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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggtgatgattgcatagtttaattgtacatgttacactagaggttcttcagctgctttcttgtcaagtttcaaataaaaacctacaattttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g56670.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 10
tgggtgatgattgcatagtttaattgtacatgttacactagaggttcttcagctgctttcttgt----caagtttcaaataaaaacctacaattttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
   ||    |    |  || ||  |  |        | ||  | || || ||||   |  |  |    |  |||| |||  ||||   | ||||  | |  |||||| |||||||| |||||||| ||||||||||||||||||||||| ||||| ||||| ||||||||||||||||| ||||||
-ccgtagc-acaaaaaggtgtacctacatgcaagtgattat-gtttgtttagctctgtggtcatggcccctgtttaaaaccaaaaatgaaaattcca-tcacagGTACGTGGAGGTTAATATGAACTCTGGTGCTACTGTTTGGCCACTCTTCAATAGTCTGCAGGCATTCTGGCCAGGGCTTCAG

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 10
tgggtgatgattgcatagtttaattgtacatgttacactagaggttcttcagctgctttcttgt----caagtttcaaataaaaacctacaattttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG------------------
   ||    |    |  || ||  |  |        | ||  | || || ||||   |  |  |    |  |||| |||  ||||   | ||||  | |  |||||| |||||||| |||||||| ||||||||||||||||||||||| ||||| ||||| ||||||||||||||||| ||||||                  
-ccgtagc-acaaaaaggtgtacctacatgcaagtgattat-gtttgtttagctctgtggtcatggcccctgtttaaaaccaaaaatgaaaattcca-tcacagGTACGTGGAGGTTAATATGAACTCTGGTGCTACTGTTTGGCCACTCTTCAATAGTCTGCAGGCATTCTGGCCAGGGCTTCAGGTTTGGTTACACATATTT

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 9
---------tg-ggtgatgattgcatagtttaattgtacatgttacact----agaggttcttcagctgc---------tttcttgtcaagt----ttcaaata-aaaacctacaattt-------taattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
         || ||  ||| |  ||   | ||| | ||| ||   | ||    |  | || || |  ||          ||| || | || |    ||||| |   ||||     ||||       |  ||| ||||||||||| || |||||| |||||| ||||| ||| |||||| |||| ||||| || |||||||| ||||| || ||||||
gtaaaagcttgtggctatgttgccaccctgtaaatatacttgactcgctgtctatcgttttttgaaatgtgtaagtatgtttatttttaaatgtatttcaagtttgaaactcttgatttgtgtttatgtttcaagGTATGTGGAAGTGAATATGGATTCTGCTGCTATTGTCTGGCCATTATTTAACAGCCTGCAGGCATTTTGGCCTGGCCTTCAG

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------tgggtgatgattgcatagtt---taattgtacatgttacactagaggttcttcagc-tgctttcttgtcaagtttcaaataaaaacc----tacaattttaat-----tccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
                         | |   |||| |  | | ||   | | | |   |  | || |     ||  | ||  |   || |   |   |  ||||| |         |  |||||| ||     |  ||||||||||||||||| ||| |||||| ||||| |||||||||| |||| |||||| | || |||||||||||||| ||||||
gtaaatgattgtggctatcatgtgctagtatatgaatctacaattccttgactttgttttattcatttattatttattagaattggttttaacccgatcacaaattaggttgggggtttaatttttatgtatctgtagGTATGTGGAGGTAAACATGGATTCTGCTGCTATTGTTTGGCCATTATTTAACAGTTTGCAAGCATTCTGGCCAGGCCTTCAG

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|88361880|gb|CI682051.1|CI682051
EST:     GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG                         GTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTNTGGCCACTATCCAA
genomic: GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTGgtaaaaatat ... ttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAA
EST: gi|88394177|gb|CI684850.1|CI684850
EST:     GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG                         GTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAA
genomic: GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTGgtaaaaatat ... ttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcagctgctttcttgtcaagtttcaaataaaaacctacaattttaattccagGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG
                                           ttttaat  putative branch site (score: 3)
                       tttcaaataaaaacct  TA-rich tract