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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgcttcatttcttatctttgatagggatcatccagaaagatgcatcctgcattcttgttgcagttgctcttacttatttttcattccgtgggcattgccacagCAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCAGAAGCTTCAGTGGAATCAGCTGGTGCAAAAGCTGCTGCATGCAGAACTC

Basic information

species Oryza sativa
transcript LOC_Os12g20150.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g20150.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G040968_T02 (Zea mays), 3'ss of exon 11
---------gtgatgcttcatttcttatctttga----tagggatc------atccagaaagatgcatcctgcat----tcttgttgcagttgctcttacttatttttcattccgt----------gggcattgccacagCAAAAAAGCAAA---TCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCAGAAGCTTCAGTGGAATCAGCTGGTGCAAAAGCTGCTGCATGCAGAACTC
          |  ||| |||  || | |  |  |    |    |||      |||  |  |  | |||  | ||     | || ||  | |||||| ||||| ||||   |||| |          |  | |  |  |||||||| ||| |    || | ||  |||||||  | || ||  || ||||||||||| || ||  | |||||| ||||||||||||||||||||||  |||   
gttaactttcttttgcctcaaatcatgtaatcaaagcatgccaatccaccacatcttgctaactacatgttacaacacatgtttttatacttgctcctactttttttcttttccctaactctaagggaccttcacttcagCAAAAGAGCTATACTTCCGTAGCAAATGGTATGTCTGGTGTGCTCGAGCTTTCAGAGGCATCGATTGAATCATCTGGTGCAAAAGCTGCTGCATGTGGAA---
















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|58686191|gb|CK074878.1|CK074878
EST:     ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAG                         CAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA
genomic: ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAGgtgatgcttc ... attgccacagCAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA
EST: gi|29669192|gb|CB665467.1|CB665467
EST:     ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAG                         CAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA
genomic: ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAGgtgatgcttc ... attgccacagCAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA
EST: gi|29666723|gb|CB662998.1|CB662998
EST:     ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAG                         CAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA
genomic: ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAGgtgatgcttc ... attgccacagCAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA
EST: gi|218500377|gb|FG965723.1|FG965723
EST:     ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAG                         CAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA
genomic: ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAGgtgatgcttc ... attgccacagCAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA
EST: gi|58652693|gb|CK041373.1|CK041373
EST:     ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAG                         CAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA
genomic: ATGAATTCTCTCTACCATCGGATATCGAGATGCCACTGCAAATGTCTAAGgtgatgcttc ... attgccacagCAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattcttgttgcagttgctcttacttatttttcattccgtgggcattgccacagCAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCAGAAGCTTCAGTGGAATCAGCTGGTGCAAAAGCTGCTGCATGCAGAACTC
                  ctcttac  putative branch site (score: 3)
                     ttacttatttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgcttcatttcttatctttgatagggatcatccagaaagatgcatcctgcattcttgttgcagttgctcttacttatttttcattccgtgggcattgccacagCAAAAAAGCAAATCAGGAGTGAATGGTAGTTTTGCTGCTCTTGAGCTTTCAGAAGCTTCAGTGGAATCAGCTGGTGCAAAAGCTGCTGCATGCAGAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC