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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttactgttttacgagccacttgtaagcacacaaacgagtacttatgaatatttgttcattgcttacactttcatgtattgcccttgttacatcgattctggctcgtcttacttgttgacttcttgtcattttttgctccagTCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAAACTGGGAAGAAACTTGTATTCTCTAAAGATCCTAGACATGGTTCTCATT

Basic information

species Oryza sativa
transcript LOC_Os02g53210.6
intron # 3
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|29674941|gb|CB671216.1|CB671216
EST:     AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAG                         TCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAA
genomic: AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAGgtatgcttta ... tttgctccagTCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAA
EST: gi|29621685|gb|CB626696.1|CB626696
EST:     AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAG                         TCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAA
genomic: AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAGgtatgcttta ... tttgctccagTCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAA
EST: gi|29621684|gb|CB626695.1|CB626695
EST:     AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAG                         TCAAGACTTTCACCTTTTGCAAACACTATAACTAGGAGAAAGGGAGATGAA
genomic: AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAGgtatgcttta ... tttgctccagTCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAA
EST: gi|218503370|gb|FG964055.1|FG964055
EST:     AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAG                         TCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAA
genomic: AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAGgtatgcttta ... tttgctccagTCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAA
EST: gi|58595254|gb|CF993562.1|CF993562
EST:     AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAG                         TCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAA
genomic: AAGACCAGGACACAAAACCTGCTCACCTGTGGCAATTGATGGTCACAAAGgtatgcttta ... tttgctccagTCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatcgattctggctcgtcttacttgttgacttcttgtcattttttgctccagTCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAAACTGGGAAGAAACTTGTATTCTCTAAAGATCCTAGACATGGTTCTCATT
                          tgttgac  putative branch site (score: 3)
                                cttcttgtcatttttt  CT-rich tract
                                       tcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttactgttttacgagccacttgtaagcacacaaacgagtacttatgaatatttgttcattgcttacactttcatgtattgcccttgttacatcgattctggctcgtcttacttgttgacttcttgtcattttttgctccagTCAAGACTTTCACCTTTTGCAAACACTAGAACTAGGAGAAAGGGAGATGAAACTGGGAAGAAACTTGTATTCTCTAAAGATCCTAGACATGGTTCTCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA