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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctcccgtgttttgttttgtagattgataatttggctctcaactctaaatgttaaatctaagttatattacatcattacatgcttagcttaatggt...

Basic information

species Zea mays
transcript GRMZM2G173424_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 5'ss of exon 5
TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctcccgtgttttgttttgtagattgataatttggctctcaactctaaatgttaaatctaagttatattacatcattacatgcttagcttaatggt------
|| ||||||||||| |||| ||||||||| |||||||| |||||||||||||| ||||||||||||||||| | |||||| ||||||||||| ||||| |||||| ||    ||  |||     || | |||| |||    |||| || |  |  |  ||  || ||  | | |||  | |   |    |||||| | |       
TTGTTTGACACAAAACACAATGGAATTTTAGGATTTGATGAATTTGCTCGTGCACTCTCAGTATTTCATCCAAGTGCTCCACTTGATGAGAAGATTGACTgtgagttcagacgtactgt-----agctagatattttactcctcatctatgcagttctaaattatgtattgtcacaataatggct-tggagcttatttgcaaaagt

upper sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G44580.1 (Glycine max), 5'ss of exon 5
TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctcccgtgttttgttttgtagattgataatttggctctcaactctaaatgttaaatctaagttatattacatcattacatgcttagctt-aatggt--------------------------------------------------------
|||||||||||||| |||| ||| ||  |||| |||||||| ||||||||||||||||| || || ||||||||||| ||| ||||||| || || || |||  | |      | || |||     |||  || ||| ||   ||  | |      ||||| ||| | | | | ||  |||  |  |    ||| |||  |                                                        
TTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATAAGATCGAATgtatgttgtacaatattttttctacaattattattttagcatacagatttt--ctgtaaatttaa-taacaatgcacaattgaaatcaagtctttaattttctttgataacctttttaaataaacaaaaattgaacccatgtgatatcatgtttcag

upper sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G39940.1 (Glycine max), 5'ss of exon 5
TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctcccgtgttttgttttgtaga--ttgataatttggctctcaactctaaatg----ttaaatctaagttatattacatcattacatgc-ttagcttaatggt-----------------------------------------------------------------------------------------
|| ||||| |||||||||| ||| ||  | |  |||||||| ||||| ||||||||||| || |||||||| ||||| ||  ||||||| || ||||| ||| ||     |     ||||| | |||  ||    || |||    |   | ||  ||    || |||   |     |||  ||  | |   |   ||| | | |  |                                                                                         
TTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaa--tgacaaatgtttagaagactttagctatctggtctactgttttatctgggttttgaatgggaagggcatt-tattgtaaagggagctagatcattttttttgtttctgtagtttatttatttccttaatgcatttgttattgatagtaatgcatatgttggggattcccaactcttcctttttgcag

upper sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 6
TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctcc-cgtgttttgttttgtagattgataatttggctctcaact---ctaaatgttaaatctaagtt-----atattacatcattacatgcttagctt-aatggt---------------------------------------------------------
 |||||||||||||||||| ||| ||  | || |||||||| ||||||||||||||||| || |||||||| ||||| ||  ||||||| || || || |||  | | | |   |||| ||   || | | || ||||     | || |   ||| ||  ||  | ||| ||     | | | ||  | |  |  |    ||| |||  |                                                         
-TATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTTCATCCAAATGCCCCTATTGATGATAAGATCGAATGtatgttgcacaaatttttttccctacaattattatttttgcatgaatttttctatattctatttttaaatttaagaacaatgcacaactggaatcaagtctttaattttctttaataacatttttaaataaaccaaaattgactccatatgatatcatgtttcagt

upper sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 6
TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctcccgtgttttgttttgtagattgataatttggctctcaactctaaatgttaaatctaagttatattacatcattacatgcttagcttaatggt
|| ||||| |||||||||| ||||||  |||| ||||| |||||||||||||||||||| || ||||| || ||||| ||  | ||||| |||||| | |||  |  ||    ||||   |||||  |  | ||   |    |       | |  ||||   | |  |||| ||  |  || ||                
TTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACAAAATTCACTgtacgtccc----ttttagcttgtatctcaaaaacaaga---ttgggataacacattaa---tgatatatactatttttttgcag---------------

upper sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 6
TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctcccgtgttttgttttgtagat-tgataatttggctct-caact---ctaa-------atgttaaatctaagttatattacatcattacatgcttagcttaatggt----------
|| |||||||||||||| | ||||||  |||| ||||| || ||||| ||||||||||| || |||||||| ||||||||| | || || || ||||| |||  |     |  | ||     || ||| ||| ||     || | ||| |   || |       ||| || || |||   ||   | |||| || |   ||| |   |   |          
TTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACAAGATTGACTgtacgtctttg-atcttacaaagttgatctgagaaaccatctatacaatttatctgatgttgacatgctacatgtaacccatgaaatatcacta-acagttaccgggaacattgttttgcag

upper sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 5'ss of exon 4
TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctcccgtgttttgttttgtagattgataatttggctctcaactctaaatgttaaatc--taagttatattacatcattacatgcttagcttaatggt--------------------------------------------------------------------------------------------
|| |||||||||||||||| ||||||  | |  |||||||| ||||| ||||| ||||| || |||||||| ||||| ||| |||| || |||||||| ||| || |   ||   |        | | | |    |||  | |             | | |   | ||  | |          | |   || | || |||                                                                                              
TTGTTTGACACAAAGCACAATGGAATACTAGATTTTGAAGAGTTTGCGCGTGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACAAAATTGACTgtaagttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctgatgatttcatgctgatgcttattgatgtatgtttgggatgccaaatcatttcttttgcag

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|211209490|gb|FL043658.1|FL043658
EST:     TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATT                         TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG
genomic: TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctccc ... gttactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG
EST: gi|211119821|gb|FL462978.1|FL462978
EST:     CTTGATGAGAAAATTGATT                         TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG
genomic: CTTGATGAGAAAATTGATTgtgagctccc ... gttactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG
EST: gi|211209489|gb|FL043657.1|FL043657
EST:     TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATT                         TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG
genomic: TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctccc ... gttactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG
EST: gi|74244689|gb|DT652603.1|DT652603
EST:     TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATT                         TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG
genomic: TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctccc ... gttactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG
EST: gi|71307467|gb|DR789938.1|DR789938
EST:     TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATT                         TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG
genomic: TGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctccc ... gttactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAG

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 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 94

TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctccc ... gttactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctccc ... gttactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 34

TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctccc ... gttactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 78

TTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGAAAATTGATTgtgagctccc ... gttactgcagTTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAG