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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataattttattcaatggtgtgggatgacccggttgggtatctgttcagtggcccatggttctctaattgttgctgttgggtagcaatagttttg...

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 24
ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaa---tataattttattcaatggtgtgggatgacccggt-tgggtatctgttcag---tggcccatggttctctaattgttgctgttgggtagcaatagttttg
||||| | |||||||||||||| || ||||| || ||||||||||| |||||||| ||||| |||||||| |||||||| |||||||||||||| |||||||||    |||||  || |     ||| |||||| |       | | | | |||| |    |  ||  | | ||  |||||  | |||| |                
ATGGATTACGCACTAAAGATAAAGAACGTGTACTGGTTCTTGGTGCCACAAATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagctataaccttgtgttggggt-tgggataatgaaaaattgctgtttgttgatttctaaccatttggtcgttaattactactgtag----------------

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataattttattcaatggtgtgggatgacccggttgggtatctgttcagtggcccatggttctctaattgttgctgttgggtagcaatagttttg-
||||  || | || |||||||| |||||| | |||||||||| ||||||||||||||||||||| || || |||||||| ||||||||  | || || |||| ||  |  || | ||   || |||    |       ||  || | |    | ||     |      ||||||  || | || | |   ||   || |  
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcgttatgtt---tgatgttaacttcttttatttcgtgttttacaaatgagatcta---tgctaattcgtgttctttgttgaaaaatattgtag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 20
ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataattttattcaatggtgtgggatgacccggttgggtatctgttcagtggcccatggttctctaattgttgctgttgggtagcaatagttttg-
||||  |||| || |||||||| |||||| | ||||||||||  |||||||||||||||||||| || || |||||||| ||||||||  | || || |||| ||  | ||| | ||   || |||  | |       ||  || | |    | ||     |      ||||||  || | ||   |   || | || |  
ATGGTTTGCGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCGGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcattatgtt---tgatgtcagcttcttttatttcgtgtttcacaaatgagatcta---tgctaatttgtgttctttcttgaaaaaaattgtag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 15
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 23
ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataattttattcaatggtgtgggatgacccggttgggtatctgttcagtggcccatggttctctaattgttgctgttgggtagcaatagttttg
| || ||| | || || || ||||| ||||| || |||||||  || |||||||||||||||||||| ||||||||||| ||||| ||||| || |  |||| | |   || |   |   | || |||  | | |    ||   |  ||    || |   |    | | |  |  | |||  ||                
ACGGTCTGAGGACAAATGAAAAGGAACGTGTTCTGGTTCTTGCAGCCACAAATAGACCTTTTGACCTTGACGAGGCTGTCATTAGAAGGTTGCCTCATAGgtaatttatatatagcttccttgt-tggactaagctttctgtcaaattgacatgtcgta-acaagtttttggtattggcttctgcag-------------

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 24
ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataattttattcaatggtgtgggatgacccggttgggtatctgttcagtggcccatggttctctaattgttgctgttgggtagcaatagttttg
||||  ||||||| |||||||  ||  | || || || ||||  || |||||||||||||||||||| || |||||||| ||||| ||||| || || |||| ||   |    |   | ||  ||| |||  | ||   |   | ||     | |||  | | |||||    |  | | |  |   |  ||         
ATGGCTTGCGCACAAAAGATACCGAAAGGGTTCTGGTGCTTGCAGCCACAAATAGACCTTTTGACCTTGATGAGGCTGTTATTAGAAGGTTGCCGCGTAGgt-aaggcatcactgagccattttgttggactatcctactttatttccacaaactgggacttagttcttctgtaatggttcatcttttacag--------

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|67025653|gb|CO454402.1|CO454402
EST:     AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGT
genomic: AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataa ... attatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGT
EST: gi|87153787|gb|DY398576.1|DY398576
EST:     AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCCGAAAGT
genomic: AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataa ... attatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGT
EST: gi|71435056|gb|DR816106.1|DR816106
EST:     AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGT
genomic: AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataa ... attatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGT
EST: gi|211048834|gb|FL187594.1|FL187594
EST:     AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGT
genomic: AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataa ... attatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGT
EST: gi|87152067|gb|DY396856.1|DY396856
EST:     AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCTGATGCATCANATAGAGAGAAAATTCTGAAAGT
genomic: AATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataa ... attatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGT

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: 49 (upstream exon), 49 (downstream exon)
Score: 358

ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataa ... attatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCGGATGTTGATCTCGACTCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataa ... attatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCGGATGTTGATCTCGACTCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 273

ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataa ... attatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCGGATGTTGATCTCGACTCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 329

ATGGACTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtgaatataa ... attatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCGGATGTTGATCTCGACTCACTT