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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttctttccctctcaaatattcacagttcttcatttgcttgtgttgtgttcttctccagtgatgatgttatgtgaccaaaccattttatgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG

Basic information

species Zea mays
transcript GRMZM2G128877_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 14
ttcttctttccctctcaaatattcacagttcttcatttgcttgtgttg-tgttcttctcca---gtgatgatgttatgtgaccaaaccattttatgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG
    | |||  |  | ||||  | | |  | |  |||||    | ||  ||||| |   ||   |   |||||||||||||| | || || || ||  |||||||| |||||| |    ||||||| |   ||||||||||||||||||||||| ||||| ||||||||||||||||||||||| || ||| |||||||||| |
----tttttttcaatgaaatgctaataagtttatatttgaacattttcctgttcgttcgcatttgctttgatgttatgtgacaatacaatgttttgtgttgcagGCGCTTGAGCCGCACTATGAGAGGGAAGATCCAGATTTCATTGATATTAGAACAAAGGCACGTGAGGTGTTGCAGAGGGAAGATGATTTAAATGAAATAG

upper sequence: GRMZM2G128877_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 15
--------------ttcttctttccctctcaaatattcacagttcttcatttgcttgtgttgtgttcttctccagtgatgatgt-----tatgtgaccaaaccattttatgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG
              |  ||  ||        |   | ||   |||| ||||||  ||  | ||||| |  | |  |||   |       | | | |      | ||||      |  |||| |||||  ||||||||||| | |||||||||||||| ||  | ||||||||||| || ||||| ||  |||| ||||| || || || ||||||||||
gtatgtcctaaagttggttactttgtaactcatcctccagctttctacatttgtatgcatagtgttttggttccatgactttccccgaatttttaatattttctttttggtatctttagGCACTTGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTG

upper sequence: GRMZM2G128877_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
ttcttctttccctctcaaatattcacagttcttcatttgcttgtgttgtgttcttctccagtgatgatgttatgtgaccaaaccattttatgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG
             || |||||||| | ||||        ||||| |||  ||  | || ||  ||  ||| || | |  |  |   ||| ||  ||  |||| || || || || ||||||||||| ||||||||||||||  | || |||||||| ||  | ||||||||||||||||| |||||||| ||||||||||
--------gtatgcttaaatattctcggttca-----aacttgtcttggtttactatctagaaatcttgt-atataaa-acgctgctttttgtttt--agGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG

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|32929207|gb|CF034019.1|CF034019
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|60338201|gb|DN205174.1|DN205174
EST:     GGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: GGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|13149764|gb|BG320086.1|BG320086
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|32831320|gb|CD970998.1|CD970998
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|32928400|gb|CF033212.1|CF033212
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|32837774|gb|CD977452.1|CD977452
EST:     CCCATCTGTGAATTGGCTCATTTCCTATTCCAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: CCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|74035379|gb|DT535868.1|DT535868
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|5296280|gb|AI783050.1|AI783050
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|5846764|gb|AI999847.1|AI999847
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|32939925|gb|CF044744.1|CF044744
EST:     ATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: ATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|211532168|gb|FL123442.1|FL123442
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|211154401|gb|FL123520.1|FL123520
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|5847131|gb|AW000210.1|AW000210
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|33092495|gb|CF052489.1|CF052489
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|5846817|gb|AI999900.1|AI999900
EST:     AGCATTTCCCATCTGGGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|5846863|gb|AI999946.1|AI999946
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|67040096|gb|CO466351.1|CO466351
EST:     ATTTCCCATTTCTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: ATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|32836684|gb|CD976362.1|CD976362
EST:     AGCATTTCCCATCTGTGAATTGGATCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAAATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|5343199|gb|AI795384.1|AI795384
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|5296225|gb|AI782905.1|AI782905
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|5325051|gb|AI783242.1|AI783242
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|211156008|gb|FL123543.1|FL123543
EST:     GAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGARAAGTTTGATCCARATTTCATTGATATTAGG
genomic: GAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
EST: gi|67025855|gb|CO454604.1|CO454604
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGG

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), 46 (downstream exon)
Score: 264

GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 416

GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 388

GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 390

GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgttcttctccagtgatgatgttatgtgaccaaaccattttatgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG
                                       attttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttctttccctctcaaatattcacagttcttcatttgcttgtgttgtgttcttctccagtgatgatgttatgtgaccaaaccattttatgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA