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

...ttctaccattattgtacgtggcagaacttcctatgatacattaatgcaagttgtgatagtaagtatttcatgtaaatatctagaaccctttgttgtgcagAAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGATGGGAAAGATATGGTGCTTTTGGGAG

Basic information

species Oryza sativa
transcript LOC_Os02g27360.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g27360.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G098215_T01 (Zea mays), 3'ss of exon 3
--ttctaccattattgtacgtggcagaacttcctatgatacattaatgcaagttgtgatagtaagtatttcatgtaaatatctagaaccctttgttgtgcagAAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGATGGGAAAGATATGGTGCTTTTGGGAG
   | |   |  |   |  ||   |  |       ||| |  ||      | |  | |  ||   | ||| ||   |  | |        |||||| |  ||||  |||||||||| ||||| ||||   | ||||||||||| ||||| ||||||||||||||||| || || ||||
aagtgtgg-acaaccatttgttcaatcaacctgagtgacaagttcccatta-tcatcaaggtttatgtttaatactataaacgcattatttttgttttctagAATGATTTATACTGTATGGGATTCCTGGATGGTGGAGTACAGACCAAAGATGGGAAAGATATGGTTCTCTTAGGAG
















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|86499644|gb|CI142277.1|CI142277
EST:     GAGACGTTTCACTGATTGTTTCTCCACATGATTATCTTTTCCAAAATGGG                         AAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT
genomic: GAGACGTTTCACTGATTGTTTCTCCACATGATTATCTTTTCCAAAATGGGgtatttaata ... tgttgtgcagAAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT
EST: gi|86493808|gb|CI136441.1|CI136441
EST:     GAGACGTTTCACTGATTGTTTCTCCACATGATTATCTTTTCCAAAATGGG                         AAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT
genomic: GAGACGTTTCACTGATTGTTTCTCCACATGATTATCTTTTCCAAAATGGGgtatttaata ... tgttgtgcagAAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT
EST: gi|88903097|gb|CI088635.1|CI088635
EST:     GAGACGTTTCACTGATTGTTTCTCCACATGATGATCTTTTCCAAAATGGG                         AAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT
genomic: GAGACGTTTCACTGATTGTTTCTCCACATGATTATCTTTTCCAAAATGGGgtatttaata ... tgttgtgcagAAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT
EST: gi|88246534|gb|CI246383.1|CI246383
EST:     GTTTCTCCACATGATTATCTTTTCCAAAATGGG                         AAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT
genomic: GTTTCTCCACATGATTATCTTTTCCAAAATGGGgtatttaata ... tgttgtgcagAAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT
EST: gi|88228038|gb|CI227518.1|CI227518
EST:     TTTCCAAAATGGG                         AAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT
genomic: TTTCCAAAATGGGgtatttaata ... tgttgtgcagAAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagttgtgatagtaagtatttcatgtaaatatctagaaccctttgttgtgcagAAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGATGGGAAAGATATGGTGCTTTTGGGAG
                                        ccctttgtt  CT-rich tract
                  tatttcatgtaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctaccattattgtacgtggcagaacttcctatgatacattaatgcaagttgtgatagtaagtatttcatgtaaatatctagaaccctttgttgtgcagAAGAATTTATACTGCATGGGGTTCCAAAACGGTGGAGTACAAACCAAGGATGGGAAAGATATGGTGCTTTTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG