ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttcttctttcatatcttatttttgctaatgttttatgataaatagtcaggcttcacgaatgtttctattatactgttaaatctgtactaacca...

Basic information

species	Zea mays
transcript	GRMZM2G038401_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G038401_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 5'ss of exon 7

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttcttctttcatatcttatttttgctaatgttttatgataaatagtcaggcttcacgaatgtttctattatactgttaaatct--gtactaac-ca--
||| |||||||| || || ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||   |  |  ||    |   | | ||   | || |||||| ||| |||  |   ||   | || | ||| | | | |  ||   ||  || || || ||  
AGGATTTGCACAGTATGTTCCAAATGAAAATCTTTTGATGACAAAAGAACAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGAGCTGCAGAGGAGgtacacactaattctt----ttacagtcttatgactgatttatgttaa-tagctaccttttgtggatatatctttcaaattcctactgctgagtgctgacacacc

upper sequence: GRMZM2G038401_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G14640.1 (Glycine max), 5'ss of exon 4

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgta-------cattttcttctttcatatcttatttttgctaatgttttatgataaatagtcaggcttcacgaatgtttctattatactgttaaatctgtactaacca
 || ||||| ||||| || || | ||| || ||| | |||||||| |||||||||||||||||||| || ||| || | ||||| || ||| | ||| ||||        ||||| ||||||| || | |   |||| ||  |||||| |  |  ||| ||    ||   | |||  |  ||  | ||||| ||    |  |||   
TGGGTTTGCTCAATATGTTCCCAGTGAGAACCTTCTCATGACAAAGGAGCAGCTTTTTGATATGACTTGTATGGCACTTGGTGGTCGGGCTTCTGAGCAGgtggtcttggcatttccttcttttatgtttacctttttctcctgtttt-tcttttatattc---tttgctgtatggctagatctttctgttgaaagaatg-taat--

upper sequence: GRMZM2G038401_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA12G06580.1 (Glycine max), 5'ss of exon 4

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttcttctttcatatcttatttttgctaatgttttatgataaatagtcaggcttcacgaatgtttctattatactgttaaatctgtactaacca-----
 || ||||| ||||| || || ||||| || ||||| |||||||| ||||||||||||||||| || || |||||| | ||||| || ||||| ||| |||||  |||     || | | | || |||||  | |  |||     |     ||    ||||    || | |||  | ||  | || |||| | ||    |     
TGGATTTGCCCAATATGTTCCCAATGAGAACCTTTTCATGACAAAGGAGCAGCTTTTTGATATCACTTGTATGACACTTGGTGGTCGGGCTGCTGAGCAGgtagttttgacatttcctttttttttttttttttacctttctctct--cctgtttttcttc-tatat-tctctgctgtatggctagatct-ttctgttgaaagaa

upper sequence: GRMZM2G038401_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA12G06530.1 (Glycine max), 5'ss of exon 7

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttcttctttcatatcttatttttgctaatgttttatgataaatagtcaggcttcacgaatgtttctat-tatactgttaaatctgtactaacca----
 || ||||| ||||| || || ||||| || ||| | |||||||| |||||||||||||||||||| || |||||| | || || || ||||| ||| |||||  |||     || |   | || |||||| | |   ||| |      |  |     |  |      || || | | ||  | || |||| | ||    |    
TGGGTTTGCCCAATATGTTCCCAATGAGAACCTTCTCATGACAAAGGAGCAGCTTTTTGATATGACTTGTATGACACTTGGCGGTCGGGCTGCTGAGCAGgtagttttgacatttcc---ttttttttttgtttac-ctttctctctcctgtttttcttctatattctttgctgtatgtatggctagatct-ttctgttgaaaga

upper sequence: GRMZM2G038401_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 5'ss of exon 7

