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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttctatacaaataagttggagatgctttattctatggcaacaatgtagacgcccaatatgatgtctcatgtgctgtcatgcctacaatgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAA

Basic information

species Oryza sativa
transcript LOC_Os08g15040.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G147726_T04 (Zea mays), 3'ss of exon 4
cattttctatacaa-ataagttggagat--gctttattctatggcaacaatgtagacgcccaatatgatgtctcatgtgctgtcatgcctacaatgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAA----------
  ||   | |||    || |||| || |  ||| || | ||  |      | | | |     || |||  | | |  || | ||||||             ||||||||||||||||||| |||||||||||||| || || ||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||          
tgttacttgtaccctgtaggttgtagctttgctgtactgtaccgtgttttttttggcattttatctgacatgttagttgttttcatgc-------------aggatcttccagGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTACACAAAATTAAGAGCCGCCAATGGGCGATTTTCAAAACATCTGCAATAAAGGGAGAGGG

upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 11
-cattttctatacaaataagttggagatgctttattctatggcaacaatgtag-acgcccaatatgatgtctcatgtgctgtcatgcctacaatgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAA
   |    |||   | |  ||      |   || |    | ||   | ||||    |     | ||   | | || ||   |  |   |    | | |||||||||||||||||||||| |||||||||||||| || || ||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||
gtgtgccttatgttactt-gtaccctgtaggttgtagctttgctgtactgtaccgtgttttttttggcattttatctgacatgttagttgttttca-tgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTACACAAAATTAAGAGCCGCCAATGGGCGATTTTCAAAACATCTGCAATAA

upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0008g07360.t01 (Vitis vinifera), 3'ss of exon 6
cattttctatacaaataagttggagatgctttattctat-ggcaacaatgtagacgcccaatatgatgtctcatgtgctg-------tcatgcctacaatg-aatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAA
           | |||  | ||   ||  | | | || | |     | | |     |      | |||  |||| || ||       |||    |  |||| ||   |||||||||| ||||||||||||||||||||  |||| ||| | || ||  | |||||||| || | ||| |||||||| ||||| ||||| |  |||||||
---------acccaatgtggtgacaattttctctgctcttgatggaattcttagaactttggttcatgattcatctgatggttcagctcactgttttaatgtaaattagGATCTTCCTGGTGCACTTGATGATGCTGCTTTAACAGAAGCTTTGGAGTTGCACAAGATAAAAAACCGCCAATGGGCTATTTTTAAAACTTGCGCCATAA

upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv11s0052g01720.t01 (Vitis vinifera), 3'ss of exon 7
---cattttctatacaaataagttggagatgctttattctatggcaacaatgtagacgcccaatatgatgtctcatgtgctgtcatgcctacaatgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAA
       | || ||  ||     ||   ||   |   ||| ||  |    |||         || || | | || |   || |  | |||    |  ||  |||||||||| ||||||||||||||||||||  | || ||  | |||||  | ||||||||||| | |||||||||||| ||||| ||||| ||||||||||
agcttcatcctctatgaactttctgcgcataaatccatctgtgaaatttgtgtgtttagttgat-tgttttttctttctcttttttccctgt--tctatatagGATCTTCCTGGTGCACTTGATGATGCTGCTGTGACTGAGGCCTTAGAGTTGCACAAGATTAAAAACCGTCAATGGGCAATTTTTAAAACTTCTGCCATAA

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|88906338|gb|CI375410.1|CI375410
EST:     AGGAGGATGAGCTAAAA-GTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: AGGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|89162128|gb|CI103664.1|CI103664
EST:     TATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: TATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|88239417|gb|CI240579.1|CI240579
EST:     AGGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: AGGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|86434337|gb|CI094680.1|CI094680
EST:     AGGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: AGGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|86511016|gb|CI153649.1|CI153649
EST:     AGGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: AGGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtagacgcccaatatgatgtctcatgtgctgtcatgcctacaatgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAA
             aatatgat  TA-rich tract