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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catctgtgctgtttccttcattcttggcataagtctaaaactacttaatattggaatcagagggagtaagcaacagcgtctgatacattttatttattagCCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTCGTTCGGAATCAAATTGAAGAACCAGAAACTCCACGATCTTCAAGGTCGA

Basic information

species Oryza sativa
transcript LOC_Os07g32400.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g32400.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G027756_T01 (Zea mays), 3'ss of exon 14
------catctgtgctgtttccttcattcttggcataagt---ctaa--aactacttaatat-tggaatcagagggagtaagcaacagcgtctgatacat-tttatttattagCCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTCGTTCGGAATCAAATTGAAGAACCAGAAACTCCACGATCTTCAAGGTCGA
       |      ||  ||  | |||| ||   || |     || |    |||  ||| |  ||| |      | | | || | ||||  || | |||| |||| || |||||||||||| ||||||||||| |||||||| | |||||  ||||||||||| |||||||  |||| |||||| |||||||||||||||||||||||||| |
gtaagttacaaacactactta-tacatttttaagattaacatccttactgtctatgtaagacatggcaaagatagaactgaggagcagcagctaacacatctttacttcttagCCTCCCAGCAGATTCTCCTCTTATGAAGATATGTCTAATAGTGGGACAGTTGTTCGGACCCAAAATGAAGACCCAGAAACTCCACGATCTTCAAGGTCAA
















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|11025721|gb|AU162322.1|AU162322
EST:     CGCCAAGAGCATCTCAGGTGTACCCTGCAGCTACTAACCACAGTTCCAAG                         CCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTC
genomic: CGCCAAGAGCATCTCAGGTGTACCCTGCAGCTACTAACCACAGTTCCAAGgtgtgtttta ... tatttattagCCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTC
EST: gi|33678909|gb|CF307148.1|CF307148
EST:     CGCCAAGAGCATCTCAGGTGTACCCTGCAGCTACTAACCACAGTTCCAAG                         CCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTC
genomic: CGCCAAGAGCATCTCAGGTGTACCCTGCAGCTACTAACCACAGTTCCAAGgtgtgtttta ... tatttattagCCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTC
EST: gi|33678127|gb|CF306366.1|CF306366
EST:     CGCCAAGAGCATCTCAGGTGTACCCTGCAGCTACTAACCACAGTTCCAAG                         CCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTC
genomic: CGCCAAGAGCATCTCAGGTGTACCCTGCAGCTACTAACCACAGTTCCAAGgtgtgtttta ... tatttattagCCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatattggaatcagagggagtaagcaacagcgtctgatacattttatttattagCCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTCGTTCGGAATCAAATTGAAGAACCAGAAACTCCACGATCTTCAAGGTCGA
                                gtctgat  putative branch site (score: 4)
                                          ttttattt  putative PPT
                                 tctgatacattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catctgtgctgtttccttcattcttggcataagtctaaaactacttaatattggaatcagagggagtaagcaacagcgtctgatacattttatttattagCCTCCCAGTAGATTCTCCTCGTATGAAGACACGTCTATCAGTGGGACAGTCGTTCGGAATCAAATTGAAGAACCAGAAACTCCACGATCTTCAAGGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC