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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgttcccaccactatcatcatgtattatcagcaattattgttgtgattgctcagttggtccaaaatattggcataattcctttactcgttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAAATCCAAGAAGGATAGAAAATATATTTTCTCATCCTCGCCAGCCTCGGTC

Basic information

species Oryza sativa
transcript LOC_Os05g03430.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03430.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G155123_T02 (Zea mays), 3'ss of exon 15
ggtgttcccaccactatcatcatgtattatcagcaattattgttgtgattgctcagt-tggtccaaaatattggcataattcctttactcgttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAAATCCAAGAAGGATAGAAAATATATTTTCTCATCCTCGCCAGCCTCGGTC
 |  ||      ||     | |  ||||    |   |  |      |||  ||  ||    |  |   |||||   |||    |||  |  |   |||||||||||||  | |  ||||  |||| ||| ||| |||  ||| || || |||| || |||||||| |||||||||||||||||||||||||| || |||||
tgaatttttttaacctgtttaacttattgct-gttgtgttctcaacgatatctgtgtactattaatgttattgttgtaacattttttgttctcaattgcagCTTCTGCTCTCCCAAGCATGAACAATGACAGATGTAATGGATCTAATCTAAACCCGAGAAGGATTGAAAATATATTTTCTCATCCTCGCCAACCACGGTC
















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|86481066|gb|CI123699.1|CI123699
EST:     GCCACAAATTCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTG                         CTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
genomic: GCCACAAATTCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTGgtttgtctcc ... ttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
EST: gi|86858340|gb|CI271186.1|CI271186
EST:     GCCACAAATTCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTG                         CTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
genomic: GCCACAAATTCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTGgtttgtctcc ... ttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
EST: gi|163919779|gb|EG710341.1|EG710341
EST:     CCACAAATTCCATCAGACAGAGACAGGGATCGAACCATTGACCGATGCTG                         CTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
genomic: CCACAAATTCCATCA-ACAGAGACAGGGATCGAACCATTGACCGATGCTGgtttgtctcc ... ttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
EST: gi|218484827|gb|FG958208.1|FG958208
EST:     GCCACAAA-TCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTG                         CTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
genomic: GCCACAAATTCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTGgtttgtctcc ... ttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
EST: gi|87027311|gb|CI269986.1|CI269986
EST:     TCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTG                         CTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
genomic: TCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTGgtttgtctcc ... ttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA
EST: gi|29689428|gb|CB685703.1|CB685703
EST:     GCCACAAATTCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTG                         CTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTTA
genomic: GCCACAAATTCCATCAACAGAGACAGGGATCGAACCATTGACCGATGCTGgtttgtctcc ... ttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgctcagttggtccaaaatattggcataattcctttactcgttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAAATCCAAGAAGGATAGAAAATATATTTTCTCATCCTCGCCAGCCTCGGTC
                                 ttcctttactcgtttt  CT-rich tract
                  aaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgttcccaccactatcatcatgtattatcagcaattattgttgtgattgctcagttggtccaaaatattggcataattcctttactcgttttttgcagCTTCTGCATTTCTGAGCACAAACATTGAAAGACGTAGCGGAGCTGATTTAAATCCAAGAAGGATAGAAAATATATTTTCTCATCCTCGCCAGCCTCGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG