ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtcttcttcctgttttttcagctgccactctgttacttgttagctcatggtgctgaactgctgaactgcatctgcttgctagccatataatacc...

Basic information

species	Zea mays
transcript	GRMZM2G134747_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g33270.1 (Oryza sativa), 5'ss of exon 3

CATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtcttcttcctgttt--tttcagctgccactctgttacttgttagctcatggtgctgaactgctgaactgcatctgcttgctagccatataatacc
 ||||||||||| ||||| |||||||||||  |||| || || ||||||||||| ||||||||||||||||||||||| ||||| ||||||| ||| |||||  |||| ||||| ||      ||   | |   |   | |||||| || |    || |||  || ||   |  |  |      |||   |  |||   |  
TATAGACTTCTACTGTTCGGTTGACAAGGTACAAGGTGCTGATGGAAAAGATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttttcttgcttccctattctcgatataatcatcttacttttttgaat-tgatgcataattgaatatgttgaatcatctgccgtctgtatggaag-

upper sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0049g01520.t01 (Vitis vinifera), 5'ss of exon 3

CATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtcttcttcctgttttttcagctgccactctgttacttgttagctcatggtgctgaactgctgaactgcatctgcttgctagccatataatacc--
|||||||||||| || ||||||||||| ||| |||| |  || ||||| |||||||||||  | || ||||||||||||||| | ||| | || || |||||| ||  | | ||| |    ||  |  |       ||  |     |   ||||       ||     |||          | | |   ||| || ||    
CATAGACTTCTACTGCTCAGTTGACAAAGTTAAAGGTGTGGATGGAAAGGATCGTGTGGTCTTGACGTTTGATGGGAAGTATTTGCCTCATACAGAGCAGgtcagttgcattttcgtacagttagaaat-tgttgttggcatacactgaatcataaaataaaaaataagaaaaatgaaaattagttgaacat-tagtagtga

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|7844018|gb|AW787345.1|AW787345

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAG
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAG

EST: gi|113571359|gb|DW741030.1|DW741030

EST:     GGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: GGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|60400889|gb|DN233696.1|DN233696

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|211469684|gb|FL432027.1|FL432027

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|31441069|gb|CD510500.1|CD510500

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|211191597|gb|FL255435.1|FL255435

EST:     ATCGTGTTGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|78544325|gb|DV621823.1|DV621823

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|26457359|gb|CA828942.1|CA828942

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|31405717|gb|CD484449.1|CD484449

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|60399029|gb|DN231845.1|DN231845

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|211044293|gb|FL125316.1|FL125316

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|12046752|gb|BF728891.1|BF728891

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|31611770|gb|CD568392.1|CD568392

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATG
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATG

EST: gi|211009982|gb|FL448376.1|FL448376

EST:     ACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|30032230|gb|CB834081.1|CB834081

EST:     ATCGTGTGGTGGTCACAAAAAATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|31406273|gb|CD485005.1|CD485005

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|7844445|gb|AW787667.1|AW787667

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|149011217|gb|EE042296.2|EE042296

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGC

EST: gi|7844017|gb|AW787344.1|AW787344

EST:     ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAG                         AAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGAT
genomic: ATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGAT

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), 46 (downstream exon)
Score: 131

CATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtct ... acatctgcagAAATCTGAACATATGATGTCTAGGCCAACCCGCAAGACATCTTGATGTGGCTGGTGAGGAGGAGAAACATGATCGTAGTGGTTGGTATCGGGCTCAGCAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 231

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 125

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtcttcttcctgttttttcagctgccactctgttacttgttagctcatggtgctgaactgctgaactgcatctgcttgctagccatataatacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG