ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgtgatcaagcattatgtgcctttatcagcatcatttggttgctagcttgctattctcagcagctcatttcttaatatggattttgtggctgg...

Basic information

species	Zea mays
transcript	GRMZM2G057853_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G057853_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g43250.1 (Oryza sativa), 5'ss of exon 6

AAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgt-attcctgtgatcaagcattatgtgcctttatcagcatcatttggttgcta-gcttgctattctcagcagctcatttcttaatatggattttgtggctgg
|||||||||| ||||| ||||| || ||||||||||| || |||||| ||||||  || |||| ||||  |||||||||||||||||||||||| |||||||  ||||| |  |||   |  ||     || |   || | | ||  |   || |  |  | || | |     |  | | | | |   ||| ||        
AAGAAGCTCACCAGCGTTGGCTCCCCCTTGTTGAGCTTGGCTCACCTCAGGATAAGGGGGATATAGTGCATGCTGTAGCATGGGCTCCTAACATCGGCAGgttgttcctttcttcagcaagcataacagttgacatgccttaatttttcaatatgtattgtgttttgaatgttttgtgt-tcactgctgatattagcatca-

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|148953595|gb|EC898949.2|EC898949

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGCGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|148930898|gb|EC873352.2|EC873352

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTTGCA-TCTGGC
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATT-GCAATCTGGC

EST: gi|93012339|gb|EB637859.1|EB637859

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGAATATCGCAGTTTGCA-CCTGCAAAGGAA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTT-GCAACCTGCAAAGGAA

EST: gi|50328004|gb|CO523130.1|CO523130

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|76294071|gb|DV033639.1|DV033639

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTTACATTGGCAG                         AACATATGAGATTATCGCAGGTGCACCCTGCAAAGGAATTGCCAATCTGGC
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGC-AATCTGGC

EST: gi|78080510|gb|DV508922.1|DV508922

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGGAATTGCA-TCTGGC
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGG-AATTGCAATCTGGC

EST: gi|76909537|gb|DV163411.1|DV163411

EST:     ATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCCTA-CATTGGCAG                         ACCATATGAGATTATCGCAGTTGCACCCTGCAAAGGAATTGCAATCTGGCA
genomic: ATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCC-TAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|71772782|gb|DR970707.1|DR970707

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ATCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|71444110|gb|DR825160.1|DR825160

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCTACCTGCTAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|149107563|gb|EE189446.2|EE189446

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATTTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|71773952|gb|DR971840.1|DR971840

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|149107564|gb|EE189447.2|EE189447

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTACCATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|148981980|gb|EE028040.2|EE028040

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|71439594|gb|DR820644.1|DR820644

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCA

EST: gi|211023881|gb|FL345725.1|FL345725

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|149074196|gb|EE162559.2|EE162559

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAAATGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|84976699|gb|DW475121.1|DW475121

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|71429467|gb|DR810517.1|DR810517

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|148953594|gb|EC898948.2|EC898948

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|60353460|gb|DN220433.1|DN220433

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

EST: gi|76283890|gb|DV023458.1|DV023458

EST:     GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAG                         ACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA
genomic: GATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCA

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: 129

AAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgt ... tctattctagACCATATGAGATTATCGCAGTTGCAACCTGCAAAGGAATTGCAATCTGGCATATAGGTTTGAACGCTGATGCTGATGGCGGACCTTCGACGCAGAACGTT

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 65

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 30

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTCCTAACATTGGCAGgtattcctgtgatcaagcattatgtgcctttatcagcatcatttggttgctagcttgctattctcagcagctcatttcttaatatggattttgtggctgg

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT