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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAGGGTGTGGCTAACCTAACTCTACATTTCCCTGAGAACTTTGGAGGTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagccttgcttatttagtttaaaaaggtaattggatatcgtgctgatgctttgatttcaaaattctgccaattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g37832.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37832.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G090647_T04 (Zea mays), 5'ss of exon 6
GTTCCAGGGTGTGGCTAACCTAACTCTACATTTCCCTGAGAACTTTGGAGGTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagccttgctt----attta-gtttaa------aaaggtaattggatatcgtgctgatgctttgatttcaaaattctgccaattgcag
|||||| |||||||||||||||||||| |||||| |||| |||||||| ||||| |||||||| || |||||||||||  | ||||||||||| ||||||||||  |||  ||| ||    ||||| |  |||      |||   | | | |   | | ||||| |||  ||| |    | ||||   |  |||
GTTCCAAGGTGTGGCTAACCTAACTCTGCATTTCTCTGACAACTTTGGTGGTGATACAACTAAAATTTATTACATTGGACTACGTGGTGAAGCCACTCAGgtacttaagttttgttttgctatttatgcataataaagaaaaaacagtggaacgccatactgattctt--attgcttcgtgctgcttgtcccag
















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|88852617|gb|CI008810.1|CI008810
EST:     GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAG                         AACCAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
genomic: GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagc ... ccaattgcagAACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
EST: gi|58678373|gb|CK067060.1|CK067060
EST:     GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAG                         AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
genomic: GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagc ... ccaattgcagAACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
EST: gi|218502566|gb|FG947236.1|FG947236
EST:     GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAG                         AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
genomic: GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagc ... ccaattgcagAACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
EST: gi|88269573|gb|CI380871.1|CI380871
EST:     GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAG                         AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
genomic: GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagc ... ccaattgcagAACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
EST: gi|88366636|gb|CI556420.1|CI556420
EST:     TATATTACATTGGGTTGCGTGGTGAAGCTACTCAG                         AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
genomic: TATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagc ... ccaattgcagAACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
EST: gi|40724664|gb|CK431262.1|CK431262
EST:     GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTATTCAG                         AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
genomic: GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagc ... ccaattgcagAACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
EST: gi|58594516|gb|CF992824.1|CF992824
EST:     GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAG                         AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
genomic: GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagc ... ccaattgcagAACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
EST: gi|87030834|gb|CI362048.1|CI362048
EST:     GTTACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAG                         AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
genomic: GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagc ... ccaattgcagAACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA
EST: gi|88831856|gb|CI369538.1|CI369538
EST:     GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAG                         AACAAAAGGGATGTTTTGGCCACAATTGTTTATGAAATAATGCCTAATCCA
genomic: GTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagc ... ccaattgcagAACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCAGGGTGTGGCTAACCTAACTCTACATTTCCCTGAGAACTTTGGAGGTGACACAACTAAGATATATTACATTGGGTTGCGTGGTGAAGCTACTCAGgtaccaaagccttgcttatttagtttaaaaaggtaattggatatcgtgctgatgctttgatttcaaaattctgccaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC