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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctgaacataagtattttttatccgctgttatgttgcttacatgacgacgggaattttgtcagccttgttacccatggcatgagcaaacttttgatgaatacctttgatgtttttgtcacactag

Basic information

species Zea mays
transcript GRMZM2G112337_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112337_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 5'ss of exon 8
GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctgaacataagt---attttttatccgctg---ttatgttgc-ttacatgac--gacgggaattttgtcagccttgtt---acccatg--gcatgagcaaacttttgatgaatacctttgatgtttttgtcacactag----------------------------------
||||| ||||| |||||||||||  | |||||||||||||| || ||||| ||||||||||| ||| ||||||||| ||||||||| ||||| | |||||  |        |||| | |||  ||   ||||  | | ||||||      |  | |  ||   | ||||   |   ||| |||   |||  |  |   | |||     |   || ||  | ||   |  ||                                    
GACGACAACAGATACAGTGCAACCAGAGGTGCACATCTGAACCTCAAGCGGGCAGAAAAGGCTCGTCTTTTGGTCAGTAAAATTCCAGgtatatcctgaatgtttacttggttttgtttcccttgtgattatactacattacatattctaaaagtagcttccactgcctgccttagacctatgctacatctggcataatatgacatggaaaattaattctattcctaatctgacttttgggttcatctgtgactgttacgagtgtag
















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|88756750|gb|DY540891.1|DY540891
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|148995697|gb|EE034920.2|EE034920
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|71771989|gb|DR969926.1|DR969926
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|67021761|gb|CO450510.1|CO450510
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|71773221|gb|DR971130.1|DR971130
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|148928684|gb|EC873287.2|EC873287
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|89249959|gb|DY621745.1|DY621745
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|71306089|gb|DR789194.1|DR789194
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|71435944|gb|DR816994.1|DR816994
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|149098529|gb|EE184515.2|EE184515
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|60351440|gb|DN218413.1|DN218413
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|149078381|gb|EE167156.2|EE167156
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|89763677|gb|DY690772.1|DY690772
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|67020793|gb|CO449542.1|CO449542
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
EST: gi|149088740|gb|EE177864.2|EE177864
EST:     GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGG                         CTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG
genomic: GAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctg ... gtcacactagCTATTGTTGACACACTGCTTGCAAAGACCCGGGCATGGGAACAAGAGCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGTGCAGAAAAGGCCCGTGTTTTGGTCAATAAAATTCCGGgtatgttctgaacataagtattttttatccgctgttatgttgcttacatgacgacgggaattttgtcagccttgttacccatggcatgagcaaacttttgatgaatacctttgatgtttttgtcacactag

- - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - -  TGAAGC