL124819.1|FL124819

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|211041270|gb|FL124817.1|FL124817

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|76283007|gb|DV022575.1|DV022575

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

EST: gi|93282356|gb|EB674620.1|EB674620

EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGGTTCAG                    
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA-----C-Ggtcagttcgc ... gcagg

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: 48 (upstream exon), 49 (downstream exon)
Score: 6

ATATATTCGTGTCCTCCGAATTAGTCCTTCCTGCAGTGTCCTCGCCGACAGGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... gcaggttcagAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAA

Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 14

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 28

Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 5

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcagcgagcataatctatttgctgtgatgatgtatatactttcttgcaggttcagAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAA

                                      ctttcttgc  CT-rich tract
         ataatctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatttctgttatgcaaataatagaaatgggggtatccttcctctcagcgagcataatctatttgctgtgatgatgtatatactttcttgcaggttcagAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAA

tgtattt
- - - - - ttatgca
- - - - - - - - - - aatagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat