Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTTTTATTCCAAGCCCTAGATGGCAGAATCCCTCAAATTATGCACCGATGATTGTACCGCAAGGTCTTGTTCAAGTACCAAGCTGGAACTCATATACTgtaagatcatttcttctcacagtcatagacatatagtggagacgtgattttcccaatcatggattgtttacgttggctttcatgctctgttaatttccta...

Basic information

species Oryza sativa
transcript LOC_Os01g68860.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68860.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G107491_T03 (Zea mays), 5'ss of exon 5
TTCTTTTATTCCAAGCCCTAGATGGCAGAATCCCTCAAATTATGCACCGATGATTGTACCGCAAGGTCTTGTTCAAGTACCAAGCTGGAACTCATATACTgtaagatcatttcttctcacagtc--atagacatatagtggagacgtgattttcccaatcatggattgtttacgttggctttcatgctctgttaatttccta
||||||||| ||||||||||| ||||| | ||| |||||||||||||| ||| ||||||| || || ||||| ||||| || |||||||| |||||| ||||||| ||||||  | |   | |   ||  | || |       ||       || || | ||   ||   | |    |  || ||     | | | |  |||
TTCTTTTATACCAAGCCCTAGGTGGCAAAGTCCTTCAAATTATGCACCAATGGTTGTACCTCATGGCCTTGTCCAAGTGCCGAGCTGGAATTCATATCCTgtaagttcatttggtatagtaatgcaatgtaaattttacaattacaaagcaatcacatttatcattttccttcaaaag--tttattaaacgatgagtctcta

upper sequence: LOC_Os01g68860.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G087032_T04 (Zea mays), 5'ss of exon 4
TTCTTTTATTCCAAGCCCTAGATGGCAGAATCCCTCAAATTATGCACCGATGATTGTACCGCAAGGTCTTGTTCAAGTACCAAGCTGGAACTCATATACTgtaagatcatttcttctcacagtcatagacatatagtggagacgtgattttcccaatcatggattgtttacgttggctttcatgctctgttaatttccta-----------------
||||||||| ||||||||||| ||||| | ||| ||||||||||| |||||||||||||| || || ||||||||| | |  |||||||| |||||||||||||| ||||||  |             |||| || || ||  || |||||  |||| ||  |    | |||||  ||||  |   ||    ||| ||||                 
TTCTTTTATACCAAGCCCTAGGTGGCAAAGTCCTTCAAATTATGCGCCGATGATTGTACCTCAGGGCCTTGTTCAAATGCAGAGCTGGAATTCATATACTgtaagttcatttggt-------------acat-taatgcag-tgtaatttttacaattataaagcaatcacgttatctttttt--cctagagattccctagaggaacagggagcgga
















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|29684893|gb|CB681168.1|CB681168
EST:     GCTGGAACTCATATACT                         GGCCAAATGATGCCTGTTTCATCTTCTGAGAGTCGACTGCAGTCCCCAGGG
genomic: GCTGGAACTCATATACTgtaagatcat ... gcttttcaagGGCCAAATGATGCCTGTTTCATCTTCTGAGAGTCGACTGCAGTCCCCAGGG
EST: gi|38476016|gb|CF960149.1|CF960149
EST:     TGATGGTACCGCAAGGTCTTGTTCAAGTACCCAGCTGGAATTCATATACT                         GGCCAAATGATGCCTGTTTCATCTTCTGAGAGTCGACTGCAGTCCCCAGGG
genomic: TGATTGTACCGCAAGGTCTTGTTCAAGTACCAAGCTGGAACTCATATACTgtaagatcat ... gcttttcaagGGCCAAATGATGCCTGTTTCATCTTCTGAGAGTCGACTGCAGTCCCCAGGG
EST: gi|218503721|gb|FG969763.1|FG969763
EST:     TGATTGTACCGCAAGGTCTTGTTCAAGTACCAAGCTGGAACTCATATACT                         GGCCAAATGATGCCTGTTTCATCTTCTGAGAGTCGACTGCAGTCCCCAGGG
genomic: TGATTGTACCGCAAGGTCTTGTTCAAGTACCAAGCTGGAACTCATATACTgtaagatcat ... gcttttcaagGGCCAAATGATGCCTGTTTCATCTTCTGAGAGTCGACTGCAGTCCCCAGGG
EST: gi|29658444|gb|CB654719.1|CB654719
EST:     TGATTGTACCGCAAGGTCTTGTTCAAGTACCAAGCTGGAACTCATATACT                         GGCCAAATGATGCCTGTTTCATCTTCTGAGAGTCGACTGCAGTCCCCAGGG
genomic: TGATTGTACCGCAAGGTCTTGTTCAAGTACCAAGCTGGAACTCATATACTgtaagatcat ... gcttttcaagGGCCAAATGATGCCTGTTTCATCTTCTGAGAGTCGACTGCAGTCCCCAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTTTTATTCCAAGCCCTAGATGGCAGAATCCCTCAAATTATGCACCGATGATTGTACCGCAAGGTCTTGTTCAAGTACCAAGCTGGAACTCATATACTgtaagatcatttcttctcacagtcatagacatatagtggagacgtgattttcccaatcatggattgtttacgttggctttcatgctctgttaatttccta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA