Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcacgaagtggggatcagtctttttttttctaacaaaaccggggctaaattaaacctacactgttgcctttccctctccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG

Basic information

species Zea mays
transcript GRMZM2G168510_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g10784.1 (Oryza sativa), 3'ss of exon 2
gtgagcacgaagtggggatcagtct-ttttttttctaacaaaaccggggctaaat-taaacctacactgttgcctttccctctccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG
           ||| | | ||  || || |  || ||   |   | ||| || || | || ||    |  |||  ||  | |||||  ||||||||||  | || || ||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||| || ||||| || |||
-----------gtgagcagcaaactattgtaattttagttatttctgggatatatatgaatctgttttcctgctattttccctccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTACATCATCAAAATCCTTCCGTGGTCCTGGTCTGGAGGAAGGCCTGAAG

upper sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 2
-----gtgagcacgaagtggggatcagtctttttttttctaacaaaaccggggctaaatt--aaacctacac--tgttgcctttccctctccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG-
        |     || | | ||      |  ||| |    |  | |   |   ||  ||  || |  |||   | |||  | |   | |   |   ||  ||||||| ||  | || |||||||| |||||||| ||||| ||||| ||||||||||||||||| ||||| || ||  | |  || ||  | ||| 
aagggtcaaagttaaaattgtgaatgaaatggtttgtagacatgatattagttttatctttgaagctaacatgatcttgagtgtatatgtgtctttcagaGTTGGAATACCATTGGTTTTCAAGTCAAGCTTTGACAAAGCTAACCGAACATCATCAAAATCATTTCGTGGCCCGGGGATGGCTGAGGGATTGAAGG

upper sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------gtgagcacgaagtggggatcagtctttttt-----tttctaacaaaaccggggctaaattaaa---cctacac--tgttgcctttccctctccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG
                                                | |    ||  ||  |   |  | ||         |   |  || | ||||  || |||  |   |  |||   | |||  | |   | |   |   ||  ||||||| ||| | || |||||||| |||||||| ||||| ||||| ||||||||||||||||| ||||| || ||  | |  || ||  | |||
gtatgtaattatctctatttatgattattttttttattaatgggaaaataaatgtgatttgatggaaatccattagaaaaagctagcaggaagaacgggtgtatatttgatagctaacatgatcttgagtgtatatgtgtcttccagAGTTGGAATACCGTTGGTTTTCAAGTCAAGCTTTGACAAAGCTAACCGAACATCATCAAAATCATTTCGTGGCCCGGGGATGGTTGAGGGATTGAAG

upper sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 2
gtgagcacgaagtggggatcagtctttttttttctaacaaaaccggggctaaattaaacctacactgttgcctttccctctccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG
||  |       ||  |   | | |  || ||| ||      | |    |  |||   | ||   | |||  || |  | ||     |||  ||||  |   ||| || |||||||| |||||||||||||| || || || || ||||||||||| || ||||||||  |    ||||| || |||
gtatgttttgtttgatggaaaatttcattgttttta------cggtttgtggattgttcatagggt-ttgttttacaatttc-----tagATTTGGGTTGAAGCTGGTTTTCAAGTCGAGCTTTGATAAAGCCAATCGAACCTCCTCAAAATCATTTCGGGGTCCTGGCATGATTGAAGGCCTGAAG

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|9952617|gb|BE639305.1|BE639305
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|91055907|gb|EB166325.1|EB166325
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|50323772|gb|CO518898.1|CO518898
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|50323794|gb|CO518920.1|CO518920
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|71307284|gb|DR789817.1|DR789817
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|9794838|gb|BE553146.1|BE553146
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         TCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|211064516|gb|FL339511.1|FL339511
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|74236361|gb|DT644275.1|DT644275
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|91050684|gb|EB161102.1|EB161102
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|21432170|gb|BQ547660.1|BQ547660
EST:     AGGAGTCACGTCCTGTTGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: AGGAG-CACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|78121994|gb|DV540378.1|DV540378
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|211382423|gb|FK948864.1|FK948864
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCACTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|31355531|gb|CD439888.1|CD439888
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|211382425|gb|FK948866.1|FK948866
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCACTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|71449637|gb|DR830687.1|DR830687
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|26457480|gb|CA829063.1|CA829063
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|91051935|gb|EB162353.1|EB162353
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|78110755|gb|DV529153.1|DV529153
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|211162593|gb|FL363072.1|FL363072
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCACTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|116816629|gb|EC859381.1|EC859381
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCACTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|31361455|gb|CD445812.1|CD445812
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|211382426|gb|FK948867.1|FK948867
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCACTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|211215731|gb|FL322482.1|FL322482
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCACTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
EST: gi|211058755|gb|FL342288.1|FL342288
EST:     GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA                         GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC
genomic: GAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTAC

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: 388

GCAGCCAAACCGTTCTTCTTGTTGGCTGGTCCCAACGTGATTGAATCGGAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 354

GCAGCCAAACCGTTCTTCTTGTTGGCTGGTCCCAACGTGATTGAATCGGAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG


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

GCAGCCAAACCGTTCTTCTTGTTGGCTGGTCCCAACGTGATTGAATCGGAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

GCAGCCAAACCGTTCTTCTTGTTGGCTGGTCCCAACGTGATTGAATCGGAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAAgtgagcacga ... tccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaaaaccggggctaaattaaacctacactgttgcctttccctctccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG
                           cactgttgcctttccc  CT-rich tract
              taaattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcacgaagtggggatcagtctttttttttctaacaaaaccggggctaaattaaacctacactgttgcctttccctctccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG