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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagatgttctgctatccaaaacagggtggttaatgtaagttatagaagaatggcagtggatacgttttaatttttgttggcattttcagGCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTGAAAAGTCGGTCCTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGAC

Basic information

species Oryza sativa
transcript LOC_Os01g36840.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36840.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G030596_T02 (Zea mays), 3'ss of exon 13
gtaagagatgttctgctatccaaaacagggtggttaatgtaagttatagaagaatggcagtggatacgttttaatttttgttggca-ttttcagGCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTGAAAAGTCGGTCCTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGAC
|||||| || ||          |  ||         || |  |||| | ||||           ||  ||||  ||||| |   |  |||||||||||||||||||| ||||| ||||||||||||||||||||||| |||||||| ||||| |||||||||||||| || |||  ||||||||||||||||||
gtaagaaatatttgaaggagtcatccaaaaatcaagatattggtta-aaaagatc---------tatattttcttttttatcatcccttttcagGCATTCTGGAGGCCAACTTTATCAAACCTACCCATGACAAGCAGGATTTTGAGAAGTCAGTCCTTTATCAAAGACTTGAGTTCCGCTTGAAAGAAATGAC
















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|116874995|gb|EC365503.1|EC365503
EST:     ATTTTGGAAAGTTGCGAACAACTCATATGGCAAAGGGCGAGGAGTTGTGG                         GCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTG
genomic: ATTTTGGAAAGTTGCGAACAACTCATATGGCAAAGGGCGAGGAGTTGTGGgtaagagatg ... gcattttcagGCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTG
EST: gi|11171117|gb|AU163632.1|AU163632
EST:     ATTTTGGAAAGTTGCGAACAACTCATATGGCAAAGGGCGAGGAGTTGTGG                         GCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTG
genomic: ATTTTGGAAAGTTGCGAACAACTCATATGGCAAAGGGCGAGGAGTTGTGGgtaagagatg ... gcattttcagGCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTG
EST: gi|116875003|gb|EC365511.1|EC365511
EST:     ATTTTGGAAAGTTGCGAACAACTCATATGGCAAAGGGCGAGGAGTTGTGG                         GCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTG
genomic: ATTTTGGAAAGTTGCGAACAACTCATATGGCAAAGGGCGAGGAGTTGTGGgtaagagatg ... gcattttcagGCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTG
EST: gi|116875534|gb|EC366042.1|EC366042
EST:     ATTTTGGAAAGTTGCGAACAACTCATATGGCAAAGGGCGAGGAGTTGTGG                         GCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTG
genomic: ATTTTGGAAAGTTGCGAACAACTCATATGGCAAAGGGCGAGGAGTTGTGGgtaagagatg ... gcattttcagGCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagttatagaagaatggcagtggatacgttttaatttttgttggcattttcagGCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTGAAAAGTCGGTCCTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGAC
                              ttttaat  putative branch site (score: 3)
                                              cattttc  putative PPT
                         atacgttttaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagatgttctgctatccaaaacagggtggttaatgtaagttatagaagaatggcagtggatacgttttaatttttgttggcattttcagGCATTCTGGAGGCAAACTTCATCAAACCTACCCATGACAAGCAAGATTTTGAAAAGTCGGTCCTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA