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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacag

Basic information

species Glycine max
transcript GLYMA13G28720.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 12
lower sequence: 13113.m00246 (Oryza sativa), 5'ss of exon 12
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaacttta---ttttacttttcaattcattgt-tcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacag
||| ||||||| |||  |||| ||||| || ||||| |||||||| ||||| ||||||||||||||||||||||| ||||| |||||||||||  | | |   |||||   | |||| |  ||||   |||| |   | | |  | ||| |   |    | | | | | |               
GAATCCACAAGCTGATCTGCAAGCTCAAGACCGTGCACATAGGATAGGTCAGAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAGgtttgtcaatcttttctttagaatattacgtaacaatcttttgtattgatatctaagataggatgacgaaaacttaatttcag--------------

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 12
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttattttacttttcaattcattg--ttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacag-----------
||| || ||||| ||  |||| || || |||||||| ||||| ||||||||||||||||||||||||||||| ||||| || ||||||||||    | || || ||  ||| |  ||| ||  || ||  ||  | ||  |   ||    || || || | ||  |||      ||| | ||            
GAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAGgttt----tatttaatttattttaagatttaaaaacactggtttagcactaagcaatatcttct-atttatttat-ataacagaatatgcttcatattctatgcag

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 12
lower sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 12
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacag
||| ||||||| |||  |||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||   |||  |  || |   ||    |      | || | | |   | ||||  || |  || |                          
GAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAGgtttgttgtttctagattaacagtaaccat------agtgctaaattc-tatgttgatatca-atttggaag---------------------

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 9
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttatt-ttactttt-caattcattgttcact-ctgtgtgt-tagtagctcatctaatcattgtaatttgtaatggtacag
||| || |||| |||  |||| |||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| ||||| |||||||||||   |||  |  || ||  ||||| |        ||| |  ||| ||   ||| | | || | ||  || ||    || ||  |         
GAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAGgtttgttgtttctagattaataattactgtagtgccaaattttatacttctacctgtatggaagataatgcaaaca----aaattacag--------

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 12
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 12
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgta-atttgtaatggtacag
|||||||||||| |||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| || || || || |||||||||     | |    || |   | | |||  | || |       |  || | | |   |  | |  ||    ||||   |||  |         
GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgtt---ggtctc---ctctccgtgaatttcaagttaa--aacagccatgagaggtttaaaattaattatgtgttgtttgtttacag--------

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 12
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 12
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacag
|||||| |||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || || || ||||||   | | ||  ||     | ||       |   |    | ||   | |   | | | || ||       | ||  | || |         
GAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAGgtt---actcttgtacccatgtgtat-----gaagtaagaatgacctggagaacttg-aactaattctgcattggtcttatgcag--------

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 12
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacag
|||||| |||||||| ||||| || || |||||||||||| |||||||||||||||||||||||||||| || || || || || ||||||    |||||   |||   |||    || |  |   |    |     | | | | | ||| || |  || || |   ||  |||  | |||
GAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAGgttc---attttgttcttgtgttttgcattaagctatctaaagatatcatatataaat-gcttatttcttctttctgggtt--aattat-cag

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 12
lower sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 12
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacag
||| || ||||| || ||||| || || ||||| || ||| ||||||| || || |||||||||||||||||||| ||||| ||  ||||    ||   | |  | | | ||| || |    | | |  |   ||||| | | ||                                    
GAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAGgt--aaaaggatgacttgtgtgttatttctttgctgactcgtt-ttctgtttctcag------------------------------------

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|254331883|gb|GR846193.1|GR846193
EST:     ATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAG                         TATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTT
genomic: ATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaatt ... aatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT