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

gtatgtgctctgcggaggaaatgttttgctaatttgcttcaacacgaaagagaggttccttctacatatttcctgtagtttaacgtactgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTAAAATGGGGGGATGATAACCATAAGTGGATTCGACCTGGACACCTCTTCA

Basic information

species	Zea mays
transcript	GRMZM2G050984_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g31550.2 (Oryza sativa), 3'ss of exon 12

gtatgtgctctgcggaggaaatgttttgctaatttgcttcaacacgaaagagaggttccttctacatattt-------cctgtag--tttaac----gtactgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTAAAATGGGGGGATGATAACCATAAGTGGATTCGACCTGGACACCTCTTCA
          |  |  |||||||||| |||     |    || | ||  ||   ||| || | |  |||||       |||||    ||||||     |    | |||||||||||||||| ||||||||||||||| || ||||| ||| | ||||| ||||||||||||||||||||||| |||||||||||||||||||| || ||||
---------gtatgatggaaatgtttggctgcccag----aataagatggacctgtttctcccatttatttacttcttcctgtcttctttaacttcaatggcttgtttcagATTGAAGGAGGTTTTATCCAAGGATTAGGTTGGGCGGCCCTGGAAGAACTAAAATGGGGGGATGATAACCACAAGTGGATTCGACCTGGACATCTTTTCA

upper sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 13

gtatgtgctctgcggaggaaatgttttgctaatttgcttcaacacgaaagagaggttccttctacat----atttcctgtagt-ttaacgtactgtattt---cagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTAAAATGGGGGGATGATAACCATAAGTGGATTCGACCTGGACACCTCTTCA
        ||         ||| |||      | | ||| || |  |         |  || | |||    | ||| | |  | ||   |   | |||||   ||||| || ||||||||||||||||| ||||| |||| |||  ||||||| || |||||||| |||||    ||||| ||||| |   ||||   ||| | ||
------attccaatttcctaatttttcctccctattcttgaaaataagttttgctgtatttttgcatgataaattcatattttgttcttgctatttattttcacagATCGAGGGAGCTTTTATCCAAGGTTTGGGTTGGGTAGCTTTAGAAGAACTTAAATGGGGAGATGAAGCACATAAATGGATCCCGTCTGGGTGCCTTTACA

upper sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 12

--gtatgt-gctctgcggaggaaatgttttgctaatttgctt-caacacgaaagagaggttccttctacatatttcctgtagtttaacgtactgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTAAAATGGGGGGATGATAACCATAAGTGGATTCGACCTGGACACCTCTTCA
  || ||| ||  | | |||  | | ||  |||  ||  |    |  || |  |  | ||||  ||| |  ||  |||   |||   |  | | || | |||||||||||||| ||| | |||||  |||| ||||  ||| ||||||||||||||||||| ||||     || || ||||||| ||||||   ||| | ||
cagtgtgttgcattacagag--atttttccgcttcttcacacatagtacaatgggaaagttctatctgctgatgaccttgtgttattctaattctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTAAAATGGGGAGATGCAGCTCACAAATGGATTCCACCTGGTTGCCTGTACA

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|78023990|gb|DV492377.1|DV492377

EST:     ATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGGTA
genomic: ATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|60395383|gb|DN228252.1|DN228252

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|67016938|gb|CO445687.1|CO445687

EST:     ATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: ATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|14204330|gb|BG838007.1|BG838007

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATT-GGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|14204197|gb|BG837874.1|BG837874

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|45567638|gb|CK985669.1|CK985669

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

EST: gi|211338067|gb|FL010980.1|FL010980

EST:     TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAG                         ATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA
genomic: TTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTA

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: 47 (upstream exon), 49 (downstream exon)
Score: 112

AGTTGAGATCGACACCCTAACTGGGGATTTTTACACAAGGACAGCTGATATTGTTATGGATCTCGGATTTTCAATTAATCCAGCAATTGACATTGGCCAGgtatgtgctc ... tgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTAAAATGGGGGGATGATAACCATAAGTGGATTCGACCTGGACACCTCTTCA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 320

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 363

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 136

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

acgaaagagaggttccttctacatatttcctgtagtttaacgtactgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTAAAATGGGGGGATGATAACCATAAGTGGATTCGACCTGGACACCTCTTCA

                                  gtttaac  putative branch site (score: 136)
                   tacatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctctgcggaggaaatgttttgctaatttgcttcaacacgaaagagaggttccttctacatatttcctgtagtttaacgtactgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTAAAATGGGGGGATGATAACCATAAGTGGATTCGACCTGGACACCTCTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA