ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GAGGCAGGTGGAGGCGAACAAGCGGAAGCTGGAGGAGCTTCAGCTCCACTACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctgtttcttgtgtcgctcgatgccttcttttctgtaggtttactttatcccaatcggcttttctgcag

Basic information

species	Zea mays
transcript	GRMZM2G173321_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G173321_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g09420.1 (Oryza sativa), 5'ss of exon 1

------GAGGCAGGTGGAGGCGAACAAGCGGAAGCTGGAGGAGCTTCAGCTCCACTACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttg--------cgctgtttcttgtgtcgctcgatgccttct--tttctgtagg--tttactttatcccaatcggcttttctgcag-------------------------------------
      | ||||||||||||||||||||||||||||||||||||| |  |||||| ||||||||||||||||| | ||      | ||||| ||||||| ||||||||  |        | |  |||||| | |   | |||  |  ||  ||| | | ||  |||  ||    |   | |  || | ||  |                                     
GCGGAGGCGGCAGGTGGAGGCGAACAAGCGGAAGCTGGAGGAGCTCCGCCTCCACCACCTCTCCGCCGCCGTCCGCGA------ATCCGCCTCCAAGCCGTCGCCGgtcagattcccctcaccatttcttttctttttggatttcccctggtttttctcggtctttgattctctctggttgttttgtttgtgggtctcttcctgatctgggcggttgccggtgggtgcag

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|211138903|gb|FL206376.1|FL206376

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGT-ATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|26456740|gb|CA828323.1|CA828323

EST:     ACCTCTCCGCCGCCGTCAGAGAAGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|76936192|gb|DV174627.1|DV174627

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|149051910|gb|EE156043.2|EE156043

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|78093455|gb|DV521829.1|DV521829

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|26457345|gb|CA828928.1|CA828928

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|211138901|gb|FL206374.1|FL206374

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|60397540|gb|DN230356.1|DN230356

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|93281470|gb|EB673734.1|EB673734

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|211138904|gb|FL206377.1|FL206377

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|211138900|gb|FL206373.1|FL206373

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|211139833|gb|FL206379.1|FL206379

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|211139832|gb|FL206378.1|FL206378

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|211138902|gb|FL206375.1|FL206375

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCG-CGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|20507484|gb|BQ279652.1|BQ279652

EST:     ACCTCTCCGCCGCCG-CAGAGAAGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

EST: gi|71333335|gb|DR803729.1|DR803729

EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

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), 47 (downstream exon)
Score: 96

GAGGCAGGTGGAGGCGAACAAGCGGAAGCTGGAGGAGCTTCAGCTCCACTACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCG

Block sizes: 28 (upstream exon), 43 (downstream exon)
Score: 23

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 27

Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 10

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCAGGTGGAGGCGAACAAGCGGAAGCTGGAGGAGCTTCAGCTCCACTACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctgtttcttgtgtcgctcgatgccttcttttctgtaggtttactttatcccaatcggcttttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG