ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgcatattttagctgaaccaattaattcagcacaaatgatgtcctaggttttttttggggaaatcttgggtacccttgccatctttgtttttt...

Basic information

species	Zea mays
transcript	GRMZM2G074790_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G074790_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 5'ss of exon 6

CAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgcatattttagctgaaccaattaattcagcacaaatgatgtcctaggttttttttggggaaatcttgggtacccttgccatctt-tgtttttt
||| ||||| ||||||||||||||||| |||||||||||||| || |||||||| ||||||||||||||||||||||||||||| ||||||||||| |||||||||||| || | || |   || || | ||| |||||  ||  |  |  |||    ||           ||    | |  |  |  | |  ||    | 
CAAGACATTAGACAATGAGCTTGAAGCGGTACAGGGAATGAAACTTTCCAGAGGCTACATATCTCCTTACTTTGTGACTGATCAGAAGACTCAGAAGTGTgtaagtctgtatttcttggtcaaatcagtgaatccagcatgaactacattgtagaaagttcgctacattccctcatttgctttgactttatgatggaaat-

upper sequence: GRMZM2G074790_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G20560.2 (Glycine max), 5'ss of exon 5

CAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgcatattttagctgaaccaattaattcagcacaaatgatgtcctaggttttttttggggaaatcttgggtacccttgccatctttgtttttt---
 || || ||||| |||||  | ||||  ||| | ||||||||| |  |||||||||||||||||||||| ||| | |||||||| ||||| | ||||||||||||   ||  | ||   ||  |   | |||   |  ||       |   | |  | |        ||||||    || | | | |     | |   |    
GAACACTTTGGATAATGAATTGGAAGTGGTAGAAGGAATGAAGTTAACCAGAGGATACATATCTCCTTATTTTATTACTGATCAGAAGACCCGGAAATGTgtaagc--gctgacttattctttagtcactaacata-tactccctccggttttgaatataagcaaaaaaatctcttctatcttggtctcaaatataagtaaat

upper sequence: GRMZM2G074790_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G01190.1 (Glycine max), 5'ss of exon 6

CAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgcatattttagctgaaccaattaattcagcacaaatgatgtcctaggttttttttggggaaatcttgggtacccttgccatctttgtttttt---
 || || ||||| ||| || | ||||  ||| | ||||||||| |  ||||||| |||||||||||||| ||| | |||||||| ||||| |||||||||||||||  ||| | | |   |    || | |  |   | | | |   ||| |   | |         ||||||    || | | | |     | |        
GAACACTTTGGATAATAAGTTGGAAGTGGTAGAAGGAATGAAGTTAACCAGAGGCTACATATCTCCTTATTTTATTACTGATCAGAAGACCCAGAAATGTgtaagt--gcagactattcttttgtcagtaacatgtactcca-tccggtcttgaatataagcaaaaaaaatctcctctatcttagtctcaaatataagcaaat

upper sequence: GRMZM2G074790_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g02240.t01 (Vitis vinifera), 5'ss of exon 6

CAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgcatattttagctgaacca---attaattcagcacaaatgatgtcctaggttttttttggggaaatcttgggtacccttgccatctttgtttttt
 || || ||||||| |||| | ||||  ||  | |||||||||||  | ||||| || ||||||||||| ||||| ||||| || ||||| |||||||||||||||    || |||    | || ||   |||     | |  |||     |  ||    ||  |           ||   |    ||   |||     |   
AAATACTTTGGACAGTGAGTTAGAAGTGGTGGAAGGAATGAAGCTAGCGAGAGGCTATATATCTCCTTATTTTGTTACTGACCACAAGACCCAGAAATGTgtaagttcagatctttatttttaaacacaaatttgcctatctaaaaaagaataataataattgatcaccctgtaactgaacaaagatgaggtctcccact---

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|18450792|gb|BM429070.1|BM429070

EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAAATCTCAAACAT
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAA-TCTCAAACAT

EST: gi|18649481|gb|BM498300.1|BM498300

EST:     ACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: ACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG

EST: gi|18450399|gb|BM428677.1|BM428677

EST:     GAGGATACATATCTCCTTACTTTGNGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG

EST: gi|78117877|gb|DV536264.1|DV536264

EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCT
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCT

EST: gi|31358270|gb|CD442627.1|CD442627

EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAGAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG

EST: gi|6021191|gb|AW066119.1|AW066119

EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG

EST: gi|87153562|gb|DY398351.1|DY398351

EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG

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: 463

CAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 125

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 127

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 113

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgcatattttagctgaaccaattaattcagcacaaatgatgtcctaggttttttttggggaaatcttgggtacccttgccatctttgtttttt

- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT