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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC

Basic information

species Oryza sativa
transcript LOC_Os12g27520.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G063792_T05 (Zea mays), 3'ss of exon 4
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
                 |||||    |  |||      |  ||   |  |  |||||    || | | |      | |  || |||   ||| ||     || |||||  |      | ||| |||| |||||||  || |||||||| || ||||||| ||||||| |||||||||| |||||||| |||||||||||||| || ||||| || ||||| || |
-----------------acctacccaagatttaccttgtgctatgcttgttcttttattgtgtattggtagcgggggtagaaaaat---atggta-----ctgatcctcttttttcatttgccagGTCTCATCCCAATCCCCAAAGGAGGGGTCCTATTACAAGCAGTTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTCGGTAGCACTACTTATGATCAAC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 7
gtatactttgttcttctac--ctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
|||||  |||||||| ||    || || ||||    |   |||     ||  | |  ||   |  ||    ||  |  |   |     |   |   |||  | || |||||  |      | ||| |||| |||||||  || |||||||| || ||||||| ||||||| |||||||||| |||||||| |||||||||||||| || ||||| || ||||| || |
gtatatcttgttcttttatatttaattcacctacccaagatttaccttgtgctatgcttgttcttttattgtgtattggtagcgggggtagaaaaatatggtactgatcctcttttttcatttgccagGTCTCATCCCAATCCCCAAAGGAGGGGTCCTATTACAAGCAGTTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTCGGTAGCACTACTTATGATCAAC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
gtatactttgttcttctacctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatc-tctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
||||| ||||||||| ||  ||  | ||||    |   |||     | | | |  ||      ||  | || | ||   | |   | | |    |||  | || |||||  |    || | ||||||||||||||||| || |||||||| || ||||||| ||||| | |||||||||| |||||||| ||||||||||||||||| ||||| || ||||| || |
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttg-taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 3
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatc-tctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
                 |||||    |  |||   ||||      | | | |  ||      ||  | || | ||   | |   | | |    |||  | || |||||  |    || | ||||||||||||||||| || |||||||| || ||||||| ||||| | |||||||||| |||||||| ||||||||||||||||| ||||| || ||||| || |
-----------------acctacccaagattt--acctt------gccctgtgcttgttgatttctgttg-taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 6
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
                 |   |  | |          |   | |  |     |  ||   |||    | |||   ||    | |    |    |   || || ||  ||     || | |   ||  | || || | || ||||      |||||| |||||||    |||||||||| |||||||| || || ||||||||||||||||| |||||||| |         
-----------------aggaaagtaagaacaccaagtggctgaaattgctatgctattaggt----cagatacagaaatgagatcactgacatccattgctgattgttt----atatttaacagAGTACAACCAGATCACCAA------GTTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 6
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
                       |||  | |  ||  |    || |    |   |     |   || |   || |   |  |  ||    || |   |   | |   |  |   || | | | ||  ||||||  | || ||||      ||||||||||||||    | ||||| || |||||||| ||||| ||||||||||||||||| || ||||| |         
----------------------gttggacctggaggataaaaaatgaaaccaagta--tggaactacccttttctagctttagcatcgattgatcaatcattgacattcattttatttttac-agAGTTCATCTAGATCACCAA------GTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 6
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
       | || | |  |   ||   |           | |  | ||   |||||    |  ||||||  |||  |||| | ||||  | ||  |||  | | ||  || ||||          |  ||||||  | ||  ||       ||||||||||||||    | ||||| || |||||||| ||||| ||||||||||||||||| || ||||| |         
------gtcgtacctggatgaataaaaatgaaactgagtatggaagtacccttttctatc--tttagc--att--gattgatcaatcat-tgacatccattttat--ttttaca----------gAGTTCATCTAGATCATCAT------GTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttcta--caatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
                         ||    | ||       |  | ||    ||   |     ||   | | | ||| ||  ||| | ||        || | | ||| |     || | |   ||  | || || | || ||||      | |||| |||||||    |||||||||| |||||||| || || ||||||||||||||||| |||||||| |         
------------------------ggaaaagtaagaacaccaagtggctgaaattg--ctatgctattaggtca-gatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccg-gtttagc-tgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
                                           |  |||    |  | | | || |  | | | | ||   |||| |||| |   |        |||     |    |  ||| |        ||||| |  | || ||| |  | ||||   ||     |||| || || ||||| || ||||||||||||||||| |||||||| ||||| |  |      
-----------------------------------------gtatatctcgaatgcaactgtgtgtgaccttaatgtggc-caactatttaag--tgctgaaggaatttggttgtgtttcctgatgcagGG-GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaat-ctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
             | || |  || | | |||   |  | || |  | | | |  ||   |  | |   |  || ||  || |||||    |  | |  || |||    | |    | |  |   |||||||||||||||| || ||||| ||||| || || |||    | || || || ||||||||||| |||||||||||||| |||||||||||||| |  |
------------gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgccct--tgttattgtaacatatatttgttgcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 7
----gtatactt-tgttcttctacctatttgaccttttagcctttttaacgtcttcttttt----acccggtt-tagctgattatgattcaacaattttatgttatctttcta-----------atccttctacaatctctgct---------agGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
     | ||||| ||||||  || || ||  |  | || ||  || |   ||  | |   |    |||   || | | |  | | | ||   |  ||   ||||  ||||| |           |||     | ||| | |  |         ||||| |  | || || ||||| || ||    | ||  ||| || |||| |  || |||||||||||||||||||||||||| |||||| | | |||    |
gtatatctacttctgttctggtagcttttcaatttgtttgcacttctgttgttctttcaatcaagaccttattgttgatattcaggcttttccttttccctgttccctttccatatcagttattatctggtcataatgtttctttctaattgcagGTTACCACACGGTCACCAAAAGATGGAATATGTTATAAGAAGTTGCCAAGATCAAGTGCTATTAAGGTGATTGATTTTGGTAGCACAGCTTTTGAGTGTC

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|86900381|gb|CI296424.1|CI296424
EST:     AGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA                         GTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAG
genomic: AGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttg ... tctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAG
EST: gi|29665166|gb|CB661441.1|CB661441
EST:     AGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA                         GTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAG
genomic: AGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttg ... tctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
                            ttctaat  putative branch site (score: 2)
                                             tctctgct  putative PPT
             aattttatgttatctt  TA-rich tract