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

gtaaattacggttctggtcatgtcccaatgtgttcatttttatggtttttgtggcctttgtgattatttgcaaacattattggtggtgcatggatatagctgtgtttggtgcatcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTTACCTTGGTTCAATGGTGCTGCTTATGTTTACGACCATTTTGTGCGGCCA

Basic information

species	Zea mays
transcript	GRMZM5G862101_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G862101_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 3

gtaaattacggttctggtcatgtcccaatgtgttcatttttatggtttttgtggcctttgtgattatttgcaaacattattggtggtgcatggatatagctgtgtttggtgcatcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTTACCTTGGTTCAATGGTGCTGCTTATGTTTACGACCATTTTGTGCGGCCA
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----------------------------------------------------------tgtgatttttttt-----ttactattgatgc-tggagataaacatgttca-cacatcaagaggataacaaagga-ttagatatgcttacttctgacggttgcttgcagGCTTCCTTTTTGGTCCTATGCAAAGTTGTTCTTCAACTGCTGGTTGGTCTTACCTTGCTTCCATGGTGCTGCTTATGTTTATGATCACTTTGTGCGGCCA

upper sequence: GRMZM5G862101_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 3

gtaaattacggttctggtcatgtcccaatgtgttcatttttatggtttttgtggcctttgtgattatttgcaaacattattggtggtgcatggatatagctgtgtttggtgcatcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTTACCTTGGTTCAATGGTGCTGCTTATGTTTACGACCATTTTGTGCGGCCA
                                                              |||   ||  | || | | |||  |   |||   ||  | |||||  |   | |  |    ||||    | ||     ||  ||  ||   ||| | |  ||||||| || |||||| |||||||||| ||| |    |  |||||||||||| |||| |  |||| ||||||||| |||||||| || ||||||||| | || 
------------------------------------------------------------aaattgaatgggatcaatttgggtcctttttgg---taattctgttt--tatctgagatatcagaaactacacctctgcttgaacatgttgtgtctgtgtg-gcagGCTCCCTTTTTGGCCATATGCAAAGCTGATTGCAACTTGCTGGTTGGTCATACCCTACTTCAGTGGTGCTGCATATGTTTATGAGCATTTTGTGAGACCT

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|211223200|gb|FL136732.1|FL136732

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223194|gb|FL136726.1|FL136726

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223203|gb|FL136735.1|FL136735

EST:     TACTCATTTGNCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGNTCTTTAACTGCTGGTTGGNCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223202|gb|FL136734.1|FL136734

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGG
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGG

EST: gi|211223197|gb|FL136729.1|FL136729

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211221143|gb|FL136724.1|FL136724

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223201|gb|FL136733.1|FL136733

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223204|gb|FL136736.1|FL136736

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCNATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAANTGTTCTTTAACTGCTGGTTGG
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGG

EST: gi|211223195|gb|FL136727.1|FL136727

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

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: 335

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTTACCTTGGTTCAATGGTGCTGCTTATGTTTACGACCATTTTGTGCGGCCA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 150

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 219

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 216

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

catcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTTACCTTGGTTCAATGGTGCTGCTTATGTTTACGACCATTTTGTGCGGCCA

                             tgctcac  putative branch site (score: 216)
                                          tctttattt  putative PPT
                                    tttagatctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattacggttctggtcatgtcccaatgtgttcatttttatggtttttgtggcctttgtgattatttgcaaacattattggtggtgcatggatatagctgtgtttggtgcatcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTTACCTTGGTTCAATGGTGCTGCTTATGTTTACGACCATTTTGTGCGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT