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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctatgctattcattaattcaccctttaccttctgaaatttcttaattttttgaacgccattcaaccccacgaagatatttgatacagtaaccacagcccagtgacattctttgctgatgctgcattaccgatttcctgtctgttcagATCTCCGTGAAGATAGGGCCTATCTTGCTGATCATCCAGCTTCTTCCATAATAACAACGGAGCAGGTTGGTGTTTTGACTGTGACAAGAGAATGACACAT

Basic information

species Oryza sativa
transcript LOC_Os01g12900.2
intron # 4
splice site 3'
intron type U2

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|7134828|gb|AU082694.1|AU082694
EST:     TCGCCGGTTTTCGCCTGGTGTNC-TGTA-TTCTTNTTGGA-CCAAGTTGG                         ATCTCCGTGAA
genomic: -CGCCGGTTTGCGCCTGGTGTTCCTGTAGTTCTTGTTGGAACCAAGTTGGgtatgctatg ... gtctgttcagATCTCCGTGAA
EST: gi|55439594|gb|CV733107.1|CV733107
EST:     TCGCCGGTTTGCGCCTGGTGTTCCTGTAGTTCTTGTTGGAACCAAGTTGG                         ATCTCCGTGAAGATAGGGCCTATCTTGCTGATCATCCAGCTTCTTCCATAA
genomic: TCGCCGGTTTGCGCCTGGTGTTCCTGTAGTTCTTGTTGGAACCAAGTTGGgtatgctatg ... gtctgttcagATCTCCGTGAAGATAGGGCCTATCTTGCTGATCATCCAGCTTCTTCCATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagcccagtgacattctttgctgatgctgcattaccgatttcctgtctgttcagATCTCCGTGAAGATAGGGCCTATCTTGCTGATCATCCAGCTTCTTCCATAATAACAACGGAGCAGGTTGGTGTTTTGACTGTGACAAGAGAATGACACAT
                   tgctgat  putative branch site (score: 3)
                                       tttcctgtctgttc  putative PPT
             attcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctatgctattcattaattcaccctttaccttctgaaatttcttaattttttgaacgccattcaaccccacgaagatatttgatacagtaaccacagcccagtgacattctttgctgatgctgcattaccgatttcctgtctgttcagATCTCCGTGAAGATAGGGCCTATCTTGCTGATCATCCAGCTTCTTCCATAATAACAACGGAGCAGGTTGGTGTTTTGACTGTGACAAGAGAATGACACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA