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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag

Basic information

species Zea mays
transcript GRMZM2G126453_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 24
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcatt-cagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag
|||| || |||||||||||||| || ||||| || ||||||||||| |||||||||||||| ||||| || |||||||| |||||||||||||| ||||||| |  | | |  | ||    ||||  |||  ||      || | || ||      |||| | ||     | |  || |  |||||  ||     | | |                                            
ATGGATTACGCACTAAAGATAAAGAACGTGTACTGGTTCTTGGTGCCACAAATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagctataaccttgtgttggggttgggataa-----tgaaaaattgc-----tgtttgttgatttctaaccatttggtcgttaattactact-gtag-------------------------------------------

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 23
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtggga--ctggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag
||||  |||| || |||||||| |||||||| |||||||||| ||||||||| ||||||||||| || || |||||||| ||||||||| | || ||  ||| |   | |||   || | ||  |   || |||  |  ||| || |  ||   | |  |    ||   |||| |  |    || ||  ||||  ||||                                              
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcat-gttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatg---catggtc-tgacttcattttttttttgtag----------------------------------------------

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag
|||| ||| | || |||||||| |||||| | |||||||||| |||||||||||| |||||||| || || |||||||| ||||||||  | || || |||||||  | |||   ||   ||        ||| |   || |||  | ||  |||      | |  | ||| | ||    ||||    ||||   |  |||| | | |                                   
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcgttatgtttgatg--------ttaacttcttttatttc-gtgttttacaaatgagatctatgctaat----tcgtgttctttgttgaaaaatattgtag-----------------------------------

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 19
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtggga--ctggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag
||||  |||| || |||||||| |||||||| |||||||||| ||||||||| ||||||||||| || || |||||||| ||||||||| | || ||  ||| |   | |||   || | ||  |   || |||  |  ||| || |  ||   | |  |    ||     |   | |  |||  ||  || | |                                                  
ATGGTCTGCGTACAAAAGATAAAGAGCGTGTACTTGTTCTTGCTGCTACAAACAGGCCTTTTGATCTTGATGAGGCTGTTATTAGGAGGCTTCCTCGACGgtgagcat-gttatgtttaatgttaacttgtattttcatgttttacagatgacatctattctaatgcatggtctgtcttcaatttttttttgtag--------------------------------------------------

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 20
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag
|||| ||||| || |||||||| |||||| | ||||||||||  ||||||||||| |||||||| || || |||||||| ||||||||  | || || |||||||  |  ||   ||   ||        | | |   || |||  | ||  ||       | |  | ||| | || |    |||  || | |  |  ||| ||                                       
ATGGTTTGCGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCGGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcattatgtttgatg--------tcagcttcttttatttc-gtgtttcacaaatgagatctatgctaatttg--tgttctttcttgaaaaaaattgtag-------------------------------------

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 23
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgt-tgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag
| ||  |    ||| | || | ||| ||||| || || ||||  || |||||| ||||||||||||| || |||||||| |||||  |||| ||||| ||||||||  |   ||  |   | |||||    |      ||||  || ||   |     |   | ||   |||  || |  | || |    ||  | ||                                              
ACGGTCTTACGACTCAGGAAAGGGAACGTGTTCTGGTCCTTGCAGCCACAAATCGGCCTTTTGACCTTGATGAGGCTGTTATTAGACGGTTGCCCCGTAGgtaaattataaatcgcttccttggactaagcttttt--ttgttaaattgacatgacagtta-taggttgtgaaaattttgtggtattgacttctgcag----------------------------------------------

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 23
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag
| ||  || | || || || ||||| ||||| || |||||||  || |||||||| ||||||||||| ||||||||||| ||||| ||||| || |  |||||| |  | | |   |   | |   |||| ||   || | |    ||||    |||    || |   |  | | | |  |  | |||| ||                                                   
ACGGTCTGAGGACAAATGAAAAGGAACGTGTTCTGGTTCTTGCAGCCACAAATAGACCTTTTGACCTTGACGAGGCTGTCATTAGAAGGTTGCCTCATAGgtaatttatatatagcttccttg--ttggacta---agcttt----ctgtcaaattgacatgtcg-taacaagtttttggtattggcttctgcag------------------------------------------------

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 23
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag
||||  | || || || ||||| || |||||  | || ||||  || || ||||||||||||||||| || |||||||| ||||||||| | ||| | |||||||  |  | | ||| |      || ||||       ||||| | | |   |     | |     | | | |  |  |   |   | ||   |  ||| |                                         
ATGGCCTACGTACAAAGGATAAAGAACGTGTATTGGTACTTGCCGCCACCAATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatcatatgatt-ataatcccttgatttgttg--tgtatgagtattagtcaacccagaaaaaccttaattccctactatgtatgttaactgccaacac----------------------------------------

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 24
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcag
|||| |||||||| |||||||  ||  | || || || ||||  || |||||||| ||||||||||| || |||||||| ||||| ||||| || || ||||||    |   | |  || |  |  |||| || ||   | |||  |   |   |     ||       |  || | |||| |||  | ||    ||                                              
ATGGCTTGCGCACAAAAGATACCGAAAGGGTTCTGGTGCTTGCAGCCACAAATAGACCTTTTGACCTTGATGAGGCTGTTATTAGAAGGTTGCCGCGTAGgtaaggcatcactgagccattttg-ttggactatcctactttatttccacaaact-----gggacttagttcttctgtaatggttcatcttttacag----------------------------------------------

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|211384433|gb|FL031621.1|FL031621
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         -TTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|32921157|gb|CF025969.1|CF025969
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|58029637|gb|CX725064.1|CX725064
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAA-TTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|32920203|gb|CF025015.1|CF025015
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|211048841|gb|FL187601.1|FL187601
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|211048838|gb|FL187598.1|FL187598
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCA-                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|32921345|gb|CF026157.1|CF026157
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|211048837|gb|FL187597.1|FL187597
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|32920665|gb|CF025477.1|CF025477
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT

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), 46 (downstream exon)
Score: 231

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 207

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 288

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT