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'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtctccttgtccaactaccaagtccgagatagctttccttagttgtacatgatgaaagcgataattgatttttctaaaatttctgttatttactgtagGTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTTGATGCAGTAGTTTACCTAATGCTGGTAAACGATCTTATTCGTGGGCTTT

Basic information

species Zea mays
transcript GRMZM2G073054_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 13
atgtctccttgtccaactaccaagtccgagatagctttccttagttgtacatgatgaaagcgat---aattgatttttctaaaatttctgttatttactgtagGTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTTGATGCAGTAGTTTACCTAATGCTGGTAAACGATCTTATTCGTGGGCTTT
    |   | | ||  | |   ||| | |   |   |   | | |  ||     |   |   ||   | ||  ||| | |   |||  ||    |  ||| ||||  |||| ||||| || ||    ||||||||||| ||||| |||||||||||||| || |||||||| ||||||   || ||| | |||| |||||| |
--agcgattagccctgc-aaagagtgcaaaggattatatttcactcatattctttctcaatcatttaattttttttcttttgcattattgaatctcgctgcagGTAGCATTTACTGGAAATTACAATGAGTATTTTGGTTTTGCAACTGATGTTGATGCTGTGGTTTACCTGATGCTGACTAATGATGTCATTCATGGGCTCT

upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 13
atgtctccttgtccaactaccaagtccgaga--tagctttc-cttagttgtacatgatgaaagcgataattgatttttctaaaatttctgttatttactgtagGTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTTGATGCAGTAGTTTACCTAATGCTGGTAAACGATCTTATTCGTGGGCTTT
   |  |  ||   | |     | ||  |    ||  |||| ||||| | | | |  | ||     |||||  ||| | |   |||  ||    | |||||||||  |||| ||||| || ||    ||||||||||| ||||| |||||||||||||| ||  ||||||| ||||||   || ||| | |||| |||||| |
---tagcagtgattagcctttgaatcgaaagattatatttcacttagatattctttctcaatcatttaatttttttcttttgcattattgaatgtgactgtagGTAGCATTTACTGGAAATTACAATGAGTATTTTGGTTTTGCAACTGATGTTGATGCTGTGATTTACCTGATGCTGACTAATGATGTCATTCATGGGCTGT
















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|67035192|gb|CO463725.1|CO463725
EST:     TTCGATTTGATGGGGTGACCTCCATGATGTATACTCACCATGGATTACAA                         GTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTT
genomic: TTCGATTTGATGGGGTGACCTCCATGATGTATACTCACCATGGATTACAAgtaagtttac ... tttactgtagGTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTT
EST: gi|101386689|gb|EB815361.1|EB815361
EST:     TTCGATTTGATGGGGTGACCTCCATGATGTATACTCACCATGGATTACAA                         GTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTT
genomic: TTCGATTTGATGGGGTGACCTCCATGATGTATACTCACCATGGATTACAAgtaagtttac ... tttactgtagGTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTT
EST: gi|211410788|gb|FL280482.1|FL280482
EST:     TTCGATTTGATGGGGTGACCTCCATGATGTATACTCACCATGGATTACAA                         GTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTT
genomic: TTCGATTTGATGGGGTGACCTCCATGATGTATACTCACCATGGATTACAAgtaagtttac ... tttactgtagGTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTT
EST: gi|211410789|gb|FL280483.1|FL280483
EST:     TTCGATTTGATGGGGTGACCTCCATGATGTATACTCACCATGGATTACAA                         GTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTT
genomic: TTCGATTTGATGGGGTGACCTCCATGATGTATACTCACCATGGATTACAAgtaagtttac ... tttactgtagGTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacatgatgaaagcgataattgatttttctaaaatttctgttatttactgtagGTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTTGATGCAGTAGTTTACCTAATGCTGGTAAACGATCTTATTCGTGGGCTTT
                            ttctaaa  putative branch site (score: 2)
                 ataattgatttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtctccttgtccaactaccaagtccgagatagctttccttagttgtacatgatgaaagcgataattgatttttctaaaatttctgttatttactgtagGTGACATTCACTGGGAACTATGGCGAGTATTTTGGATTTGCCACTGATGTTGATGCAGTAGTTTACCTAATGCTGGTAAACGATCTTATTCGTGGGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG