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

...caataccagctttacatcttgatgatgacccatgtcactattttttataagcataaaattatctcgatacctgtctgattctcttatatgtttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATGTGGCAAGAGTTGAGGCTATTGAGGCTGCAGGGTCACGAGGCACAAATGT

Basic information

species Oryza sativa
transcript LOC_Os07g08880.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G097726_T03 (Zea mays), 3'ss of exon 1
caataccagctttacatcttgatgatgacccatgtcactattttttataagca---taaaattatctcgatacctgtctgattctcttatatgtttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATGTGGCAAGAGTTGAGGCTATTGAGGCTGCAGGGTCACGAGGCACAAATGT
 |||      |||   | |  || | |  |  | ||| |  |||    |||||   |||| |    ||   |      ||||||| | |  |||||||| ||||||| || || ||||||||||||||||||||| | ||||||||||| |||||||||||||||||||| ||||| || ||||| || |||||||| |||||
-aatggggtatttttgtttatataagg--ctttctcattgctttgacgaagcagcgtaaagtgccttccggattcaattgattctttaaattgtttcttacagCTGGCGATTGCGTGCTAATGAGGGCATCTGATGCTTCAAAGCCACCTTATGTGGCAAGAGTTGAGGCAATTGAAGCAGCAGGATCTCGAGGCACCAATGT
















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|88324893|gb|CI644902.1|CI644902
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|88736691|gb|CI760199.1|CI760199
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|55434340|gb|CV730291.1|CV730291
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|58603106|gb|CK013634.1|CK013634
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|33822155|gb|CF336893.1|CF336893
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|55432497|gb|CV729270.1|CV729270
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|325493451|gb|JG457975.1|JG457975
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|88328018|gb|CI648425.1|CI648425
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|88407773|gb|CI607907.1|CI607907
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|88743386|gb|CI766894.1|CI766894
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|88392298|gb|CI612772.1|CI612772
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|88392287|gb|CI612761.1|CI612761
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|88392479|gb|CI611745.1|CI611745
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|86910171|gb|CI292979.1|CI292979
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|58679044|gb|CK067731.1|CK067731
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
EST: gi|88760851|gb|CI770407.1|CI770407
EST:     GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGC                         CTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG
genomic: GCGGATCCTCGAGTCCTACACCATCAAGGGCTCCGACAAAGTCATCAAGCgtgaggctcc ... tttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataagcataaaattatctcgatacctgtctgattctcttatatgtttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATGTGGCAAGAGTTGAGGCTATTGAGGCTGCAGGGTCACGAGGCACAAATGT
                           gtctgat  putative branch site (score: 4)
                                           tgtttctt  putative PPT
       ataaaattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caataccagctttacatcttgatgatgacccatgtcactattttttataagcataaaattatctcgatacctgtctgattctcttatatgtttcttgcagCTGGGGACTGTGTGCTAATGAGGGCATCTGATACATCAAAGCCACCCTATGTGGCAAGAGTTGAGGCTATTGAGGCTGCAGGGTCACGAGGCACAAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG