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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaaatcaaagttcagtctaatggcccctgggattttcaaatactgttcactgaccattgggtattccag

Basic information

species Glycine max
transcript GLYMA19G27360.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaaat----caaagttcagtctaa--tggcccctgggattt--tcaaatactgttcactgaccattgggtattccag
|| |||||||||||||||||||| |||||||||||| | ||||  ||||||||||| ||||||||||| || ||||| ||| ||||||| || ||| ||   |      | |    |||| ||  ||  |  ||     |  || ||||   |   |||   || |  |    |||
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttat-gttttcatcag

upper sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaaatcaaagttcagtctaatggcccctgggattttcaaatactgttcactgaccattgggtattc--cag
|| ||||||||||||||||||||||||||||||||| | ||||  ||||||||||| |||||||||||||| ||||| ||| |||||||    |||   | | |     ||   | | |||||   |   ||  |  | |  | ||  |||| |||  | | | |  |||
GTATTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTGTCTTTGTGGAGAGCATTCTTAGATATGGTCTGCCGCCATCATTCCTGgtaat----tctctcagactt----ttttttgtgatggcaaatattatgcttcagt-ttcttgtctgatcatatgttttgcatcag

upper sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G128995_T01 (Zea mays), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaaatcaaagttcagtctaatggcccctgggat--tttcaaatactgttcactgac-cattgggtattccag
|| |||||||||||||||||||| |||||||||||| | ||||  |||||||| || ||||||||||| |||||||| ||| ||||||| | ||      |       ||| |   | ||||    | | ||  || |   |  |||    | |    ||  | ||  |||
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATCCTTAGATATGGTCTCCCTCCATCATTCCTGgtaatttgct-----gaggctgttgttta---tgatggtaaatagtatacttccgtttcttgtctgatcatatgttttgcatatcag

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

upper sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 9
lower sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaa--atcaaagttcagtctaatggcc---cctgggattttcaaatactgttcactgaccattgggtattccag
|||||||| ||||||||||| || ||||||||||||  ||| |||||||||||| ||||||| ||| | |||||  | ||||||||||  ||    || ||   ||   | || ||   | |   |   |||   || | |     |   | |||  |  |||  | ||||||
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagctatgctattttagagaattcctctaccctactatctcccttaccaaattactttctcttgtct-ttccag

upper sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 9
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaaatcaaagttcagtctaatggcccctg------ggattttcaaatactgttc----actgaccattgggt--attccag
|||||||| ||||||||||| ||||||||||| ||| | ||||| ||||| || || ||||||||  |||| ||||||||||||||||   |  | |  ||   |||  |||  |||      ||||       | ||||||   || || |     | ||    ||| |   ||| |||
GTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTGgtaaataaaccattcaactccaacattccttcttggaatccctccctcacgaattttcttttattgattgaggattggttgttgagatgatttcag

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|58018243|gb|CX704985.1|CX704985
EST:     GTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTG                         GCATGCGTTTTAGCTCCTTCTGTAAAATCCGAGAAGAAAGTACGTTCTATC
genomic: GTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatact ... ggtattccagGCATGCGTTTTAGCTCCTTCTGTAAAATCCGAGAAGAAAGTACGTTCTATC
EST: gi|21639034|gb|BM140080.1|BM140080
EST:     GTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTG                         GCATGCGTTTTAGCTCCTTCTGTAAAATCCGAGAAGAAAGT
genomic: GTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatact ... ggtattccagGCATGCGTTTTAGCTCCTTCTGTAAAATCCGAGAAGAAAGT
EST: gi|6846822|gb|AW349112.1|AW349112
EST:     GTTTATTTGCTGAGAGCATNNNNAGATATGGTCTGCCTCCATCCTTCTTG                         GCATGCGTTTTAGCTCCTTCTGTAAAATCCGAGAAGAAAGTACGTTCTATC
genomic: GTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatact ... ggtattccagGCATGCGTTTTAGCTCCTTCTGTAAAATCCGAGAAGAAAGTACGTTCTATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaaatcaaagttcagtctaatggcccctgggattttcaaatactgttcactgaccattgggtattccag

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