ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTCAATGAAGATGACTTGTGCAAATTGCTTCCATATGTCAGTCGTCGTCGTCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctgtggtggactaatggtttatctatctcaaacaacattgaacatctgtgaaaaacctgtattctttcagcttattaaaatgcttgacaaata...

Basic information

species	Zea mays
transcript	GRMZM2G160316_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G160316_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g07380.1 (Oryza sativa), 5'ss of exon 2

TTCAATGAAGATGACTTGTGCAAATTGCTTCCATATGTCAGTCGTCGTCGTCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctgtggtggactaatggtttatctatctcaaacaacattgaacatctgtgaaaaacctgtattcttt-cagcttattaaaatgcttgacaaata--
||    ||||| ||  |||| ||  | || ||||  |||||||||||||| ||||||||||| |||||| || | ||||||||||| ||||| |||||||||||||||| |  |||| ||||  |  | |||  ||   |   ||  |    |  |        | ||||  |    |    | | | |||| || |  |   
TTTGCGGAAGACGAGCTGTGTAAGCTTCTCCCATCAGTCAGTCGTCGTCGCCAGACACCTGAGCTTTGTAGAATACTTGGGTTGTCACAGAACATGCCAGgtcagtgctatcatggattaatcatgcacctagttc---cgttatgtattgaccataggggttttctatttgtcattgtcactcagattgctagagagcttat

upper sequence: GRMZM2G160316_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g07360.1 (Oryza sativa), 5'ss of exon 2

TTCAATGAAGATGACTTGTGCAAATTGCTTCCATATGTCAGTCGTCGTCGTCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctgtggtggactaatggtttatct-atctcaaacaacattgaacatctgtgaaaaacctgtattctttcagcttattaaaatgcttgacaaata
||     |||||||  |||| ||  | ||||| |  |||||||||||||||||||||||||| |||||| || | ||||| ||||| ||||| |||||||||||||||| |  | || ||||  |  | ||  |  ||   | |||  |  ||   || ||    | ||||  |     | | | | ||| ||    || |
TTTGCACAAGATGAGCTGTGTAAGCTACTTCCCTCAGTCAGTCGTCGTCGTCAGACACCTGAGCTTTGTAGAATACTTGGATTGTCCCAGAACATGCCAGgtcagtgctatcatcgattaataatgcagcttgttccattgagcatcaataataaatggaat-tttctatttctctttgtcactcagatgtttagagaaca

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|31557940|gb|CD527152.1|CD527152

EST:     AACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         G-GTCATTGAAGTTCTGG-GGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: AACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|211250452|gb|FK978630.1|FK978630

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGCAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|87153317|gb|DY398106.1|DY398106

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAATGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|19770478|gb|BQ035199.1|BQ035199

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAA-TGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAATGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|29543979|gb|CB604359.1|CB604359

EST:     TCAGACACCTGAAC-TTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         G-GTCATTGAAGTTCTGG-GGAAAG-GGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|31406338|gb|CD485070.1|CD485070

EST:     TCAGACACCTGAACTTTGTCGA-TGCTTGGGTTGTCGCAGAAAATGCCAG                         G-GTCATTGAAGTTCTGG-GGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|91056387|gb|EB166805.1|EB166805

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|8930234|gb|BE224998.1|BE224998

EST:     TGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|61118818|gb|DN559779.1|DN559779

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|76282460|gb|DV022028.1|DV022028

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|211250451|gb|FK978629.1|FK978629

EST:     TCAG-MACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|5928808|gb|AW056100.1|AW056100

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|60400787|gb|DN233594.1|DN233594

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|19436599|gb|BM953009.1|BM953009

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAATGGAAGAC
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGAC

EST: gi|20300669|gb|BQ163612.1|BQ163612

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAATGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|22818834|gb|BU498924.1|BU498924

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGGGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|19436600|gb|BM953010.1|BM953010

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAATGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|67018089|gb|CO446838.1|CO446838

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|8577162|gb|BE129799.1|BE129799

EST:     CGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT
genomic: CGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

EST: gi|22491645|gb|BU051568.1|BU051568

EST:     TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAG                         GTGTCATTGAAGTTCTGGTGGAAAATGGAAGACCTATTGATGCAATTAATT
genomic: TCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATT

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: 46 (upstream exon), 49 (downstream exon)
Score: 851

TTCAATGAAGATGACTTGTGCAAATTGCTTCCATATGTCAGTCGTCGTCGTCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctg ... ttgaaatcagGTGTCATTGAAGTTCTGGTGGAAAGTGGAAGACCTATTGATGCAATTAATTTGGCTTATGTGTTTGAGCTTACTGAACAATTTGAACCAGTACACCTTCT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 259

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 411

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 305

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAATGAAGATGACTTGTGCAAATTGCTTCCATATGTCAGTCGTCGTCGTCAGACACCTGAACTTTGTCGATTGCTTGGGTTGTCGCAGAAAATGCCAGgtcagtgctgtggtggactaatggtttatctatctcaaacaacattgaacatctgtgaaaaacctgtattctttcagcttattaaaatgcttgacaaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgaaaaa