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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtataaactgtgaaaaagaagtgcaaatttgttatttcttgttcctcatatggttgaagaggtcttgtttctcactgtgaattatacttgtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG

Basic information

species Oryza sativa
transcript LOC_Os06g09330.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 7
---agtat----aaactgtgaaaaagaagtgcaaatttgttatttcttgttcctcatatggttgaagaggtcttgtttctcactgtgaattatacttgtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG
   ||| |    | |  |    ||  || |   |   | ||  ||       |||   || || |||  ||    ||||||| |||  || || ||  |   |||||||||| ||||| ||||||||||||||||||| ||   |||| |  |||||||||||||||||||| ||||||||||| ||||| ||||||||
gttagtttctcaacatcgcagcaagcaattctcagcattttccttacaagaactcccttgttttaaggtgt----tttctcaatgttgataattctcat---tgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACGTCAGATGCAGAAAAGAGACGTTTAGCAAAAGCTTCCCTTGCTTACAATTGTGAGAG

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G453855_T03 (Zea mays), 3'ss of exon 4
----agtataaactgtgaaaaagaagtgcaaatttgttatttcttgttcctcatatggttgaagaggtcttgtttctcactgtgaattatacttgtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG
      |  | | |     ||  || |       | |   ||       ||    || || |||  ||    ||||||| |||  || || ||  | |||||||||||| ||||| ||||||||||||||||||| ||   |||| |  |||||||| ||||||||||| ||||||||||||||||| ||||||||
agttgctcaacattacagcaagcaattcttggcatttcccttgccagaacttccttgttttaaggtgt----tttctcaatgttgataattctcatacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAGAGGCGTTTAGCAAAAGCTTCCCTTGCCTACAATTGTGAGAG

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G116919_T02 (Zea mays), 3'ss of exon 6
----agtataaactgtgaaaaagaagtgcaaatttgttattt-cttgttcctcatatggttgaagaggtcttgtttctcactgtgaattatacttgtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG
      |  | | ||    ||  || |       | |   || |  |  | |||| || || |||  ||    ||||||| |||  || || ||  | |||||||||||| ||||| ||||||||||||||||||| ||   |||| |  |||||||| ||||||||||| |||||||||| |||||| ||||||||
agttgctcaacattgcagcaagcaattcttggcatttcccttgccagaacttcat-tgttttaaggtgt----tttctcaatgttgataattctcatacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAGAGGCGTTTAGCAAAAGCTTCCCTTGTCTACAATTGTGAGAG

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G045039_T01 (Zea mays), 3'ss of exon 3
----agtataaactgtgaaaaagaagtgcaaatttgttatttcttgttcctcatatggttgaagaggtcttgtttctcactgtgaattatacttgtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG
      |  | | ||    ||  || |       | |   ||       ||    || || |||  ||    ||||||| |||  || || ||  | |||||||||||| ||||| ||||||||||||||||||| ||   |||| |  |||||||| ||||||||||| ||||||||||||||||| ||||||||
agttgctcaacattgcagcaagcaattcttggcatttcccttgccagaacttccttgttttaaggtgt----tttctcaatgttgataattctcatacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAGAGGCGTTTAGCAAAAGCTTCCCTTGCCTACAATTGTGAGAG

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|87015788|gb|CI279540.1|CI279540
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|87010686|gb|CI312378.1|CI312378
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|86495662|gb|CI138295.1|CI138295
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|86599367|gb|CI251325.1|CI251325
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|86514651|gb|CI157284.1|CI157284
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|86855623|gb|CI268950.1|CI268950
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|88995570|gb|CI022893.1|CI022893
EST:     CTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|88206366|gb|CI206215.1|CI206215
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|87035120|gb|CI189743.1|CI189743
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|89186387|gb|CI262219.1|CI262219
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|87035496|gb|CI190118.1|CI190118
EST:     CATTCTCACGGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: CATTCTCACGGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
EST: gi|88223516|gb|CI223365.1|CI223365
EST:     GGGCCTCCTTTCATTCATG                         ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG
genomic: GGGCCTCCTTTCATTCATGgtaagctctt ... gtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatatggttgaagaggtcttgtttctcactgtgaattatacttgtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG
                        ttctcac  putative branch site (score: 2)
                                   aattatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtataaactgtgaaaaagaagtgcaaatttgttatttcttgttcctcatatggttgaagaggtcttgtttctcactgtgaattatacttgtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG