ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CTTGTCGAAGGAAAAGTACATGTCCAAGGAAGAGAAGCAGACATCAATCAATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttcgttttttatataggagtcttctgattgctgaacatccatcttgtataaattcaggaagaaagcgttgtccctacacctaatgaacctagt...

Basic information

species	Zea mays
transcript	GRMZM2G459291_T02
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G459291_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g34470.1 (Oryza sativa), 5'ss of exon 6

CTTGTCGAAGGAAAAGTACATGTCCAAGGAAGAGAAGCAGACATCAATCAATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttcgttttttatataggagtcttctgattgctgaacatccatcttgtataaattcaggaagaaagcgttg--tccctacacctaatgaacctagt------
 ||||| ||||| || |||||||||||||| || || ||||||||||| |||||||| ||||||||||| |||||  ||||||||||||||||||||||||||   | | |  || | || |   || |||| |  ||||         || ||  ||    | | ||||||| ||   |   |  ||||| |||||  |||      
TTTGTCAAAGGAGAAATACATGTCCAAGGATGAAAAACAGACATCAATTAATCATTTCCATGAGAAGCTATTTAAGTTGAAGGACATGATGAAGACAGAGgtaggtgat-gagttatgtagacatgtgttcttaccgctgt-------cctagttgaagcctatggagaaagcattaaatatttggacctattgaactcagtactaag

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|60354947|gb|DN221920.1|DN221920

EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG

EST: gi|78021401|gb|DV489788.1|DV489788

EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG

EST: gi|6227239|gb|AW155838.1|AW155838

EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG

EST: gi|148945620|gb|EC890877.2|EC890877

EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG

EST: gi|76018399|gb|DT945569.1|DT945569

EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG

EST: gi|60348894|gb|DN215867.1|DN215867

EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGGGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG

EST: gi|74239921|gb|DT647835.1|DT647835

EST:     ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGG-ATAGGTTCATGGAGGAA
genomic: ATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAA

EST: gi|60359077|gb|DN226050.1|DN226050

EST:     AAACTGAAGGACATGATGAAGACAGAG                         GCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG
genomic: AAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTG

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: 36 (upstream exon), 46 (downstream exon)
Score: 71

CTTGTCGAAGGAAAAGTACATGTCCAAGGAAGAGAAGCAGACATCAATCAATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttc ... ctgagcatagGCCGGGAAAAGGAGAGCTGAGAAAAGGCATAGGTTCATGGAGGAATTTGTGGCTGAATTCTACGAAGAGTGGAGTGGCAGGGCTTGAGGTTGAACAACCA

Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 212

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 127

Block sizes: 31 (upstream exon), 48 (downstream exon)
Score: 123

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTCGAAGGAAAAGTACATGTCCAAGGAAGAGAAGCAGACATCAATCAATCATTTTCATGAGAAGCTTTTTAAACTGAAGGACATGATGAAGACAGAGgtaatggttcgttttttatataggagtcttctgattgctgaacatccatcttgtataaattcaggaagaaagcgttgtccctacacctaatgaacctagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA