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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggccaactgtattttccaatattaactccacattcattttatattatcaaatatgtttttcacgctatgccactgtgatcgcaaatattgtatttcagCTGGCGTTGTTATGTTTACAAGATCACTTGCTCCATTGAAACGCCATGGTATACGTGTCAATGTACTCTGCCCTGAG

Basic information

species Oryza sativa
transcript LOC_Os09g28570.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G179045_T01 (Zea mays), 3'ss of exon 4
----atggccaactgtatttt--ccaatattaactccacattcattttatattatcaaatatgtttttcacgctatgccactgtgatcgcaaatattgtatttcagCTGGCGTTGTTATGTTTACAAGATCACTTGCTCCATTGAAACGCCATGGTATACGTGTCAATGTACTCTGCCCTGAG
    |     || | |||||         | |  |  |  |  ||  || | | |     |||| | | || || ||  ||    | |  || | |||||     |  || || |||||||||||| |||||||||||||| |||| ||  |||| || |||||||||||||| |||||||||
cgcaacttgtaaatatatttagatttgggtcatgtatagctcaatgctaaactgttcggcatgtgtgt-acactgtgtgacctcaaacttaatttttgta-----gGGGGTGTGGTTATGTTTACACGATCACTTGCTCCACTGAAGCGGTATGGCATTCGTGTCAATGTACTGTGCCCTGAG

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 4
atggccaactgtattttccaat--attaactccacattcattttatattatcaaatatgtttttcacgctatgccactgtgatcgcaaatattgtattt-cagCTGGCGTTGTTATGTTTACAAGATCACTTGCTCCATTGAAACGCCATGGTATACGTGTCAATGTACTCTGCCCTGAG
|     |||| |   |   |||  || ||    |   |     || |  |||   |   |  |||  |  |||||  | ||||| ||  |  | | ||  |||  || || ||||||||||||||||||||| |||||||||||||||||||| | ||||||||||| |||||||| |||
aatattaactatggctattaatttatgaaggataatatgtacataaaccatctgctgcatggttccag--atgcc-ttatgatctcacttcgtttcttgacagGGGGTGTGGTTATGTTTACAAGATCACTTTCTCCATTGAAACGCCATGGTGTTCGTGTCAATGTGCTCTGCCCGGAG

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G179045_T02 (Zea mays), 3'ss of exon 4
----atggccaactgtatttt--ccaatattaactccacattcattttatattatcaaatatgtttttcacgctatgccactgtgatcgcaaatattgtatttcagCTGGCGTTGTTATGTTTACAAGATCACTTGCTCCATTGAAACGCCATGGTATACGTGTCAATGTACTCTGCCCTGAG-----------------------
    |     || | |||||         | |  |  |  |  ||  || | | |     |||| | | || || ||  ||    | |  || | |||||     |  || || |||||||||||| |||||||||||||| |||| ||  |||| || |||||||||||||| |||||||||                       
cgcaacttgtaaatatatttagatttgggtcatgtatagctcaatgctaaactgttcggcatgtgtgt-acactgtgtgacctcaaacttaatttttgta-----gGGGGTGTGGTTATGTTTACACGATCACTTGCTCCACTGAAGCGGTATGGCATTCGTGTCAATGTACTGTGCCCTGAGGTATTAAGATTTGCATGACTGGA

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|29670807|gb|CB667082.1|CB667082
EST:     CGCAGGCCTTTATCCTATGAACTTTGATCCCATATATAGTGGAACAAAAG                         CTGGCGTTGTTATGTTTACAAGATCACTTGCTCCATTGAAACGCCATGGTA
genomic: CGCAGGCCTTTATCCTATGAACTTTGATCCCATATATAGTGGAACAAAAGgtgcatatac ... tgtatttcagCTGGCGTTGTTATGTTTACAAGATCACTTGCTCCATTGAAACGCCATGGTA
EST: gi|58688798|gb|CK077485.1|CK077485
EST:     CGCAGG-CTTTATCCTATGAACTTTGATCCCATATATAGTGGAACAAAAG                         CTGGCGTTGTTATGTTTACAAGATCACNTTGCTCCATTGAAACGCCATGGT
genomic: CGCAGGCCTTTATCCTATGAACTTTGATCCCATATATAGTGGAACAAAAGgtgcatatac ... tgtatttcagCTGGCGTTGTTATGTTTACAAGATCAC-TTGCTCCATTGAAACGCCATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcaaatatgtttttcacgctatgccactgtgatcgcaaatattgtatttcagCTGGCGTTGTTATGTTTACAAGATCACTTGCTCCATTGAAACGCCATGGTATACGTGTCAATGTACTCTGCCCTGAG
                                       aaatattgtatttca  TA-rich tract