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

...gtataagtttagttactttaacaataatcgtatgacatttcctgtgtatcttttttttgacacacacataacattatgatgtatttgctttatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGCAAAATTCCTCGAGAGAAAACTTCAGCAACCTGATGGCTTGGACTCCCTG

Basic information

species	Zea mays
transcript	GRMZM2G020606_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G020606_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g47340.1 (Oryza sativa), 3'ss of exon 1

gtataagtttagt-tactttaacaataatcgt-atga-catttcctgtgtatcttttttttgacacacacataacattatgatgtatt-tgctttatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGCAAAATTCCTCGAGAGAAAACTTCAGCAACCTGATGGCTTGGACTCCCTG
    | | ||  | ||  | ||  || ||| | |||    |||  | | | |  |  |  |||||    | | | |   | |  || | | ||   | |||||||||||| |||||||||||| ||||||| |||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||  |||| || |||
----aggcttgctctatgtaaagtatgatcttcatgggtttttgttctttgttatgctcatgacatgaccctgaaaggctcaaatactgtactcctttaaatagGATGGCTCATCCTGGAGGACCACTAACTACAAACAAGGCTGCTGCTTTAGCAAAATTCCTTGAGAGAAAGCTTCAGCAGCCTGATGGGCTGGAATCTCTG

upper sequence: GRMZM2G020606_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0020g01600.t01 (Vitis vinifera), 3'ss of exon 1

----gtataagtttagttactttaacaataatcgtatgacatttcctgtgtatcttttttttgacacacacataacattatgatgtatt--tgctttatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGCAAAATTCCTCGAGAGAAAACTTCAGCAACCTGATGGCTTGGACTCCCTG
     |  |||   ||  |||||     |     |       | |||  |  |   ||||    |       |   ||| | ||  | |  || ||| |    |||| |||| || ||||| ||| || | || |||||||||||||||||||| ||||| |||||||| ||||| || ||  | |||| ||| ||||  ||| | 
aggaatgaaagaacagg-acttttgtgttggaaattcatttctgccttagggttactttt----cgtgggtgttg-attttcattcactggtgttttttggtgtagGTTGGCTCACCCTGGTGGACCATTGACGACAAACAAGGCTGCTGCTTTGGCAAAGTTCCTCGAAAGAAAGCTCCATGAGCCTGGTGGATTGGCTTCCTTA

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|71331155|gb|DR802412.1|DR802412

EST:     AAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGCCCCCAGCCGAG                         GATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGC
genomic: AAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGCCCCCAGCCGAGgtaccgcgcg ... tatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGC

EST: gi|37376807|gb|CF624961.1|CF624961

EST:     AAGTTCGCGCTGTTTCTTCCGCCTCCTCCCTTTTCCCGCCCCCAGCCGAG                         GATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGC
genomic: AAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGCCCCCAGCCGAGgtaccgcgcg ... tatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGC

EST: gi|211299732|gb|FL213380.1|FL213380

EST:     AAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGACCCGAGCCGAG                         GATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTCTAGC
genomic: AAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGCCCCCAGCCGAGgtaccgcgcg ... tatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGC

EST: gi|28187621|gb|CB179231.1|CB179231

EST:     AAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGCCCCCAGCCGAG                         GATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGC
genomic: AAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGCCCCCAGCCGAGgtaccgcgcg ... tatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGC

EST: gi|161591214|gb|EY959425.1|EY959425

EST:     AAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGCCCC-AGCCGAG                         GATGGCCCATCC
genomic: AAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGCCCCCAGCCGAGgtaccgcgcg ... tatcaaatagGATGGCCCATCC

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: 45 (upstream exon), 44 (downstream exon)
Score: 81

CGGCGGCCGGCGACCTGTCCGACGATGAGAAGCGGGCGATGAGGGGCAGCAAGTTCGCGCCGCTTCCTCCGCCTCCTCCCTCTTCCCGCCCCCAGCCGAGgtaccgcgcg ... tatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGCAAAATTCCTCGAGAGAAAACTTCAGCAACCTGATGGCTTGGACTCCCTG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 69

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtatcttttttttgacacacacataacattatgatgtatttgctttatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGCAAAATTCCTCGAGAGAAAACTTCAGCAACCTGATGGCTTGGACTCCCTG

                    acataac  putative branch site (score: 69)
                                      tttgcttt  putative PPT
                           attatgatgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataagtttagttactttaacaataatcgtatgacatttcctgtgtatcttttttttgacacacacataacattatgatgtatttgctttatcaaatagGATGGCCCATCCTGGAGGAGCACTAACCACAAACAAGGCTGCTGCTTTAGCAAAATTCCTCGAGAGAAAACTTCAGCAACCTGATGGCTTGGACTCCCTG

- - - - - - - - - -aacaata
- - - - - - - - - - - - - - - - tgacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgctt