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

gtatgttagaagtgtcttttggttgaacttgtttgaagctctgcctggacactctttagttttataaagaggaatcctgtgattgtttggggagttgttcagtcaggtgtatattaagacactgcattgctcttacccctcgctttgctcttactactttttttgctggcattcttttgtgcatggtgtccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTGGTCGTGATCGGTATGGTGGATCTGAGTCGAAGTGCTATGAATGTGGTGA

Basic information

species	Zea mays
transcript	GRMZM2G080930_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G080930_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 3'ss of exon 3

gtatgttagaagtgtcttttggttgaacttgtttgaagctctgcctggacactctttagttttataaagaggaatcctgtgattgtttggggagttgttcagtcaggtgtatattaagacactgcattgctcttacccctcgctttgctcttactactttttttgctggcattcttttg--tgcatggtgtcc---aaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTGGTCGTGATCGGTATGGTGGATCTGAGTCGAAGTGCTATGAATGTGGTGA
                                                                                                   || |||  |  |||    |    ||||    |  | ||  |    ||    ||| |   |   ||    | |||  ||    ||| ||||  |      |||||| |||||||||||||||||||| || || || || || ||| | || || |||||||||||  ||||||| ||||||  |||||||||||| ||||||||
---------------------------------------------------------------------------------------------------caatcatcttcata----ggttgtgcaagctttgtccctgtgtagttagaattaatttatgcattatcaggatttgttcaaatgcgtggttcctcttttaatagGCAAGAATGGATGGAGAGTTGAGCTCTCACGGAACTCAAGTAGCCGCGGAGGTCGTGATCGACATGGTGGGTCTGAGATGAAGTGCTATGAGTGTGGTGA

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|211113501|gb|FL364717.1|FL364717

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211105696|gb|FL316276.1|FL316276

EST:     TGATTTTGATGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGNGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211260063|gb|FL327809.1|FL327809

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211310251|gb|FL338861.1|FL338861

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|18964300|gb|BM660926.1|BM660926

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTC
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTC

EST: gi|211072623|gb|FL332514.1|FL332514

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211375406|gb|FL332329.1|FL332329

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211215612|gb|FL316847.1|FL316847

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211138186|gb|FL349860.1|FL349860

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211274557|gb|FL349470.1|FL349470

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211432430|gb|FL327491.1|FL327491

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211416748|gb|FL321413.1|FL321413

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211470387|gb|FL342153.1|FL342153

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211047373|gb|FL359874.1|FL359874

EST:     TGATTTTKACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

EST: gi|211091140|gb|FL328973.1|FL328973

EST:     TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG                         GTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG
genomic: TGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTG

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), 48 (downstream exon)
Score: 150

TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATGgtatgttaga ... tccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTGGTCGTGATCGGTATGGTGGATCTGAGTCGAAGTGCTATGAATGTGGTGA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 128

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 75

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttgctcttactactttttttgctggcattcttttgtgcatggtgtccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTGGTCGTGATCGGTATGGTGGATCTGAGTCGAAGTGCTATGAATGTGGTGA

    ctcttac  putative branch site (score: 75)
       ttactacttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttagaagtgtcttttggttgaacttgtttgaagctctgcctggacactctttagttttataaagaggaatcctgtgattgtttggggagttgttcagtcaggtgtatattaagacactgcattgctcttacccctcgctttgctcttactactttttttgctggcattcttttgtgcatggtgtccaaaatagGTAAGAATGGATGGAGAGTTGAACTATCTCGTAATTCCAGTGGTCGTGGTGGTCGTGATCGGTATGGTGGATCTGAGTCGAAGTGCTATGAATGTGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA