ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatccttatgatcatgtatgctccttgtttataagcattctttgtttctgcag

Basic information

species	Zea mays
transcript	GRMZM2G095252_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 5'ss of exon 7

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatcc--tta--tgatcatgtatgctccttgtttataagcattcttt-gtttctg-cag--------------------------------------------
|||||||| ||||| |||||||| ||||| || |||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| || ||||||||| || |  |||| || ||| | ||||    ||   |||||||  ||||| ||| ||||| |  |||||   |  |||| | |                                            
AACAAGCTTAGAGGGTCATTGAAAATTGCCGCTATCAAAGCCCCTGGTTTTGGTGAGCGCAAGACCCAGTACTTGGATGATATTGCCATTCTAACTGGAGgtgaggtggacttgcgatctggtgcatttggttgggtgatcattaatgctgcttatttatgatgattctggagcatctggctggatgattaatgctgcttatttataatgattttttttctctgcag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 6

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatcc--ttatgatcatgtatgctccttgtttataagcattctttgtttctgcag------------------------------------
||||| || ||||||||| |||||||||| ||  | || |||||||| ||||||||||||||||  |||||| | ||||||||||||||| | ||||||||||  | ||  |     | |   || |    || ||    |||||      | ||| |      | ||||||||   |                                     
AACAAACTTAGAGGATCACTGAAGATTGCAGCACTGAAGGCCCCTGGGTTTGGAGAGCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatataaaaatttcatgcctttgattttggaagtgtatatatgcttttttttctatctttttgtttccagatgttgataagatatgtattttctcaattggtttacag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 6

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatcc--ttatgatcatgtatgctccttgtttataagcattctttgtttctgcag------------------------------------
||||| || ||||||||| |||| ||||| ||  |||| |||||||| |||||||| |||||||  |||||| | ||||||||||||||| | ||||||||||  | ||  ||  ||| | | || |    || ||    ||| |  |    |||| |     || ||||||||                                         
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgta-tatgcgtttctctatcttttttgtttccaggtgatgataagatatgtattttctcaattgatttacag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 7

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagc---atccttatgatcatgtatgc--tccttgt-ttataagcattctttgtttctgcag----
|||||||| |||||  || ||||||| || ||  ||| ||| || || ||||||||||||||||  || ||| | |||||||||||||| || ||||||||| ||||     | | ||   ||||   ||  ||| |   || | ||   |  || | || |    ||| | | | |  ||      
AACAAGCTTAGAGGTACACTGAAGATAGCAGCTCTCAGAGCTCCAGGGTTTGGAGAGCGCAAGAGCCAATACCTTGATGATATTGCCATTCTAACTGGAGgtaagttctgtctgcattgatgagccctatgtttacgcatatatttgtagtttttatcttgtcctaattttctatcttcgcttgcag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 7

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatccttatg-----atca-----tgtatgctccttgtttataagcattctttgtttctgcag--------------------------------
|||||||| |||||  || |||||||||| ||  ||||||| ||||| ||||||||||||||||  || ||| | || ||||||||||| || |||||||||  || |   ||   |   | |  | |  ||||     ||||     |||   |||||  |||  || ||||  | | |  |  |                                 
AACAAGCTTAGAGGCACACTGAAGATTGCAGCTCTCAAAGCTCCTGGATTTGGAGAGCGCAAGAGCCAATACCTTGACGATATTGCCATTCTAACTGGAGgtaggtcatgtttttataacaaaaaacctatatgtgggtatcaatcaatgtgccctcctgatttggaatcatt--tggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 6

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatccttatgatcatgtatgctccttgtttataagcatt-------ctttgtttctgcag----------
|| |||||||| ||  |||| |||||||||||  | ||||| ||||| |||||||||||||| |  || ||  | ||||||||||| ||||| ||||||||| |||  |  |   | |        | | | || |  ||  || | |||||| | |  |||        | || ||| | |            
AATAAGCTCAGGGGGGCATTAAAGATTGCTGCACTGAAAGCTCCTGGATTTGGAGAGCGCAAAAGCCAATATCTTGATGATATTGCTATCCTCACTGGAGgttagtctatttagtgatgattgttttgcatctgctattgagtgtttcttgttaaaactcatgtataatacattatttttacttgggtattcag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 7

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagt-taaacttccgttctagagcatccttatgatcatgtatgctcc---ttgtttataagcattctttgtttctgcag-------------------
|| ||||| ||||| ||||| |||||||||||  | ||||||||||| ||||||||||||||||  |||||| ||||||| ||||| || || ||||||||| ||  || |   |  ||  |     |  || |  || | ||   |     ||  ||   ||  || ||    | | | |                   
AATAAGCTTAGAGGGTCATTAAAGATTGCTGCACTTAAAGCCCCTGGATTTGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatagataacattttcactatttttttttcttcttctaaattttattttacttgagagttttattctaatattctgtcattattatatttgcaca

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ32217 (Selaginella moellendorffii), 5'ss of exon 6

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatccttatgatcatgtatgctccttgtttataagcattctttgtttctgcag
|||  |||  | || ||  | |||||||  |||||||| ||||| || ||||||||| | ||||| |||||  | || |||||||||||||| ||||||||| |||  |  ||   || |    ||      ||  | | |    |  |   |  ||                    
AACCGGCTTCGTGGCTCTCTCAAGATTGTGGCCATCAAGGCCCCAGGATTTGGAGAGAGGAAGACGCAGTATCTCGAGGATATTGCCATCCTCACTGGAGgtaagtagagttttttttgttttccagaggcttgtgcttatcgatttgtacatcgtag-------------------

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ16507 (Selaginella moellendorffii), 5'ss of exon 6

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatccttatgatcatgtatgctc-cttgtttataagcattctttgtttctgcag
|||  |||  | || ||  | |||||||  |||||||| ||||| || ||||||||| | |||||||||||  | || |||||||||||||| ||||||||| ||   |  ||   || |      |||  | | |  ||  |      |||| |||                     
AACCGGCTTCGTGGCTCTCTCAAGATTGTGGCCATCAAGGCCCCAGGATTTGGAGAGAGGAAGACTCAGTATCTCGAGGATATTGCCATCCTCACTGGAGgtaaggagagttttttttgt----tttccagaggcttgtgcttatcgatttgtatatcgtag----------------

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|32803187|gb|CD955423.1|CD955423

EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|32837509|gb|CD977187.1|CD977187

EST:     ACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: ACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|32932965|gb|CF037777.1|CF037777

EST:     ACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCGGAGATGAAGTTGGGCTGTCACTTGACAAGGTTGACAAAT
genomic: ACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|33092673|gb|CF052667.1|CF052667

EST:     ACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: ACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|32934171|gb|CF038983.1|CF038983

EST:     ACTTGGATGATATTGCCATCCTTACTGGAG                         CACCTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: ACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|211046936|gb|FL343169.1|FL343169

EST:     TGGAGAGCGCAAGACCCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|498197|gb|T20345.1|T20345

EST:     TTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: TTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|32935108|gb|CF039920.1|CF039920

EST:     ACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: ACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|32931097|gb|CF035909.1|CF035909

EST:     TGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: TGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|32935122|gb|CF039934.1|CF039934

EST:     ACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: ACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|32838764|gb|CD978445.1|CD978445

EST:     ACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: ACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|211173892|gb|FL341459.1|FL341459

EST:     TGGAGAGCGCAAGACCCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

EST: gi|33097092|gb|CF057052.1|CF057052

EST:     GTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT
genomic: GTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAAT

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: 342

AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAATCAGTCCTTGGAACAGCAGCAAAGGTTGTCCTTACTAAAGAGTCGACAAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 884

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

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 397

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatccttatgatcatgtatgctccttgtttataagcattctttgtttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA