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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcacatacggacatcttgttttcgttctttctacatttgttttcatttttcagatctcaggtatcattttactaactttggcaacttttcaatccgcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCTGTGCAAATGTCATTACGCTCCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g40030.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 1
---------ttcacatacggacatcttgttttcgttctttctacatttgttttcatttttcagatctcaggtatcattttactaactttggcaacttttcaatccgcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCTGTGCAAATGTCATTACGCTCCTTCAG
         |   || |  |||||  ||| ||  |  | |     |||||||||  ||||||||||  |    |  |  |||||| ||||| || || |||||  |||||| ||||||||||||||||||||||||| || |||||||| || ||||| || ||||||||||| ||||||||||||
atgagccaatgtccacatagacatgatgtcttgctattgt-----tttgttttccattttcagatccga---tttgtggtactaattttggtaa-ttctcaatttgcagTGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG

upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 1
-----ttcacatacggacatcttgttttcgttctttctacatttgttttcatttttcagatctcaggtatcattttactaactttggcaacttttcaatccgcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCTGTGCAAATGTCATTACGCTCCTTCAG
        ||  | |  ||        |  |   || |   || |||| |||||| |||| | ||    |   | |||||| ||||| | ||| |||||  |||||||||||||||||||||||||||||||| || ||||| ||||||||||| ||||| |||||||| || |||||||||
accaaagaaccaatgtccacagaaagatgatgtgttattgcttcgtttccatttt-cagaaccca---tttgctgtactaattttggta-cttctcaatttgcagTGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTTGTGCGAATGTCATCACACTCCTTCAG

upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0008g05570.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------ttcacata-----cgga--catcttgttttcgttctttctacatttgttttcatttttcagatct---caggtatc-----attttact--aactttg----gcaacttttcaatcc-gcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCTGTGCAAATGTCATTACGCTCCTTCAG
                               ||||  |       |||  | | |  ||| |||  ||   | | || |  | ||| ||   || |   ||   |||     |||||||   ||||       |||| | ||   |   |||||  |  | ||||| || ||||||||||| || ||||| ||| ||||||| ||||||| |||||| || ||| |||||
gtgccctctcttctctaaattgcatcttaatttcatgtgaattctggagtcgtttcatttgcgtaattataataattatcattattattttaattttttcattaatcgatccattttacgtgaactcctctatgcaattctttgtttttgcagTTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTTGTGCAAGTGTCATCACACTCTTTCAG

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|88422800|gb|CI573962.1|CI573962
EST:     CATGACGCGGCGCGGCGCGGTCGCCGCGCTCTCCTACATGGCCTGCTCCG                         TGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCT
genomic: CATGACGCGGCGCGGCGCGGTCGCCGCGCTCTCCTACATGGCCTGCTCCGgtacgttccc ... caatccgcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCT
EST: gi|58667565|gb|CK056251.1|CK056251
EST:     GCCGCGCTCTCCTACATGGCCTGCTCCCG                         TG-TGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCC
genomic: GCCGCGCTCTCCTACATGGCCTGCT-CCGgtacgttccc ... caatccgcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCC
EST: gi|88422801|gb|CI573963.1|CI573963
EST:     CATGACGCGGCGCGGCGCGGTCGCCGCGCTCTCCTACATGGCCTGCTCCG                         TGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTACCCT
genomic: CATGACGCGGCGCGGCGCGGTCGCCGCGCTCTCCTACATGGCCTGCTCCGgtacgttccc ... caatccgcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttcagatctcaggtatcattttactaactttggcaacttttcaatccgcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCTGTGCAAATGTCATTACGCTCCTTCAG
                         tactaac  putative branch site (score: 0)
                                        cttttc  putative PPT
                 tatcattttactaa  TA-rich tract