ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccgacaatttcagccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgtttgtg...

Basic information

species	Zea mays
transcript	GRMZM2G025470_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G025470_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g51500.2 (Oryza sativa), 5'ss of exon 2

CGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccgacaatttcag--ccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgtttgtg
||||||||||| |||||||||||||||||||||||| | ||||| |||||||||||||||||||||||||| || ||||||||| | |||||||||||||||||||||| ||||||     | |||| |||| ||  ||||  ||||| |  |||      | ||   |||| | |  | | |      |      ||    
CGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacacaaaactctattaaattca--

upper sequence: GRMZM2G025470_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g51500.3 (Oryza sativa), 5'ss of exon 2

---CGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccgacaatttca--gccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgtttgtg
   ||||||||||| |||||||||||||||||||||||| | ||||| |||||||||||||||||||||||||| || ||||||||| | |||||||||||||||||||||| ||||||     | |||| |||| ||  ||||  ||||| |  |||      | ||   |||| | |  | | |   || |  | |   |   
AACCGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAgtggtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacaca--aaactctattaaat---

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|14203831|gb|BG837508.1|BG837508

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA---                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|211410514|gb|FL261735.1|FL261735

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAAT
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAAT

EST: gi|109179560|gb|EC380070.1|EC380070

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|13126514|gb|BG317084.1|BG317084

EST:     AATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|211407976|gb|FL261730.1|FL261730

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA---                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|13126515|gb|BG317085.1|BG317085

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|32921127|gb|CF025939.1|CF025939

EST:     AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA---                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|32914897|gb|CF019709.1|CF019709

EST:     AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|32851133|gb|CD990814.1|CD990814

EST:     AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|211407973|gb|FL261727.1|FL261727

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA---                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|18178381|gb|BM379591.1|BM379591

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|32851050|gb|CD990731.1|CD990731

EST:     AATTACAATGCATGTGGTAGGGCGACCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|16377623|gb|BI992025.1|BI992025

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|32845497|gb|CD985178.1|CD985178

EST:     AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|78117275|gb|DV535662.1|DV535662

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA---                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|211410522|gb|FL261743.1|FL261743

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

EST: gi|14203827|gb|BG837504.1|BG837504

EST:     AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC

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: 48 (upstream exon), 47 (downstream exon)
Score: 51

CGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccga ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTCTCTGATAAGGCGTCTGCTTGGTGCTGTACAATCTGTGTGTACACATAAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 238

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 82

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccgacaatttcagccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgtttgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaataa