ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...gtaacatagaactgtacttggaatttattatttctctgcatcagcaggtcaacgtttcataaattctggttttaatcatctgcttgatttgtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG

Basic information

species	Zea mays
transcript	GRMZM2G128171_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G128171_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g23740.1 (Oryza sativa), 3'ss of exon 1

--gtaacatagaactgtacttggaatttattatttctctgcatcagcaggtcaacgtttcataaat-tctggttttaatcatctgcttgatttgtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG
     |  ||  |||  |      ||   |||  | | ||   || ||| ||| | ||||| | || ||| || ||| ||||| |  | || | | || |||||||||||||||||||||||||||| |||||||||||||  |||||||||||||| |||||||| ||||||||||| ||||| |||
ctcagatgtattactagaaaaaccatgc-ttaaatatttgtg-catcagttcagcatttcaaagatatctagtgttactcatcggtct-atctatctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG

upper sequence: GRMZM2G128171_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 2

gtaacataga-actgtacttggaatttatta-tttctctgcatcagcaggtcaacgtttcataaattctggttttaatcatctgcttgatttgtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG
 ||||  |   | ||||||    | ||| || ||||  |   | |  | ||  ||   |     ||| || ||   ||||  | |||  ||||||    ||||||||| |||||||| ||||||||||| || |||||||  ||||||   || || |||||||| |||||||| || ||||  |||
-taaccaattcattgtactaattacttagtaatttccttatgttattatgttcactaatatgtcattatgtttacgatcacttccttt-tttgttgtaatagGTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG

upper sequence: GRMZM2G128171_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G01750.1 (Glycine max), 3'ss of exon 1

gtaacataga-actgtacttggaatttatta-tttctctgcatcagcaggtcaacgtttcataaattctggttttaatcatctgcttgatttgtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG
 |||| ||   | |||| |    | | | ||  |||  |  || || | ||  ||   |     ||| || ||   ||||  | ||   ||||||    ||||||||| |||||||| ||||||||||| || |||||||  ||||||   || || |||||||| |||||||| || || |  |||
ttaacctattcattgtagtaattactaagtaacttccttatattagtatgtacactaatatgtcattatgtttacgatcacttcctc--tttgttgtaatagGTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG

upper sequence: GRMZM2G128171_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 1

--gtaacataga-actgtacttggaatttattatttctctgcatcagcaggtcaacgtttcataaattctggttttaatcatctgcttgatttgtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG
     |  || |   | ||||  ||| |||    ||       |  || | | ||  | | |  ||||    || |     |   | || |||   |  | |||||||||||||||||||| |||||||| ||||||||||  || || ||||| || ||||| ||||| ||||| |||||||| |||
tttcgatttatatgttttactgagaaattagagcttactgatgtgtgctgttgaa--tctgactaattgcatttatggaattggacatggttttaataat-agGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG

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|211249331|gb|FL145209.1|FL145209

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211249326|gb|FL145204.1|FL145204

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211249337|gb|FL145215.1|FL145215

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTA--AA-GACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211251557|gb|FL145220.1|FL145220

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211242633|gb|FL145173.1|FL145173

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|32805924|gb|CD958158.1|CD958158

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211247093|gb|FL145191.1|FL145191

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211242629|gb|FL145169.1|FL145169

EST:     AAGGAGRTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211244865|gb|FL145185.1|FL145185

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211244868|gb|FL145188.1|FL145188

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|78117464|gb|DV535851.1|DV535851

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211247094|gb|FL145192.1|FL145192

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGARAGACTTNGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211244858|gb|FL145178.1|FL145178

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211247098|gb|FL145196.1|FL145196

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211249327|gb|FL145205.1|FL145205

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAARAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211247101|gb|FL145199.1|FL145199

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211242628|gb|FL145168.1|FL145168

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211249329|gb|FL145207.1|FL145207

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211249334|gb|FL145212.1|FL145212

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211247099|gb|FL145197.1|FL145197

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211251558|gb|FL145221.1|FL145221

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

EST: gi|211249328|gb|FL145206.1|FL145206

EST:     AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTG                         GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG
genomic: AAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAG

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), 49 (downstream exon)
Score: 254

CGCTTGCGGACGGCGACGACGTGGTGGCCCTTACCGAATCCACGTTCGAGAAGGAGGTCGGAAAGGACCGCGGCGCCCTCGTCGAGTTCTACGCCCCCTGgtttgagctc ... gtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 491

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 842

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aggtcaacgtttcataaattctggttttaatcatctgcttgatttgtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG

                                          tttgttt  CT-rich tract
         tttcataaatt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatagaactgtacttggaatttattatttctctgcatcagcaggtcaacgtttcataaattctggttttaatcatctgcttgatttgtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - -gtacttg
- - - - - - - - - - - - - - - - - -ctgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctggt