ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTCATTGATTGCAAATCTGTCAGCGGCAAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatatatcttttgagcacttgttttgtttttgctaaaccactctttttagtttgctgggaggatttatgtatgtttagtttgaagttctaaagttt...

Basic information

species	Zea mays
transcript	GRMZM2G540538_T02
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G540538_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 7

GTCATTGATTGCAAATCTGTCAGCGGCAAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatatatcttttgagcacttgttttgtttttgctaaaccactcttt-ttagtttgctgggaggatttatgtatgt-ttagtttga--agttctaaagttt--
 ||| || |||||||  | ||||| |||||||| ||||||||||||||||| |||| ||| |||||||||||||||||||      || | |||||   || |    ||||||| |   ||   ||  | | ||   | || |||||| |||   | | || |  |  | || |  |   |  
ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAGgta------atttattgagatattctgagctttttgccaccacatatttcatcacttaatttgggggatttctgtgcatatcagctgcattaattgtgcaaactct

upper sequence: GRMZM2G540538_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G33910.3 (Glycine max), 5'ss of exon 4

GTCATTGATTGCAAATCTGTCAGCGGCAAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatat-----atcttttgagcacttgttttgtttttgctaaaccactctttttagtttgctgggaggatttatgtatgtttagtttgaagttctaaagttt----
|||  |  | || ||  |  |||| ||||| || ||||||||||| ||| | ||||||||||| || |||||||||||||   | |      ||| |  ||    | |||| ||| ||      |    |   |   |   |  | ||| | |  | | |||| | || | || |           
GTCTCTTGTGGCGAACTTAGCAGCTGCAAATTGCTACAAATCTGATCATTTGAAGAGACCAGAAAATTGGGCACTAGgtaccctgtcattggtctatgcaggctctcttttatttctgtctccacttcatagctgactaattcagtggactgacat-tttttattgtgcaattttttctcacgcag

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|18654569|gb|BM499374.1|BM499374

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGNGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|9952767|gb|BE639350.1|BE639350

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTG
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTG

EST: gi|211299293|gb|FK964182.1|FK964182

EST:     AACTGTTTACAA-TCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAA-TACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AACTGTT-ACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|28361646|gb|CB240002.1|CB240002

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|18648924|gb|BM497743.1|BM497743

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTA
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTA

EST: gi|211406117|gb|FK964261.1|FK964261

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAAGGCAAA-TACATCTACATTGCTGGATTTTTCCTTACAGTGT
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAA-GGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGT

EST: gi|60358287|gb|DN225260.1|DN225260

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|28931167|gb|CB334528.1|CB334528

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|18654717|gb|BM499522.1|BM499522

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACA
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACA

EST: gi|60355538|gb|DN222511.1|DN222511

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|18649011|gb|BM497830.1|BM497830

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|30031919|gb|CB833770.1|CB833770

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGG-AAAATACATCTACATTGCTGG
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGG

EST: gi|30087102|gb|CB885310.1|CB885310

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACA
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACA

EST: gi|5555550|gb|AI881501.1|AI881501

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|18649868|gb|BM498687.1|BM498687

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         CTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|211535006|gb|FL000875.1|FL000875

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGA-CTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACA
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACA

EST: gi|18649867|gb|BM498686.1|BM498686

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTG
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTG

EST: gi|18384280|gb|BM417479.1|BM417479

EST:     AA-CTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAGAATACATCTACATTGCTGGATTTTTCCT
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCT

EST: gi|20811213|gb|BQ295691.1|BQ295691

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|18654570|gb|BM499375.1|BM499375

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|18654716|gb|BM499521.1|BM499521

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|211406116|gb|FK964260.1|FK964260

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAA
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAA

EST: gi|211408679|gb|FK964274.1|FK964274

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTT
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTT

EST: gi|211301441|gb|FK964208.1|FK964208

EST:     AA-CTGGTACAGATCTGAGCATCTAAAGAGACCAGAGAACTGG-CACTAG                         TTGAAA-GGCAAA
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAA

EST: gi|24773803|gb|CA409057.1|CA409057

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGCCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|28361834|gb|CB240190.1|CB240190

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|78544692|gb|DV622190.1|DV622190

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|15313680|gb|BI478902.1|BI478902

EST:     AGAG-ACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|78543652|gb|DV621150.1|DV621150

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|40335337|gb|CK369407.1|CK369407

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGATAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|24961588|gb|CA483591.1|CA483591

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|9953243|gb|BE639826.1|BE639826

EST:     AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG                         TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC
genomic: AAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGC

EST: gi|211535002|gb|FL000871.1|FL000871

EST:     ACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGGCACTAG
genomic: ACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGG-CACTAG

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: 38 (upstream exon), 47 (downstream exon)
Score: 840

GTCATTGATTGCAAATCTGTCAGCGGCAAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG

Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 1179

Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 894

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 1273

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGATTGCAAATCTGTCAGCGGCAAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAGgtataatatatcttttgagcacttgttttgtttttgctaaaccactctttttagtttgctgggaggatttatgtatgtttagtttgaagttctaaagttt

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA