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

...ttccatggaattggaaactcatgtggagcttgtgatatgatgaagttggacaggcgtccctgataagtattcctcattttttttacttcccatttgacagGGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT

Basic information

species Zea mays
transcript GRMZM2G068277_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068277_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 6
ttccatggaattggaaactcatgtggagcttgtgatatgatgaagttggacaggcgtccctgataagtattcctcattttttttacttcccatttgacagGGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT
     |  |||||  |||   |       | |   ||  ||     |     ||  | | ||| | | ||| ||||   | |    ||||| |||| |||||| || ||||| || |||||||| || ||||||||||| | ||| || || || |||||||| ||||| ||||||||||| ||||| ||||||
caatgtccaattgtcaacctttacttgtttggacttaaaatattaataacagggaattcatgagacgcattactcacaatatgattttcccttttggcagGGTGAAGTTAATTATTGAAGAGATTGAAAAGGAAGAGGCCCTTCTACTAGACGATCTTGCTTCGATGGATAGAAAATTTGCCGAACACTATAAT
















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|6194463|gb|AW146567.1|AW146567
EST:     ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAG                         GGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA
genomic: ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAGgtagactttc ... catttgacagGGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA
EST: gi|71443221|gb|DR824271.1|DR824271
EST:     ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAG                         GGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA
genomic: ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAGgtagactttc ... catttgacagGGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA
EST: gi|5895704|gb|AW036950.1|AW036950
EST:     ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAG                         GGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA
genomic: ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAGgtagactttc ... catttgacagGGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA
EST: gi|60337416|gb|DN204389.1|DN204389
EST:     ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAG                         GGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA
genomic: ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAGgtagactttc ... catttgacagGGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA
EST: gi|60347346|gb|DN214319.1|DN214319
EST:     ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAG                         GGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA
genomic: ATTCGTCATCCCTCAGTCAAATTTCAAGTGCTAGGCTTCCAGAAAGgtagactttc ... catttgacagGGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggacaggcgtccctgataagtattcctcattttttttacttcccatttgacagGGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT
            ccctgat  putative branch site (score: 4)
                      tattcctcattttttt  putative PPT
                            tcattttttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccatggaattggaaactcatgtggagcttgtgatatgatgaagttggacaggcgtccctgataagtattcctcattttttttacttcccatttgacagGGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- -catggaa
- - - - - - - - - -catgtgg
- - - - - - - - - - - - - -gcttgtg
- - - - - - - - - - - - - - - - - - -tgatgaa