ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TAAAAGAACCTTCTACCAATGTTGTCCTAGCTGATCATGTTACAACAAAGAAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaatatttttcttacaagcacttggagatcatgcccgaaaaattataatattaataaaaaactagttttgtgtgtgcgtgtgtgtgtgttaag...

Basic information

species	Zea mays
transcript	GRMZM2G028730_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G028730_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g20230.1 (Oryza sativa), 5'ss of exon 3

TAAAAGAACCTTCTACCAATGTTGTCCTAGCTGATCATGTTACAACAAAGAAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaatattt---ttcttacaagcacttggagatc-atgc--ccgaaaaattataatattaataaaaa-actagttttgtgtgtgcgtgtgtgtgtgttaag
|||||||||| || |||||| | ||| |||| |||||||||||||| ||||||||| || || |||||||||||||||||||||| ||||||||||||||||||||  || | |      |||| |  ||      |||| |||   || | | |     |||   | |   | ||  | |  |      || |  |  |       
TAAAAGAACCATCAACCAATATGGTCTTAGCCGATCATGTTACAACGAAGAAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaaaactcaacaccttaaacacataccatgatctatgttacccagatacggggatacggacacgtatacgcgatacggcgacacggggatacg-------

upper sequence: GRMZM2G028730_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv19s0015g00910.t01 (Vitis vinifera), 5'ss of exon 4

TAAAAGAACCTTCTACCAATGTTGTCCTAGCTGATCATGTTACAACAAAGAAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaatatttttcttacaagcacttggagatcatgcccgaaaaattataatattaataaaaaactagttttgtgtgtgcgtgtgtgtgtgttaag
| || || || ||  ||||||| |||||    ||| || || |  || |||||||| || | ||  | ||||| ||||||||||||||||| ||||||||||||| |       ||   | |   |   |  |  ||  |    |     |  | | || ||   | || |  ||| |   | | |              
TCAAGGAGCCATCAGCCAATGTAGTCCTCTTGGATTATATTGCCTCAGAGAAATGGCAGGATATCATAGATTTTGATGACCACCTTGATGACATTAGCAAgtaagaa-----ccttctgtgcttccctctctatttctagagttatttccttcatttttgatctgatacaatctttcttcctccttacag----------

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|32922316|gb|CF027128.1|CF027128

EST:     AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGAGTTTTCATGATTGATCTCGC
genomic: AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

EST: gi|78109108|gb|DV527525.1|DV527525

EST:     AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC
genomic: AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

EST: gi|78109107|gb|DV527524.1|DV527524

EST:     AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC
genomic: AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

EST: gi|211420632|gb|FL480897.1|FL480897

EST:     AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGDATTTTCATGATTGATCTCGC
genomic: AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

EST: gi|149085223|gb|EE174731.2|EE174731

EST:     AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC
genomic: AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

EST: gi|32849729|gb|CD989410.1|CD989410

EST:     AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC
genomic: AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

EST: gi|93280885|gb|EB673149.1|EB673149

EST:     AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC
genomic: AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

EST: gi|37380718|gb|CF627188.1|CF627188

EST:     AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC
genomic: AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

EST: gi|76917162|gb|DV166707.1|DV166707

EST:     AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC
genomic: AAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

EST: gi|166458199|gb|EG240769.1|EG240769

EST:     AGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAA                         GGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC
genomic: AGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGC

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: 46 (upstream exon), 48 (downstream exon)
Score: 32

TAAAAGAACCTTCTACCAATGTTGTCCTAGCTGATCATGTTACAACAAAGAAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaa ... tttttggtagGGATTGGTCGAACCCAGGCCTCCTTGACTGAATTTTCATGATTGATCTCGCTATACTGTTTTGGAACTTCGCTAGAAATGAGGTGGTGAAGCTCGTCCTG

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 78

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 61

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAAAGAACCTTCTACCAATGTTGTCCTAGCTGATCATGTTACAACAAAGAAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaatatttttcttacaagcacttggagatcatgcccgaaaaattataatattaataaaaaactagttttgtgtgtgcgtgtgtgtgtgttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaaa