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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgccatgtagaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag

Basic information

species Oryza sativa
transcript LOC_Os02g04710.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G065494_T01 (Zea mays), 5'ss of exon 13
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgccatgta--gaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag
|| |||||||||||||||||||||||||| |||||||||||||| ||||||||    | |||   ||| | || ||  | | |   | |   |   |  ||||    |   | ||   ||| |                                
CTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgcaataactt-tccgtcgtgctgatctttacttataaaacaaactgaagaaacataaaactcattttgcag------------------------------

upper sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G023798_T01 (Zea mays), 5'ss of exon 13
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgc--catgtagaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag
|| |||||||| ||||||||||||||||| |||||||||||||| ||||||||      ||||  | ||| || ||  ||| |   | |    ||  | ||||    |   | |     || |                                
CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgcagtaacct-ttcatcgtgctgatttgtacttataaaacaaattgaagaaacataaaacccatcttgcag------------------------------

upper sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA01G00430.2 (Glycine max), 5'ss of exon 14
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattaca-acccatccatt----gtcctcttttcttgctttgccatgtagaaggtgaactgatctttctttcc-ttctctcctttgtatgtgtataaaatttatag
 | |||||||||||||| || ||||| ||||| || ||||||||||||||||  || | |  |   |  | |    ||  | |     | |  | |||  ||       |    || ||| |||    | | |  | | |   | | ||   | |||||
ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCCgtaagcaatcaaatgcttgtgaaatataagttttatccatcttccattccacctactccaccattcaattttttttttaactttttaatgtttccttatgtatggtgtatag

upper sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv09s0054g01550.t01 (Vitis vinifera), 5'ss of exon 13
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgccatgtagaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag--------------------------------------------------------------------------------------------------------
 | |||||||||||||| || ||||| |||||||| |||||||||||||||||  |||    |  | || |      || |  || ||    ||||| ||      ||  | | | ||  | | |||       | |   | || |   | |                                                                                                         
TTAATCAATCCTGCTGAAACTTTTGGTGACATTGTCATTGATTATCCgtaagattttaagcactcttcagt------ttctaatgttt----atgtataat----tctagtttgttttcacctatctggaaaaaaagaacaaaagaaaaaaaaaagaggtgggttgttgagggaaggggtggggggtgttgtgggttgtcttgtagtttgatttgatggagaaaatcttatatgctgttacctgggtggcactgcag

upper sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv09s0054g01110.t01 (Vitis vinifera), 5'ss of exon 15
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgccatgtagaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag------
 | |||||||||||||| || |||||||||||||| |||||||||||||||||  |||    |  | || |      || |  || ||    | | | ||    |  |  | |||    || |||         |     |  |||   | ||      
TTAATCAATCCTGCTGAAACTTTTGGGGACATTGTCATTGATTATCCgtaagattttaagcactcttcagt------ttctaatgttt----acgcataattctagtt--tgttttcacccatctggaaaaaaaaaaaaaaagaaaaaaaaaggaaaaa

upper sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv09s0018g00630.t01 (Vitis vinifera), 5'ss of exon 13
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgccatgtagaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag----
 | ||||||||| |||| || ||||| ||| |||| |||||||||||||||||  |||     ||  | ||    |||  | ||   |    ||        |    || | |  |    ||           |    | | |||| | |||     
TTAATCAATCCTACTGAAACTTTTGGTGACGTTGTCATTGATTATCCgtaagattttaag---cactctttagtttctaatgtttactcataattc------tagtttgttttcacccatctagaaaaaaaaatg-aagaaaaaaaataataaaaaa

upper sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv09s0054g01090.t01 (Vitis vinifera), 5'ss of exon 14
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgccatgtagaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag----------------------------------------------------------------------------------------------------------
 | |||||||||||||| || ||||| |||||||| |||||||||||||||||  ||      ||| | |     |||  | ||        ||||| ||      ||  | | | |   | | |||       |   | | ||||   | |                                                                                                           
TTAATCAATCCTGCTGAAACTTTTGGTGACATTGTCATTGATTATCCgtaagattttgag---cattcttcagtttctgatgtt-------tatgtataa----ttctagtttgtttccacctatctggaaaaaaaaagaaaaaaagaaaaaaaaaggaggtgggttgttgggggaaaggggtaggtggtgttgtgggttgtcttttagtttgatttgatggagaaaatcttatatgctgttactgggtggcactgcag

upper sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 14
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgccatgtagaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag
 | |||||||||||||| || ||||| |||||||| ||||||||||||||||| |||    | | |  |||       |||      ||    |||      | |    |  ||    |   |||||   |  ||||  |||  |        
TTAATCAATCCTGCTGAAACTTTTGGCGACATTGTTATTGATTATCCgtaagatatt--ggcactttgattaatgctatttgcaatattcttttgt------ttatgcaactttatagtttatctctaactaatatgactatgtag-------

upper sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv09s0054g01120.t01 (Vitis vinifera), 5'ss of exon 12
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgccatgtagaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag----
 | ||||||||| |||| || ||||| ||| |||| |||||||||||||||||  |||    |  | || |      || |  || ||    | | | ||    |  |  | ||        |         | | |   | || | | | |     
TTAATCAATCCTACTGAAACTTTTGGTGACGTTGTCATTGATTATCCgtaagattttaagcactcttcagt------ttctaatgttt----acgcataattctagtttgttttcacccatctagaaaaaaagaaagaaaaaaagaataaaaaaaga

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|58652903|gb|CK041583.1|CK041583
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTC
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTC
EST: gi|58674498|gb|CK063185.1|CK063185
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|58598317|gb|CK008845.1|CK008845
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|2309779|gb|C25934.1|C25934
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGGATGCACTTCAGCAGCA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCA
EST: gi|55411924|gb|CV724300.1|CV724300
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|58674549|gb|CK063236.1|CK063236
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|29676836|gb|CB673111.1|CB673111
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|58673098|gb|CK061784.1|CK061784
EST:     CTTATCAATCCTGCTGAGAACTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|38471634|gb|CF955765.1|CF955765
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|58664360|gb|CK053046.1|CK053046
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|58593382|gb|CF991690.1|CF991690
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|38474351|gb|CF958483.1|CF958483
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|702331|gb|D48622.1|D48622
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|58688613|gb|CK077300.1|CK077300
EST:     GAGCTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: GAGCTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
EST: gi|27545624|gb|CA763832.2|CA763832
EST:     CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCC                         TTATGTGGAACGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA
genomic: CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAA

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: 69 (upstream exon), 74 (downstream exon)
Score: 39

CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacatt ... aaatttatagTTATGTGGAATGCACTTCAGCAGCAATTCAGGCCCTGACAGCATTTAAAAAGCTCTACCCTGGACACCGCAAGAGTGAAATAGACAACTGTATAAGCAAA




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