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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgttgctggagatgatctgcagtttttctaaagtgcacatggcatattgtttgcttattatcattaccatttcagaacacttcttttttgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGACATTGTCTGCAAGCGTGCAGAACTTGGTTACAACTATGGTGTGATCCTTA

Basic information

species Oryza sativa
transcript LOC_Os06g13810.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 8
aatgttgctggagatgatctgcagtttttctaaagtgcacatggcatattgtt-tgcttattatcattaccatttcagaac--acttcttttttgt-actgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGACATTGTCTGCAAGCGTGCAGAACTTGGTTACAACTATGGTGTGATCCTTA
 || |  ||   |||    | || ||| ||  |      | |      ||||  |  || |   ||| |  |||||| ||   |  |||| ||||  | |||||||||||||||||||| |||| ||||| | ||||||  |||||||||| || ||  |||||||||||||||| |||||||||||||||||||| |||||||
-atatatct---gataggttacattttctcacattatagctttattgtttgtcataattctgtgcatcattatttcacaaataatgtcttctttgccattgtagGTTGCTGCAAAGAAGCAAACCCTTAAGAATGTCACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTA

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 1
aatgttgctggagatgat-ctgcagtttttctaaagtgcac-atggcat-attgtttgc--ttattatcattaccatttcagaa----cacttcttttttgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGACATTGTCTGCAAGCGTGCAGAACTTGGTTACAACTATGGTGTGATCCTTA
         | |||  |   ||   | | |   | || ||  ||||  | ||||||     || |   ||| |  |||||| ||        | |||||   | ||||||||||||| ||||| ||||| ||||| | ||||||  |||||||||| || ||  |||||||||||||||| |||||||||||||||||||| |||||||
---------gcagactacattgttatctctgataggttcattatggttttattgttcataattctgtgcatcattatttcacaaataatgtctttttttgccattgtagGTTGCTGCGAAGAAAGAAACCCTTAAGAATGTCACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTA

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 8
aatgttgctggagatgatctgcagtttttctaaagt--gcacatggcatattg--tttgcttattatcattaccatttcagaacacttcttttttgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGACATTGTCTGCAAGCGTGCAGAACTTGGTTACAACTATGGTGTGATCCTTA
    || |   |   | |     |||     | |     |||||| |  |||   |  | ||||  | | | | | ||           |  ||| |  || ||||| ||||  ||||| | ||| | || | |||||| ||||||||    ||  || ||||||| ||||| ||||||||||||||||| ||||| || || |
-tcatttcaatatggggttattggttcagagagacctcacacatgcctcattagatcagtttatatttact-caactttgatctggaaatacttttt--tgcagGTTTCTGCCCAGAAGCAGACTTTGAAGAATGTCACAGACTACATGGTGGATGTTATCTGCAAACGTGCTGAACTTGGTTACAACTACGGTGTCATACTGA

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------aatgttgctggagatgatctgcagtttttctaaag----tgcacatggcatattg-tttg---cttattatcattaccatttcagaacacttcttttttg-----tactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGACATTGTCTGCAAGCGTGCAGAACTTGGTTACAACTATGGTGTGATCCTTA
                                | |  |  ||    | |  ||||  |||||  |||    ||||  |    |  || ||||    | ||  |    || ||| ||  |   ||  |  ||      | ||| |||||||||| ||||||   || || |||| ||| || |||||||||   ||  |||||||||| ||||||||||||||||||||||||||||| || ||||
gtatctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGATGTTGTCTGCAAACGTGCAGAACTTGGTTACAACTATGGTGTTATACTTA

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|88504577|gb|CI432083.1|CI432083
EST:     TGGAGTGTGCTCTGCAAACACATCGTAATGTTGCACTCATTGGAGAAGAG                         GTTGCGGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
genomic: TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAGgtttgtaatt ... tgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
EST: gi|29689204|gb|CB685479.1|CB685479
EST:     TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAG                         GTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
genomic: TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAGgtttgtaatt ... tgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
EST: gi|157650204|gb|EX449838.1|EX449838
EST:     TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAG                         GTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
genomic: TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAGgtttgtaatt ... tgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
EST: gi|58657805|gb|CK046485.1|CK046485
EST:     TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAG                         GTTGCTGCAAGAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGA
genomic: TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAGgtttgtaatt ... tgtactgtagGTTGCTGCAA-AGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGA
EST: gi|2800921|gb|AA754215.1|AA754215
EST:     TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAG                         GTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
genomic: TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAGgtttgtaatt ... tgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
EST: gi|33796706|gb|CF324221.1|CF324221
EST:     TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAG                         GTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
genomic: TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAGgtttgtaatt ... tgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
EST: gi|5003496|gb|AU068645.1|AU068645
EST:     TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAG                         GTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC
genomic: TGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAGgtttgtaatt ... tgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgtttgcttattatcattaccatttcagaacacttcttttttgtactgtagGTTGCTGCAAAGAAGGAAACTCTTAAAAGTGTCACCGACTACATTACCGACATTGTCTGCAAGCGTGCAGAACTTGGTTACAACTATGGTGTGATCCTTA
                                    cttcttttttgtact  CT-rich tract
           ttattatcatta  TA-rich tract