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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattcatgtgtaggaattaaatattccagtgagtttaaccagccatatattttcctataagaacttgttaactttatttagttcatgttctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGCCTCCTGTTATGCCCAATCCAGCGGGCATGGTATATCCTCCACGACCGGC

Basic information

species Oryza sativa
transcript LOC_Os09g38790.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 2
-----ttattcatgtgtaggaattaaatattccagtgagtttaaccagccatatattttcctataagaacttgttaactttatttagttcatgttctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGCCTCCTGTTATGCCCAATCCAGCGGGCATGGTATATCCTCCACGACCGGC
     | | |    | || ||| | ||  || |  |   | || |   ||| | |      |||||    ||    ||||||  |      ||||| |  ||||||||||||||||||| | |||||| ||||||| ||||||||   | ||||||||  | ||||||| ||| |    ||||||| || |||||| ||||| ||
atgcataaattgaatttaagaactgaaacttgctattt-tgtaccattccagaaagagcgttataa----tttcccactttacctgacatttgttccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGCCTGTTATTATGCCTAATTCGCTAGGCATGGCATTTCCTCCGCGACCAGC
















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|29655595|gb|CB651870.1|CB651870
EST:     TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAG                         AGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
genomic: TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctat ... ctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
EST: gi|29624560|gb|CB629571.1|CB629571
EST:     TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAG                         AGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
genomic: TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctat ... ctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
EST: gi|29630516|gb|CB635525.1|CB635525
EST:     TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAG                         AGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
genomic: TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctat ... ctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
EST: gi|58664656|gb|CK053342.1|CK053342
EST:     TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGGCCACTATGGAGAAG                         AGGAAGACCCTTCATCGAAGGTAGCCCAAGTGGAAGTGGCATCGCTAAGGC
genomic: TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctat ... ctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatattttcctataagaacttgttaactttatttagttcatgttctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGCCTCCTGTTATGCCCAATCCAGCGGGCATGGTATATCCTCCACGACCGGC
                                           ttctaaa  putative branch site (score: 2)
                    ttgttaactttattta  TA-rich tract