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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccttgaaagctcagtattgagtcaatagctgttacatattttgattcttcccacaaatttttgcagGAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAATCTGGGAAGAAACAAAACGCAAGACCAGTTGATTTGGATCCACATGGTG

Basic information

species Oryza sativa
transcript LOC_Os01g43030.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43030.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G047093_T01 (Zea mays), 3'ss of exon 18
gtaaaccttgaaagctcagtattgagtcaatagctgttacatattttgattcttcccacaaatttttgcagGAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAATCTGGGAAGAAACAAAACGCAAGACCAGTTGATTTGGATCCACATGGTG
||||  ||   |  ||||  || |  ||| |   |     || || ||||| |  || || |||  | |||||||||||||||||||| |||||||| ||| |||||||| ||| |||||||||||| ||||||||| | ||||||||||||||| |||||||||||||||
gtaa-tctcagacactca-cataggatcactgtttacctaattttctgattttgtcc-catattcctccagGAGGCTGAAGAGAAACAAGAGGATGAAACAGCTTCATCTAACAGTTCAAAATCTGGCAAGAAACAACATGCAAGACCAGTTGATCTGGATCCACATGGTG
















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|87005314|gb|CI285536.1|CI285536
EST:     GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGG                         GAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAA
genomic: GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGGgtaaaccttg ... atttttgcagGAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAA
EST: gi|29635309|gb|CB640318.1|CB640318
EST:     GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGG                         GAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCANAA
genomic: GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGGgtaaaccttg ... atttttgcagGAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAA
EST: gi|33794849|gb|CF323303.1|CF323303
EST:     GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGG                         GAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAA
genomic: GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGGgtaaaccttg ... atttttgcagGAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAA
EST: gi|87023633|gb|CI286384.1|CI286384
EST:     GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGG                         GAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAA
genomic: GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGGgtaaaccttg ... atttttgcagGAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAA
EST: gi|58694649|gb|CK083336.1|CK083336
EST:     GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGG                         GAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAA
genomic: GGAAGAAACTGAGACAAAAACAGAAAAAGGCAGAAGCTCGTGCCAAAAGGgtaaaccttg ... atttttgcagGAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtattgagtcaatagctgttacatattttgattcttcccacaaatttttgcagGAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAATCTGGGAAGAAACAAAACGCAAGACCAGTTGATTTGGATCCACATGGTG
                           ttttgat  putative branch site (score: 4)
                                              tttttgc  putative PPT
                    ttacatattttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaccttgaaagctcagtattgagtcaatagctgttacatattttgattcttcccacaaatttttgcagGAGGCTGAAGAGAAACAGGAGGATGAGACAACTTCATCTCACACTTCAAAATCTGGGAAGAAACAAAACGCAAGACCAGTTGATTTGGATCCACATGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA