Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcttctaaattccagcttttggatcataatctaaagtcttcacaatgttaataacccttcattcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCA

Basic information

species Zea mays
transcript GRMZM2G111511_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111511_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g56400.1 (Oryza sativa), 3'ss of exon 3
gtaggcttctaaattccagcttttggatcataatctaaagtcttcacaatgttaata---acccttcattcaa-acagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCA
||||||  || |  | |  ||||||||| ||||||||  |||| ||||| ||| | |   | ||||||| ||| ||||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||| ||||||||||||||||||||| |||| ||||| || |||||||
gtaggcagctgacatgctccttttggattataatctattgtctgcacaaggttcacaaacatccttcatccaacacagAGGCCAATCCAAACTCTGAGTGGCGGGCAGAAGCAGAGAGTTGCAATTGCCGGTGCTTTAGCTGAAGCATCCAAAGTACTACTACTGGATGAGCTGACCA

upper sequence: GRMZM2G111511_T05 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G15900.1 (Glycine max), 3'ss of exon 4
----gtaggcttctaaattccagcttttggatcataatctaaagtcttcacaatgttaataacccttcattcaaa-----cagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCA
      ||| |   ||  |  |||  |   |  |   | | || | | ||  |  | ||    |||||  | | |     |||||  |  ||||||||||||||||||| ||||| ||||| ||||| |||||||||||  | |||||||| |  |||||  |  || |||| || || || |
gtattaaggatgacaaccttgagcactcaaacaaatgtgtgaattatacaataaatgaactttccttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA

upper sequence: GRMZM2G111511_T05 (Zea mays), 3'ss of exon 1
lower sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 3
------gtaggctt-ctaaattccagcttttggatcataatctaaagtc---ttcacaatgttaataaccct--tcattcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCA
       || |     | ||   ||     | | | |||   |  |||    || || |   ||   |   |  |  |     ||||| || || |||||||| |||||||| |||||||| ||| |||| ||||||||||| ||||||||||| | ||||||  || || |||| || || || |
gtcagtttatgtacattgaacaacaataagttgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA

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|18173493|gb|BM348881.1|BM348881
EST:     TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|211373270|gb|FL465535.1|FL465535
EST:     TAAGGGTATCAAAATCTTTGGATGCTGTTGGGATGTTGAGCTACTYTCAG                         AGGCCAATCCAAACTYTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|17931952|gb|BM268912.1|BM268912
EST:     TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|211053231|gb|FL127757.1|FL127757
EST:     TAAGGGTATCAAAATCTTTGGATGCTGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|60394524|gb|DN227394.1|DN227394
EST:     TAAGGGTATCAAAATCTTTGGATGCTGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|14243054|gb|BG840773.2|BG840773
EST:     TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|18169738|gb|BM339578.1|BM339578
EST:     TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|14242742|gb|BG840544.2|BG840544
EST:     TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTCTGAGTGGCGGGCAGAAACAGAGAGTTGC
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGC
EST: gi|32866994|gb|CF006676.1|CF006676
EST:     TAAGGGTATCAAAATCTTTGGATGCTGTTGGGATGTTGAGCTACTCTCAG                         AGGCCGATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|74238567|gb|DT646481.1|DT646481
EST:     TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|18165876|gb|BM335715.1|BM335715
EST:     TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTATGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
EST: gi|17932020|gb|BM268980.1|BM268980
EST:     TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAG                         AGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT
genomic: TAAGGGTATCAAAATCTTTGGATGCCGTTGGGATGTTGAGCTACTCTCAGgtaggcttct ... attcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttggatcataatctaaagtcttcacaatgttaataacccttcattcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCA
                                 taataac  putative branch site (score: 1)
                                       cccttcattc  CT-rich tract
                            aatgttaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcttctaaattccagcttttggatcataatctaaagtcttcacaatgttaataacccttcattcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA