ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttctttagcataactgcacactattctacgtttgatcattaataaaatgtgttttttggtatttaaggttttggatgatgatggacccccccccccccttctgattgcag

Basic information

species	Zea mays
transcript	GRMZM2G023232_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g08840.1 (Oryza sativa), 5'ss of exon 6

TTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttctttagca-taactgcacactattctacgtttgatcattaataaaatgtgttttttggtatttaaggttttggatgatgatggacccccccccccccttctgattgcag
 || ||||| ||||||||||||||||| || ||||| || |||||||| || ||||| || || |||||||||||||| ||||| |||||||||||||| |||   ||| | | ||| |   ||      ||| |   |||     ||  |    | |||| || |  ||| |    ||| |||     || ||                        
GTTTATTGCCAAGCTTCAGGAGGTTGAGGATTGGCTGTACGAAGATGGTGAAGATGAGACAAAAGGGGTTTATATTGCAAAGCTGGAAGAACTTAAAAAGgtacctcttttattgcacttcttggtttacattgtgtctttatgtgttggtttggtttgttcttggacattgag---ttttgatatgcctgaacttttttag----------------

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA13G43630.2 (Glycine max), 5'ss of exon 7

TTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttctttagcataactgcacactattctacgtttgatcattaataaaatgtgttttttggtatttaaggttttggatgatgatggacccccccccccccttctgattgcag
 || | |||||| ||||||||||| ||||||||||| ||||| ||||| || ||||||||||| || || || ||||| ||||||||||| || || || ||| |   | ||  | ||      | |  ||         || |  | ||    | ||    |  |   |    ||||| ||  ||  |        |||| ||| | | |      
ATTTACTGCTAAACTTCAGGAGGTGGAAGACTGGCTATATGAGGATGGTGAAGATGAAACTAAAGGCGTATACATTGCCAAGCTAGAAGAGCTCAAGAAGgtaagaaattttagggat-----tagaaaatctctgacccgagc--tgatctggtatgc---taaggcctggttgttttagagaatact---tttatccccacccgtgtaaaa----

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G22100.1 (Glycine max), 5'ss of exon 6

TTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttctttagc-ataactgcacactattctacgtttgatcattaataaaatgtgttttttggtatttaaggttttggatgatgatggacccccccccccccttctgattgcag-----------------------------------------------------------------
||| | |||||| |||||||| || ||||| ||||| ||||| || || || ||||||||||| || || |||||||| ||||| |||||||| ||||| ||  |     |||    ||||  | |  |||     | ||      | ||       | || |         | ||    |  |     | |       ||      | |  |||||                                                                  
TTTTACTGCTAAACTTCAGGAAGTGGAAGATTGGCTTTATGATGAGGGTGAAGATGAAACTAAAGGTGTATATATTGCCAAGCTTGAAGAACTCAAAAAGgttaggaagttttgttgataagggaatcctagctcccattcctcagtcaaactgtaatattgtgcaaggaaaagggaccagagtacctcttgctgttatcctttgtgtttttttgcacaaacataaatggtgtgaggtatttccatgctagttttaacataggcaatctcaatgtgattgcag

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA15G01750.1 (Glycine max), 5'ss of exon 7

TTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttctttagcataactgcacactatt-ctacgtttgatcattaataaaatgtgttttttggtatttaaggttttggatgatgatggacccccccccccccttctgattgcag
 || | |||||| ||||||||||| ||||||||||| ||||| ||||| || ||||||||||| || || || ||||| |||||||||||||| || || ||| |   | ||  |  | |    |  || |  ||     |||||    ||    | ||||||     ||       |    || ||     |   |                     
ATTTACTGCTAAACTTCAGGAGGTAGAAGACTGGCTATATGAGGATGGTGAAGATGAAACTAAAGGTGTATACATTGCCAAGCTAGAAGAACTCAAGAAGgtaagaacttttaggggttaaaaaaatctctgactctagctgatctggtatggcct-tgttttagaaaatacttttatccccatcatagcaaaaatctttt-----------------

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 6

TTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttctttagcataactgcacactattctacgtttgatcattaataaaatgtgttttttggtatttaaggttttggatgatgatggacccccccccccccttctgattgcag
 || | |||||| || |||||||| ||||| ||| | |||||||| || ||||||||||| || || ||||| ||||| || || || |||||||| || |||      ||||  | ||||| || |   ||     |||  |  || ||    |  ||||| ||||   | | ||     || |  || |                          
GTTTACTGCTAAACTGCAGGAGGTAGAAGATTGGTTGTATGAAGACGGTGAGGATGAAACAAAAGGTGTTTACATTGCCAAACTCGAGGAACTTAAGAAGgtaattacacttt--cttaactccaaatggtttc---tttagt--ttgatcttcttagttttatggt---tgacgtgaaaaataaaaattgcag-----------------------

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|211440101|gb|FK975188.1|FK975188

EST:     AGAAGAACTTAAAAAA                         GTTGGKGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|9952046|gb|BE638629.1|BE638629

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGGTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|67032981|gb|CO461730.1|CO461730

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|18661122|gb|BM501223.1|BM501223

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|32843014|gb|CD982695.1|CD982695

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|20803202|gb|BQ294252.1|BQ294252

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|67021901|gb|CO450650.1|CO450650

EST:     GGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAAACT-AAAAAA                         GTGGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAAGT-
genomic: GGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAA-CTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAA-GTT

EST: gi|37375721|gb|CF624316.1|CF624316

EST:     TTATATTGCTAAGCTAGAAGAACTNNNNNNN                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: TTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|83278270|gb|DV942278.1|DV942278

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|61119613|gb|DN560574.1|DN560574

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|67016035|gb|CO444784.1|CO444784

EST:     GGGATGAAACTA-GGNGGTTTATATTGCTAAGCTAGAAGAACTTAAAAA-                         GTTGGTGATCCTATTTAGCTGCGCTTCA
genomic: GG-ATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCA

EST: gi|67025370|gb|CO454119.1|CO454119

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACT-AAAAAA                         GGTGGTGATCCTATTGAGCTGCGCCTTCA-GGAATGGGAGATTAGAAGTTC
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGC-TTCAAGGAATGGGAGATTAGAAGTTC

EST: gi|211139744|gb|FL308469.1|FL308469

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|60354460|gb|DN221433.1|DN221433

EST:     GAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: GAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|32932457|gb|CF037269.1|CF037269

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GGTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|211343665|gb|FL392042.1|FL392042

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|213174387|gb|FM187872.1|FM187872

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

EST: gi|33098111|gb|CF058071.1|CF058071

EST:     AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAA                         GTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT
genomic: AGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCT

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: 712

TTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttc ... ctgattgcagGTTGGTGATCCTATTGAGCTGCGCTTCAAGGAATGGGAGATTAGAAGTTCTGCTGTTAGCCAACTGGTATACTGCATCAATAGCTTCAGAGAAGCTGCAC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 339

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 374

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 443

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGGATGAAACTAAGGGGGTTTATATTGCTAAGCTAGAAGAACTTAAAAAAgtatgccttctttagcataactgcacactattctacgtttgatcattaataaaatgtgttttttggtatttaaggttttggatgatgatggacccccccccccccttctgattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC