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

gtatgctagcttatggcgctgttcaaaatgacattagagatgcaatgagtccagatttttttggtaacctttgcattcttgtatgataatgctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGTTGCCGCGGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG

Basic information

species	Zea mays
transcript	GRMZM2G092719_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g08440.1 (Oryza sativa), 3'ss of exon 3

gtatgctagcttatggcgct--gttcaaaatgacattagagatgcaatgagtccagatttttttggtaacctttgcattcttgta---tgataatgctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGTTGCCGCGGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG---
||||||    ||||  |     |  ||   ||||||| ||  |||| | | |  ||||  |||   || |||||| || ||| ||   |||  |||   ||||||||| |||||||| ||||| |||||||| ||||| || ||||||||||||||||||| | | ||    |  || ||||| || ||||||||||||   | |    
gtatgcggtgttattacttcaagaacacgttgacattggaagtgcattca-tgaagataatttca-tatcctttgtatgcttatacactgagtatgtcttttgcagGTTGATCTGTTTTTCTACAGAGACCCTGAGGAGGCCAAGGAGCAGGAGGAGGAAGCTCCAGCA---CAAGACTTTGCTGCCATCACTGATTACACCGCACCTG

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G04890.1 (Glycine max), 3'ss of exon 3

gtatgctagcttatggcgctgttcaaaat--gacattagagatgcaatgagtccagatttttttggtaacctttgca----ttcttgtatgataatgctgttt----gcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGTTGCCGCGGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG---
        ||  |   | ||||| || ||  |   ||  |  || |  |||   | |||||| || |    |||       || |||  | | | |  |  ||    |||||| |||||||||||||||||||| |||||||| || ||  | || |||||||| |  ||  ||||   ||| | ||||   ||||| |||| | | | ||   
--------gccca---ctctgtttaacatctggggtttaatttggagagagcaaatatttttgtgctggattttttgaagtttattggcttaaattttttctttggtgcagGTTGATCTGTTCTTCTATAGAGAACCAGAGGAGGCTAAACAACAAGAGGAGGAGGAAGCTCCGGCGGTTGATTATGCC---ATCACGGATTTCAATGCAGGTG

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|29544057|gb|CB604437.1|CB604437

EST:     TTCTGCAAATGAGGCGCACTATCCTTCCTGGGCACAAGT-GGAAGTCATG                         GTCGGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGA
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTC-GATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGA

EST: gi|30306898|gb|CD001571.1|CD001571

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|60344945|gb|DN211918.1|DN211918

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|149000198|gb|EE037342.2|EE037342

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|31910441|gb|CD651425.1|CD651425

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|166417765|gb|EG085079.1|EG085079

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTACAGAGACCCAGAGGAAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAG

EST: gi|60394692|gb|DN227562.1|DN227562

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTACAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|8367495|gb|BE050440.1|BE050440

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTACAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|71773593|gb|DR971491.1|DR971491

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|71773592|gb|DR971490.1|DR971490

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|18659186|gb|BM500199.1|BM500199

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTACAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|50330906|gb|CO526032.1|CO526032

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|30705679|gb|CD058872.1|CD058872

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|211518212|gb|FL037249.1|FL037249

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTACAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|33093619|gb|CF053613.1|CF053613

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTACAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|211518209|gb|FL037246.1|FL037246

EST:     TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

EST: gi|29544201|gb|CB604581.1|CB604581

EST:     AAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATG                         GTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: AAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG

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: 634

CAAGGGGAGGAACAGCATTGGATGTCTGTTCTGGCTTCTGTCCAGGATGGTTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgtatgctagc ... ctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGTTGCCGCGGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 623

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 614

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 566

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gagtccagatttttttggtaacctttgcattcttgtatgataatgctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGTTGCCGCGGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG

               tggtaac  putative branch site (score: 566)
      agattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctagcttatggcgctgttcaaaatgacattagagatgcaatgagtccagatttttttggtaacctttgcattcttgtatgataatgctgtttgcagGTCGATCTGTTCTTCTATAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGTTGCCGCGGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG