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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattcaacctactgcttattgacacattagctgattttttaatatcttggttatggtctttgatgttctgactttattcctcatcttggttcatatcagGAATTGGGTGGCAACTCTTTATGGGTTGATCGTTTTCTTGCACGGTTTGCTGCATTTTTTTACTACTTCATGACTGTTGCGATGTACATGGTGAGCCCAA

Basic information

species Oryza sativa
transcript LOC_Os04g57320.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57320.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G010555_T01 (Zea mays), 3'ss of exon 4
gaattcaacctactgcttattgacacattagctgattttttaatatctt-----ggttatggtctttgatgttc-tgactttattcctcatc--ttggttcatatcagGAATTGGGTGGCAACTCTTTATGGGTTGATCGTTTTCTTGCACGGTTTGCTGCATTTTTTTACTACTTCATGACTGTTGCGATGTACATGGTGAGCCCAA
        |||| || |  ||  || ||||  |      ||| | ||||     || |        |  |  |  ||  || || |||  ||  |||| |||||| |||||||||||||| ||||||| ||| ||||  |||||||||| ||||||   ||||| ||||||||||||||||||||||| ||||||||| |||||||| 
-------gccta-tgttgttttccatattaattatcgccttagtttctttacatggattcaacacctactacttatgtattgatcccttttcccttggctcatattagGAATTGGGTGGCGACTCTTTGTGGTTTGACTGTTTTCTTGCTCGGTTTATGGCATTCTTTTACTACTTCATGACTGTTGCAATGTACATGCTGAGCCCAC

upper sequence: LOC_Os04g57320.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G102349_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------gaattcaacctactgcttattgacacattagctgattt-tttaatatcttggttat--ggtctttgatgttc-tgactttattc--ctcat----------cttggttcatatcagGAATTGGGTGGCAACTCTTTATGGGTTGATCGTTTTCTTGCACGGTTTGCTGCATTTTTTTACTACTTCATGACTGTTGCGATGTACATGGTGAGCCCAA
                                                                         |  || |   || | | |  ||     ||  || |||  |||   || ||  ||||  | || ||  | | | ||| || || |  || ||          ||||| |||||||||||||||||||||||| || ||||| ||||| |||| ||||| || |||   || |||||||||||||||||||||||||||||||||||| |||||||| 
gtacgcatctttccagtaaaatccatgtgtgccagatcttcctttcagtgctattatgtcaaagttatatcacggcttaattttattccgttctgttggtttgactaattaattttccatattaattatcagttcatttctttacatgaattcatcctacttatggattgagcccttggctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATGGCGTTTTTTTACTACTTCATGACTGTTGCGATGTACATGTTGAGCCCAC
















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|87007304|gb|CI278975.1|CI278975
EST:     GCTGAGAGCTGGAATGAGTTCCATCACCTCTTAATCATGGAA                         GAATTGGGTGGCAACTCTTTATGGGTTGATCGTTTTCTTGCACGGTTTGCT
genomic: GCTGAGAGCTGGAATGAGTTCCATCACCTCTTAATCATGGAAgtatgtctct ... ttcatatcagGAATTGGGTGGCAACTCTTTATGGGTTGATCGTTTTCTTGCACGGTTTGCT
EST: gi|29661402|gb|CB657677.1|CB657677
EST:     TGCACTTTGCTGAGAGCTGGAATGAGTTCCATCACCTCTTAATCATGGAA                         GAATTGGGTGGCAACTCTTTATGGGTTGATCGTTTTCTTGCACGGTTTGCT
genomic: TGCACTTTGCTGAGAGCTGGAATGAGTTCCATCACCTCTTAATCATGGAAgtatgtctct ... ttcatatcagGAATTGGGTGGCAACTCTTTATGGGTTGATCGTTTTCTTGCACGGTTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttggttatggtctttgatgttctgactttattcctcatcttggttcatatcagGAATTGGGTGGCAACTCTTTATGGGTTGATCGTTTTCTTGCACGGTTTGCTGCATTTTTTTACTACTTCATGACTGTTGCGATGTACATGGTGAGCCCAA
                     ttctgac  putative branch site (score: 2)
                          actttatt  TA-rich tract