ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ATAAAGACGACTTCCCATATGTGGAAACCCGTTATTCTTATGGTTCGCCACCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtcctacttaattctagagtaaacctccaactatctgatttacattcttacacttgtattactgcaaatagtataagaactgcctggctgaatctt...

Basic information

species	Zea mays
transcript	GRMZM2G109429_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G109429_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g66960.1 (Oryza sativa), 5'ss of exon 3

ATAAAGACGACTTCCCATATGTGGAAACCCGTTATTCTTATGGTTCGCCACCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtcctacttaattctagagtaaacctccaactatctgatttacattcttacacttgtattactgcaaatagtataagaactgcctggctgaatctt----
|||||||||||||||| ||||||||| | ||||||   ||||| || |||||||||||||| ||||||||  |||| || || ||||||||||| |||||| || |   |     |   ||| ||||  ||    ||||| |   |   |  | ||  | | |  ||| |  || | |||  |||| ||| |||     |    
ATAAAGACGACTTCCCTTATGTGGAAGCTCGTTATGTCTATGGCTCTCCACCAAAGCTCATTATGCTTGATGACAAAGGCGACCAGAAGGAGACTATAAGgtaaattggaga-gctgtcagaataaatttcttgttatctaag--aggatgatgcagatttctctctgaacctaat-taattactggctgactggcctcttcac

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|86473154|gb|DY239524.1|DY239524

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|37382347|gb|CF628115.1|CF628115

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|78027093|gb|DV495480.1|DV495480

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|28422521|gb|CB251924.1|CB251924

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|33095813|gb|CF055807.1|CF055807

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|13558509|gb|BG549865.1|BG549865

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGA
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGA

EST: gi|211122267|gb|FL373642.1|FL373642

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|148934019|gb|EC878027.2|EC878027

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|5058588|gb|AI737064.1|AI737064

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|37388132|gb|CF631272.1|CF631272

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|211444189|gb|FL421109.1|FL421109

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|60349419|gb|DN216392.1|DN216392

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|211214746|gb|FL397473.1|FL397473

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACAYTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|211401574|gb|FL440163.1|FL440163

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|13558052|gb|BG549408.1|BG549408

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCA
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCA

EST: gi|211264271|gb|FL294955.1|FL294955

EST:     CCAAAGCTCATAATGCTTGACAACNAGGGTGAACAGAAGGAGACCATAAG                         GATTTGATAACTGG
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATT-GATAACTGG

EST: gi|13558051|gb|BG549407.1|BG549407

EST:     CAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAG
genomic: CAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACC-ATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAG

EST: gi|211173040|gb|FL404342.1|FL404342

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACA
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACA

EST: gi|13562227|gb|BG550447.1|BG550447

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|148934022|gb|EC878030.2|EC878030

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|78090328|gb|DV518702.1|DV518702

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTTCTCAAGGAGAAAG
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTT-CTCAAGGAGAAAG

EST: gi|148953620|gb|EC898976.2|EC898976

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|18181460|gb|BM382670.1|BM382670

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|211489672|gb|FL462920.1|FL462920

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

EST: gi|78090327|gb|DV518701.1|DV518701

EST:     CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAG                         GATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT
genomic: CCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGT

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: 364

ATAAAGACGACTTCCCATATGTGGAAACCCGTTATTCTTATGGTTCGCCACCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtccta ... aaattggcagGATTGATAACTGGAAGCGAGAGCACATTCGGCAGTTTCTCAAGGAGAAAGTGAAGCCAGTGAAATTAGACAGCTGAGTTCTTGCGATAAGTGCCTGAATA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 379

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAAGACGACTTCCCATATGTGGAAACCCGTTATTCTTATGGTTCGCCACCAAAGCTCATAATGCTTGACAACAAGGGTGAACAGAAGGAGACCATAAGgcaagtcctacttaattctagagtaaacctccaactatctgatttacattcttacacttgtattactgcaaatagtataagaactgcctggctgaatctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccaac