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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatcgtttacataaatatctcgtgccatggacctcttgagtttgcagtaaagaaattgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os10g33640.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
gtaagcatcgtttacataaatatctc---gtgccatggacctcttgagtttgcagtaaagaaattgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
                |||  |||||   |  |||| || | | |   |    |||  ||      |  |||  ||  | || |||||||| |||||  | ||||||||||| ||||||||||| ||||| |||||||||||||| ||||||||||| |||||| |||||
---------------gtaagcatctccttgcaccatcgatcgcattgatg---agtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 7
-----------gtaagcatcgtttacataaatatctcgtgccatggacc-----tcttgagtttgcagtaaagaaat--tgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
            |  || || ||||  |  |  |    |      |  |     |    | |||    | | | |||  ||  |  |   || |    ||||||||||||||||| || ||||| |||||||| ||||| ||||| || || ||||||||||| || |||  ||| ||||| |||
agcatattgagttttgcttcatttatgtggaatttgtatatataaggtcagggttacatattttattttgatgcaatgatggttgttacaaaattcacagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTTTTATTCTGATGATCCAATGTTAACATGCAGGAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 6
--------------------gtaagcatcgtttacataaatatctcgtg-----ccatggacctcttgagtttgcagta----aagaaatt------gaataatttcaac-tatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
                     ||    || ||| || ||||| || |       |  ||    |||  | ||   | ||    || |  ||        ||  |   ||  | || |||||||| || ||||| || |||||||||||| ||||||| ||||| || || ||||| ||||| || |||   ||||| ||||||
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G34920.1 (Glycine max), 3'ss of exon 6
---------------gtaagcatcgtttacataaatatctcgtgccatggacctcttgagtttgcagtaaagaaattgaataatttca---actatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
                || | || ||||| | | | |  |       |  |  |      |||    |  | | | ||   | | | |   | |   |||||||||||||||||| || |||||||||||| ||||||| ||||| || || ||||||||||| || ||| |||| || || |||
aaaaaaatctttattttatgtatagtttataaataaactttaacgagtaaatattaaatatttaagtttgacacaatgctcattgtgataaaattcatagGTGGTCACTTGGAGCTATTATGTATGAAATGTTAGTGGGATATCCACCTTTTTATTCTGATGATCCAATGTCAACATGTAGGAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 7
--------------------------------------------------gtaagcatcgtttaca----taaatatctcgtgccatggacctcttgagtttgcagtaaagaaattgaata--atttcaac-tatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
                                                  |  | |  | ||  |     ||||  | | ||| ||  | | |  |||  |||    || | | |  |||    | ||||    || |||||||| |||||||| || |||||||||||||| ||||| ||||| || || ||||| ||||| || |||   ||||| ||||||
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatg-cattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 6
---------------gtaagcatcg-tttacataaatatctcgtgccatggacctcttgagtttgcagtaaagaaattgaataatttca---actatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
               | ||  |     |   ||  |||| |  ||  ||  |  |      |||    | || | | ||  |  ||| |   | | | |||||||||||||||||| || |||||||||||| ||||||| ||||| || || ||||||||||| || ||| |||| ||||| |||
tttgtatgtaaaaaggcaaataaaaactcttatgtatattttatga-ataaatattaaatatttaagtttaacacaatgtttgttttgataaaatttgtagGTGGTCACTTGGAGCTATTATGTATGAAATGTTAGTGGGATATCCACCTTTTTATTCTGATGATCCAATGTCAACATGCAGGAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 6
------------gtaagcatcgtttacataaatatctcgtgccatggacc----tcttgagtttgcagtaaagaaat--tgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
             | ||| || ||||  |  |  |   |  |    || |    |    | ||||   | | | |||  ||  |  |   ||      ||||||||||| ||||| || ||||| |||||| | ||||| ||||| || || ||||||||||| || |||  ||| || || |||
aagcttattgggtttagcttcatttatgtggaatttgtggacataagatcaggttacatattttgttttgatgcaatgatggttgttacaaaactcacagGTGGTCACTGGGAGCTATTATGTACGAAATGTTGGTGGGATATCCACCTTTTTATTCTGATGATCCAATGTTAACATGTAGGAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagcatcgtttacataa-atatctcgtgccatgg-acctcttgagtttgcagtaaagaaat-tgaataatttc----aactatct------agGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
||| |    |   |  |      ||| || |  |      |||| |  |   | || |    | |  |||||||        | |||      |||||||||||||| || ||||||||||||||||| ||||| | ||| ||||| ||||| || ||||| ||||||||||| ||||||
gtaggtgcagcaaatctgttgggtcttgttctgttttgtttcttcaactcaaaatacattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G20470.1 (Arabidopsis thaliana), 3'ss of exon 6
-----gtaagcatcgt-ttacataaatatctcgtgccatggacctc--ttgagtttgcagtaaaga---aattgaataatttcaa-------ctatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
       | | | | | ||  |  | ||| | ||| ||  | |  |  ||| | ||  | ||       |||  | |  | ||||       |||| ||||||||| ||||| || || ||||| ||||||||||| || ||||| || || ||||| ||||| |||||| |||| || ||||||
tagtcaaagggaccatcttgaagcattatttggtgacactgtctgcatttgtgctttgaataggacgctaatgcagttttctcaatgaaatgctatgtagGTGGTCTCTTGGTGCTATAATGTACGAAATGCTAGTAGGATATCCGCCGTTTTATTCAGATGATCCTATGTCAACCTGTAGAAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 7
gtaagcatcgtttacataaa--tatctcgtgccatggacctcttgagtttgcagtaaagaaat---tgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
||| |    |   || ||    ||| |   | | | ||  ||||  || |  |  ||  | ||   |||||||| |  |  || ||||||||| ||||| || || |||||||||||||| ||||| | ||| || || ||||| ||||| || ||||||||||| || |||
gtaggtgaagccaacctattcctatttgtggtctttgatttctttggtgtaaataaataatatgggtgaataatcttgag-atttagGTGGTCTCTTGGCGCCATTATGTATGAAATGCTTGTGGGGTTTCCGCCCTTTTATTCAGATGACCCAATGACAACTTGTAGGAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 6
----------------gtaagcatcgtttacataaatatctcgtgccatggacctcttgagtttgcagtaaag-aaattg-aataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
                   ||  |  |||| || | |||     | ||     ||| | | |||     | |  |||||   ||  ||| |  |    |||||||||||||| || ||||||||||||||||| ||||| ||||| || || ||||||||||| || ||| |||| || || |||
agatccttggaactaaaacagagtgatttaaattattatggaaagtcagaacactccttaattttttccagaccaaattatgattcttttatttccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 6
--------------gtaagcatcgtttac-ataaatatctcgtgccatggacctcttgagtttgcagtaaagaaattgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
                   |||| | | | || |     |    |||||||     | ||||| |  | |   ||     |  ||  |  | || |||||||| ||||| || |||||||| |||||||| ||||| ||||| || || ||||| ||||| |||||||||||||| || |||
gttggttctctaaaactgtcatcatcttctatgatctgttttccccatgga-----ttagtttcc--tcatataaccatctgtttgaatttctccagGTGGTCTCTTGGTGCTATCATGTACGAAATGCTTGTGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 6
----gtaagca-tcgtttacataaatatctcgtgccatg----gacctcttgagtt----tgcagtaaagaaattgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
    |||   | | ||   | |      ||     |||       | | || ||||    |            |||||         || |  ||||||||| | |||||||||||||| || ||||| || || || || ||||| || || ||||| ||||||||||| ||  | |||
gtatgtagcaagttgtgctccttggcccctgaatgcatttcctagctttttaagttgttttttttccggaggtttgaacgtaagtttctctgcagGTGGTCATTGGGAGCAATCATGTACGAGATGCTGGTTGGGTACCCTCCATTTTACTCCGATGAACCTATGACAACATGTCGCAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------gtaagcatcgtttacataaatatctcgtgccatggacctcttgagtttgcagtaaagaaattgaata-atttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
                        |  | | ||      |   | ||     | |   | |   |||      | |  | || || | ||        |  ||||||||||| |||||||||||||| || ||||| || || || ||||| ||||| |||||||| || |||||||||||  | |||
aattactcgagatactttatactcgactaggttgggaggaagccccgcatgttaggttttt---gttcagcccagaacagttcaacatatgattttcctgcagGTGGTCACTAGGAGCAATCATGTACGAGATGCTGGTTGGTTACCCCCCTTTCTACTCTGATGAACCCATGACAACTTGTCGCAAG

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------gtaagcatcgtttaca---taaatatctcgtgccatggacctcttgagtttgcagt-aaagaaattgaa--taatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
                                     ||  | | | | |     ||  |   | |    ||  |  |||||   |||   | ||| |  |||||  ||| ||   |||   |||||||||||||||||||||||||| || |||||||| ||||| || ||||| || ||||| || ||||||||||||||  | |||
gtatgtgacaagtcgttctcctgaatctttctctttttatccttggctcatgatgtacttgcttagcttgataaagttcttg---ttgtgttcaaaaaggttgaacgtaagttttcctac--agGTGGTCACTTGGAGCAATCATGTACGAGATGCTAGTTGGCTACCCTCCATTTTACTCTGACGAACCTATGACAACTTGTCGCAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 14 (downstream exon)
Score: 1

GCATACTCCACTGTCGGTACACCGGACTACATTGCTCCAGAAGTTCTTCTAAAAAAGGGTTATGGAATGGAGTGTGATTGgtaagcatcg ... aactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccatggacctcttgagtttgcagtaaagaaattgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
                         taaagaaattgaataa  TA-rich tract