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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactagattttgaaagcacttgattcacaagtagagcatttttcactattttgtttacttcatctgattagatgcttaatgttatattttcatttacagGTGAAAACCTGAACATACTAAAGCAGGAAGTGAAAAGCCAACGCAAGCATGTTAAAAGCTTGCAGAAAAAGTCTCTCTGGTCGAAGAATTTGGAAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g65330.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 6
tgactagattttgaaagcac-ttgattcacaagtagagcatttttcactattttgtttacttcatctgatta-gatgcttaatgttatatt-ttcatttacagGTGAAAACCTGAACATACTAAAGCAGGAAGTGAAAAGCCAACGCAAGCATGTTAAAAGCTTGCAGAAAAAGTCTCTCTGGTCGAAGAATTTGGAAGAG
|| |   |||| |   | |   || || |  |||| | |||||| |||| |||||||    |||| |||| |  ||||| |||||     | || |||| ||||||| ||| || ||||||||||||||||||||||||||||| |||||||||||||||| |||  |||||||||||| ||||| |||||||||||||||
tgcc--aatttggcctgtatgctgtttgatgagtata-cattttgcactgttttgttgttatcatttgataacaatgctgaatgtggctctgttaatttgcagGTGATAACATGCACATACTAAAGCAGGAAGTGAAAAGCCAAAGCAAGCATGTTAAAAGTTTGAGGAAAAAGTCTCTGTGGTCTAAGAATTTGGAAGAG

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G148773_T02 (Zea mays), 3'ss of exon 5
tgactagattttgaaagcacttgattcacaagtagagcatttttcactattttgtttacttcatctgatta---------gatgcttaatgttatatt-ttcatttacagGTGAAAACCTGAACATACTAAAGCAGGAAGTGAAAAGCCAACGCAAGCATGTTAAAAGCTTGCAGAAAAAGTCTCTCTGGTCGAAGAATTTGGAAGAG
       |   || | |   ||| || |  |||  |   |||| || | |||||||    |||| |||| |          ||| | |||||       || |||| ||||||| ||| || |||||||||||||||||||||||||||||| ||||||||||||||| |||  |||||||||||| ||||| |||||||||||||||
-------agcctgtatg---ttgtttgatgagtgtacatttttgcagtgttttgttgctgtcatttgataacaaattaacaatgatgaatgtggctccgttaatttgcagGTGATAACATGCACATACTAAAGCAGGAAGTGAAAAGCCAACACAAGCATGTTAAAAGTTTGAGGAAAAAGTCTCTGTGGTCTAAGAATTTGGAAGAG
















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|29680203|gb|CB676478.1|CB676478
EST:     TTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG                         GTGAAAACCTGAACATACTAAAGCAGGAAGTGAAAAGCCAACGCAAGCATG
genomic: TTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAGgttagtgtgt ... tcatttacagGTGAAAACCTGAACATACTAAAGCAGGAAGTGAAAAGCCAACGCAAGCATG
EST: gi|33799472|gb|CF325594.1|CF325594
EST:     TTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG                         GTGAAAACCTGAACATACTAAAGCAGGAAGTGAAAAGCCAACGCAAGCATG
genomic: TTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAGgttagtgtgt ... tcatttacagGTGAAAACCTGAACATACTAAAGCAGGAAGTGAAAAGCCAACGCAAGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattttgtttacttcatctgattagatgcttaatgttatattttcatttacagGTGAAAACCTGAACATACTAAAGCAGGAAGTGAAAAGCCAACGCAAGCATGTTAAAAGCTTGCAGAAAAAGTCTCTCTGGTCGAAGAATTTGGAAGAG
                             gcttaat  putative branch site (score: 4)
                                          ttttcattt  putative PPT
                               ttaatgttatattttc  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactagattttgaaagcacttgattcacaagtagagcatttttcactattttgtttacttcatctgattagatgcttaatgttatattttcatttacagGTGAAAACCTGAACATACTAAAGCAGGAAGTGAAAAGCCAACGCAAGCATGTTAAAAGCTTGCAGAAAAAGTCTCTCTGGTCGAAGAATTTGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA