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

gtgctccttttttttctctctctataaccaatctacaacttgcttgaactctttaaatagctggccctcttcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATAAATCCTGGGAGGATGACTTTGTTTGGTACCCTTTTGATTATCTGGGGTA

Basic information

species	Zea mays
transcript	GRMZM2G070890_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G070890_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g37480.1 (Oryza sativa), 3'ss of exon 2

gtgctccttttttttctctctcta-taaccaatct----------acaact----tgcttgaactctttaaatagctggccctcttcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATAAATCCTGGGAGGATGACTTTGTTTGGTACCCTTTTGATTATCTGGGGTA
|| ||| |||||||| | |    | |  ||||  |          | || |       |||      || | |  ||  | | ||||| || ||||| ||||| |||||||||||||||| ||||||||| ||  ||||  ||||||| |||||||||||||| |||||||||||||||||| ||||||||||| 
gtactctttttttttttttaataactggccaactttcttaagcagataattgtgacaattgttacactttactctctttctcacttctcaaccagATTCTTGCTGGAAGCTACTTCTGTGCTGCTGGAGCACTTGTTGGTGTCATAAACCCTGGGAGGATGACCTTGTTTGGTACCCTTTTGGTTATCTGGGGTC

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|30032255|gb|CB834106.1|CB834106

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|8318776|gb|BE025341.1|BE025341

EST:     TGACAGAAGCAAAAAATGCTTCGGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|32908647|gb|CF013460.1|CF013460

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGGTCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|5525651|gb|AI861544.1|AI861544

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|16927012|gb|BM080075.1|BM080075

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|8318775|gb|BE025340.1|BE025340

EST:     TGACAGAAGCAAAAAATGCTTCGGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|31406373|gb|CD485105.1|CD485105

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|74240707|gb|DT648621.1|DT648621

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|76021511|gb|DT948681.1|DT948681

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|211472795|gb|FL222251.1|FL222251

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|6020755|gb|AW065563.1|AW065563

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|91869972|gb|EB400635.1|EB400635

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|78021866|gb|DV490253.1|DV490253

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|19770170|gb|BQ034891.1|BQ034891

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|37419378|gb|CF647370.1|CF647370

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|32908451|gb|CF013264.1|CF013264

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGGTCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|76021510|gb|DT948680.1|DT948680

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|5268989|gb|AI770953.1|AI770953

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|26455738|gb|CA827321.1|CA827321

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|211219760|gb|FK951131.1|FK951131

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCAT
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCAT

EST: gi|148967227|gb|EE018425.2|EE018425

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|211221824|gb|FK951139.1|FK951139

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCT
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCT

EST: gi|211472793|gb|FL222249.1|FL222249

EST:     TGACAGAAGCAAAAA-TGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATCCTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|5871090|gb|AW017531.1|AW017531

EST:     GCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: GCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|29130621|gb|CB381325.1|CB381325

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|5819300|gb|AI987506.1|AI987506

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|211223889|gb|FK951159.1|FK951159

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|16919885|gb|BM074403.1|BM074403

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|78021639|gb|DV490026.1|DV490026

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|32908815|gb|CF013628.1|CF013628

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGGTCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

EST: gi|149098823|gb|EE184836.2|EE184836

EST:     TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAG                         ATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA
genomic: TGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATA

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: 113

TAAAAGCAAGACATTTCCGAGTTGGAATGACCTGTTTGACATGTACAACCTGACAGAAGCAAAAAATGCTTCTGCAGTAGTTGATCTCCAGCGTCTAGAGgtgctccttt ... tcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATAAATCCTGGGAGGATGACTTTGTTTGGTACCCTTTTGATTATCTGGGGTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 127

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaccaatctacaacttgcttgaactctttaaatagctggccctcttcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATAAATCCTGGGAGGATGACTTTGTTTGGTACCCTTTTGATTATCTGGGGTA

 ctataac  putative branch site (score: 127)
                                   ctggccctcttctt  putative PPT
                        tctttaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctccttttttttctctctctataaccaatctacaacttgcttgaactctttaaatagctggccctcttcttaatcagATACTTGCCGGAAGCTACTTCTGTGTTGCTGGAGCGCTCATTGGCATCATAAATCCTGGGAGGATGACTTTGTTTGGTACCCTTTTGATTATCTGGGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG