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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtctatggaaccataccctctttgatatgttctgtttggataatttgaattcttcatttactatacttctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTGTTTCCGAACTTTCCTGGCGAGGATCCAAAAATGCTATCCAGTTTTAAGG

Basic information

species Zea mays
transcript GRMZM2G147811_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147811_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 11
gtgcgtctatggaaccataccctctttgatatgttctgtttggataatt-tgaatt--cttcatttactatacttctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTGTTTCCGAACTTTCCTGGCGAGGATCCAAAAATGCTATCCAGTTTTAAGG
  | ||||||| ||||||   |||    |     | ||  || ||  || || |||  ||| | ||| | | ||| |  ||||||||||||| |||| | |||||||||||||| ||||||||| ||||||| ||| || | ||||| ||||||||||||||||||||||||||||  ||||| |
--gtgtctatgcaaccatgttctcaaatactctgtttgagtgcattgttatggattatcttaacttattcttctttttcttgcagGCTGTGACAAGGATGATTTTGAACATTAAGCCAAAGGATATTGGTTCCTTGATTTCAAACTTCCCTGGCGAGGATCCAAAAATGCTATCCAACTTTAAAG
















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|88753404|gb|DY537545.1|DY537545
EST:     ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACG                         GCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
genomic: ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACGgtgcgtctat ... ctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
EST: gi|32832656|gb|CD972334.1|CD972334
EST:     ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACG                         GCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
genomic: ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACGgtgcgtctat ... ctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
EST: gi|32945651|gb|CF050470.1|CF050470
EST:     ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACG                         GCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTT
genomic: ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACGgtgcgtctat ... ctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTT
EST: gi|160481281|gb|EY254203.1|EY254203
EST:     ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACG                         GCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
genomic: ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACGgtgcgtctat ... ctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
EST: gi|166555098|gb|EG040904.1|EG040904
EST:     TGCTACCGAGGAGGATCCTGTGACAAAAACG                         GCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
genomic: TGCTACCGAGGAGGATCCTGTGACAAAAACGgtgcgtctat ... ctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
EST: gi|32932428|gb|CF037240.1|CF037240
EST:     ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACG                         GCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
genomic: ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACGgtgcgtctat ... ctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
EST: gi|60345986|gb|DN212959.1|DN212959
EST:     ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACG                         GCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG
genomic: ATCAAGATCTCAATTTTCATGCTACCGAGGAGGATCCTGTGACAAAAACGgtgcgtctat ... ctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatgttctgtttggataatttgaattcttcatttactatacttctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTGTTTCCGAACTTTCCTGGCGAGGATCCAAAAATGCTATCCAGTTTTAAGG
 ctttgat  putative branch site (score: 5)
                                          cttctgttt  putative PPT
                ataatttgaattcttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtctatggaaccataccctctttgatatgttctgtttggataatttgaattcttcatttactatacttctgtttgcagGCTGTGAGAAGGTTAATTTTGAACATTAAACCAAAGGATGTTGGTTCTTTGTTTCCGAACTTTCCTGGCGAGGATCCAAAAATGCTATCCAGTTTTAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT