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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgctctgctagtctctgactctttgttgtgatacttaactctatcttgtgtgtcttgttgtctgatctctctattgcatcag

Basic information

species Zea mays
transcript GRMZM2G177912_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgctctgctagtctctgactctttgttgtgatactta-actct-atcttgtgtgtcttgttgtctgatctctctattg-catcag
|| ||||||||||||||||||||||| || |||||  | ||||||||||||||||||||||| ||||| || ||||| ||||||||||||   ||| ||  |   |      |  | || | | ||  ||| | ||      | |  | |  | || | | | | ||  ||||||
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag

upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G05470.1 (Glycine max), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgctctgctagtctctgact-ctttgttgtgatacttaactctatcttgtgtgtcttgttgtctgatctctctattgcatcag
||||||||||||||||||||||| || || |||||  ||||||  ||||||||||| ||||| |||||||||||||| ||| |||||||   |||| |||   ||  | | |  | |  |||  | |     | ||         |   ||  |    |   |||| ||    
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCACCATCTTTCTTGgtaatatactcttctaaaatcaaagtgcagtctaatgacccctgggattttcaaacactgatcactgagta--ttgggtattccag---

upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgctctgctagtctctgactctttgttgtgatacttaactctatcttgtgtgtcttgttgtctgatctctctattgcatcag
||||||||||||||||||||||| || || |||||  ||||||  ||||||||||| ||||| |||||||| ||||| ||| |||||||   |||| |||   ||  | |  |   | | ||      ||     ||     |  ||||  |||| |  |   |     |||
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaaatcaaagt--tcagtctaatggccc-ctgggattttcaaatactgttcactgaccattgggt-attccag

upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G07260.1 (Glycine max), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgta-atccgctctgctagtctctgactctttgttgtgatacttaactcta-tcttgtgtgtcttgttgtctgatctctctattgcatcag
|||||||| |||||||||||||| || || |||||  |||||   ||||||||||| ||||| ||||| |||||||| ||| ||||| ||   | |  ||   |  |  || |    |    |  ||   || | | || | | |||     |    |||     |     |||
GTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACTGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTGgtagatatacccatctgtacaatagctttcaccttcattttttccttcaaatattttatctctgacccttgattcttgtggtcattccag

upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G26220.1 (Glycine max), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgta-atccgctctgctagtctctgactctttgttgtgatacttaactct----atcttgtgtgtcttgttgtctgatctctctattgcatcag
|||||||| |||||||||||||| || || |||||  |||||   ||||||||||| ||||| ||||| |||||||| ||| ||||| ||   | || ||   |     || |  | |       ||   |||    || || | |  ||| |  |    |||     |     |||
GTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTGgtagatatacccttctgtacaacagctttcagcttcatcttttccttcttcgaatattttatcacttatccttgattcttgtggtcattccag

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|148969237|gb|EE019991.2|EE019991
EST:     GCATATTTGTAGAGAGCATTTTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATT
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|76288289|gb|DV027857.1|DV027857
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|211233368|gb|FL465080.1|FL465080
EST:     AGAGGGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTAAGGAGCATC
genomic: AGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|60338311|gb|DN205284.1|DN205284
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|60340364|gb|DN207337.1|DN207337
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|211430021|gb|FL445207.1|FL445207
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTAAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|40337132|gb|CK371202.1|CK371202
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|71327561|gb|DR800389.1|DR800389
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|78120130|gb|DV538514.1|DV538514
EST:     CATATTTGTAGAGAGCATTCTTAGAT-CGGGTCTGCCGCCATGGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: CATATTTGTAGAGAGCATTCTTAGATAC-GGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgctctgctagtctctgactctttgttgtgatacttaactctatcttgtgtgtcttgttgtctgatctctctattgcatcag

- - - - - - - - - - - - - - - - - - - - - - - AGAGCA