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttct---tctttcatatcttatttttgct-aatgttttatgataaatagtcaggcttcacgaatgtttctattatactgttaaatctgtactaacca
 || |||||||||||||| ||||| ||||| ||| | ||||| |||||||| || ||||| ||||| ||||||||  | || |||||||| || ||| ||||| | |  ||   |  | |  || | | || | ||  |      ||   | |  ||     |||| || |||||  | | |   ||   ||||  ||  |   
CGGATTTGCACAATACGTTCCAAACGAAAACCTTCTCATGACCAAAGAGCAACTCTTTGACATGACTTGCATGACTCTCGGAGGCCGTGCAGCTGAGCAGgtaaaatccctaattgctactaatgtgaattatcctcgacagaaaatataagaatgttgttgttcaaga-tgttttaagtttctggtcctatctcaacgtag--

upper sequence: GRMZM2G038401_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S456_6V6.1 (Physcomitrella patens), 5'ss of exon 8

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgta-----cattttcttctttcatatcttatttttgctaatgttttatgataaatagtcaggcttcacgaatgtttctattatactgttaaatctgtactaacca
||| ||||| |||||  | || || || |||||  | |||||||| ||||| ||||| ||||||||||| |||||| | || || |||||||| ||| |||||     |   |  || |||  | | || |||||  |  |  |||    |   |  |   |  |   | ||  |    | |    | |   | |||        
AGGTTTTGCTCAATATTTACCGAACGAGAATCTGCTCATGACAAAGGAGCAACTTTTGGATATGACATGTATGACACTTGGAGGTCGTGCTGCGGAGCAGgtattggacgagtcttttttttttttttttttttttttttttcttttctttgcttctttttgtcttgggtatcctctcttgaagagggttgctgtgtctc-----

upper sequence: GRMZM2G038401_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S346_22V6.1 (Physcomitrella patens), 5'ss of exon 8

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttcttctttcatatcttatttttgctaatgttttatgataaata-----gtcaggcttcacgaatgttt---ctattatactgttaaatctgtactaacca-----------------------------------------------------------------------------------------
||| ||||| || ||  | |||||||| |||||  | |||||||| ||||||||||| || |||||||| |||||| | || || ||||| || ||| ||||| |     |  |||  | ||||  | |||   | |   | |   ||| |       || | | ||  | |||||   || | |   |  |     | ||||  | |                                                                                         
AGGTTTTGCTCAGTATTTACCAAATGAGAATCTGCTTATGACAAAGGAGCAGCTTTTGGACATGACATGTATGACACTTGGAGGTCGTGCCGCTGAGCAGgtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacag

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|211346930|gb|FK977754.1|FK977754

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|60358258|gb|DN225231.1|DN225231

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|211346929|gb|FK977753.1|FK977753

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|31353784|gb|CD438141.1|CD438141

EST:     CTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGCTTTCTCAGAATGACCTGGAGAAAGT
genomic: CTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTG-GTGCTCAGAATGACCTGGAGAAAGT

EST: gi|32928350|gb|CF033162.1|CF033162

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|71332347|gb|DR803114.1|DR803114

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|60343952|gb|DN210925.1|DN210925

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|211346933|gb|FK977757.1|FK977757

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|61118761|gb|DN559722.1|DN559722

EST:     AGCTTTTTGATATGACATACATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|60355707|gb|DN222680.1|DN222680

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGNAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|32934811|gb|CF039623.1|CF039623

EST:     AGCTTTTTGATATGGCATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGGATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|211346936|gb|FK977760.1|FK977760

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|60394632|gb|DN227502.1|DN227502

EST:     AGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|67013763|gb|CO442512.1|CO442512

EST:     AGCTTTTTGATATGACATGCATGACATTANGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGNAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|94473016|gb|EB701974.1|EB701974

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|6637060|gb|AW261332.1|AW261332

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAG
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAG

EST: gi|78544110|gb|DV621608.1|DV621608

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

EST: gi|213169945|gb|FM183968.1|FM183968

EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 177

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 262

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttcttctttcatatcttatttttgctaatgttttatgataaatagtcaggcttcacgaatgtttctattatactgttaaatctgtactaacca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG