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'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccaaagcgtgatgcttactgatcttactattttctttcctatatgtcagatagaggtcaacagtgtctgattactacctgtaatgacaaagttgcatttactgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG

Basic information

species Oryza sativa
transcript LOC_Os08g41390.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 6
gtatgccaaagcg-tgatgcttactgatcttact-attttctttcctatatgtcagatagaggtcaacagtgtctgattactacctgtaatgacaaagttgcatttactgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG
||||||  ||| | | |   |   | ||  || | ||  |  |  || |  ||     |    |      ||  |   |    | || | | || || ||   ||||||||| | |||||||||| |  ||||| |||||||||||  |  | |||||||||||||||||||| |||   ||||||||| |||||||||| |||||||
gtatgctcaagtggtcaaagtacttaattgtaatgatgctagtagctgttggttcttgactcctttcagttgattaggtttatcttgcactcactaaattatgtttactgtt-ggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGCATGACGAA---GAGCCATTTAAATTCAAGACCGATGAAG
















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|454468|gb|D28191.1|D28191
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAANGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58677816|gb|CK066503.1|CK066503
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58695757|gb|CK084444.1|CK084444
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58695816|gb|CK084503.1|CK084503
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|29630489|gb|CB635498.1|CB635498
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58686617|gb|CK075304.1|CK075304
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58682283|gb|CK070970.1|CK070970
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|2427305|gb|C71768.1|C71768
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTNTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|29628610|gb|CB633621.1|CB633621
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAATGTGCAGTTGTTGAAG                         TCAAAATAACTGGAAAACTTCAAGATGGTACAATATTTACAAAGAACGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacagtgtctgattactacctgtaatgacaaagttgcatttactgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG
        gtctgat  putative branch site (score: 4)
             attacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccaaagcgtgatgcttactgatcttactattttctttcctatatgtcagatagaggtcaacagtgtctgattactacctgtaatgacaaagttgcatttactgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG