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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttgaaacttgtagtgactatgatactgcttcctattttacacatcattcacaaggcattttctgtctttctcag

Basic information

species Glycine max
transcript GLYMA17G05410.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 13
TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttgaaacttgtagtgactatgatactgcttcctattttacacatcattcacaaggcat--tttctgtctttctcag
 || || ||||| ||  | || ||||| || ||||||||||| || ||||| ||||||| ||| ||||| || ||||| || |||||||||||  | ||||| | ||  | | || |  |  |   ||||    |  | |||||     |    |   | |  |   || |   ||| ||||
CGATGTTATTCTGCAGCTGATAGACAAAGCAGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTCACCAACAATGAAGATCTGCAGgt-tcttgcatatttctgattgcc--gatagctatctcaattttgtttgttgaacttgaagtttgacttgtaattttatcag

upper sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 14
TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttgaaacttgtagt-gactatgatactgcttcctattttacacatcattcacaaggcattttctgt--ctttctcag
||| || ||||||||| | || ||||| || ||||||||||| || ||||| ||||||| ||| ||||| || |||||||| ||||| |||||| ||||||| ||| | | |  | |||| ||  |  ||  |   | || ||||       ||| |     |||||| ||    ||| ||||
TGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGACCTACAGgtttgtgt-atatatatagttgagcaaaatcatctctacttttttttttga-atttatggttcattttttgcaattttatcag

upper sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 13
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 13
TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttgaaacttgtagtgactatgatactgcttcctattttacacatcattcacaaggcattttctgtctttctcag--------
 || ||||| ||||| || || |||||||| || |||||||||||||||||||| |||||||| |||||||||||||| ||||| ||||||||| | |||||   | | ||| ||||   ||  |  ||| || ||    | ||  |   |||||| |||    || |    ||  |           
AGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgt---tcttaaaattgttaggataaatatattgtttatcctatt-tatgacattcaaaagttgcttacaaatttctttgatccgacag

upper sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 13
lower sequence: AT5G22770.2 (Arabidopsis thaliana), 5'ss of exon 14
TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttgaaacttgtagtgactatgatactgcttcctattttacacatcattcacaaggcattttctgtctttctcag---------
||| ||||| ||||| || || |||||||| || ||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||| | ||||| | | | |   ||||   ||  |  ||| || ||   ||  ||   || |    ||| |    ||   | |||||  |         
TGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgtttatataa---ttgttaggaaaaatatattgttt---atcctatttatgacattcaaagttgcttacatatttctttgacctgacag

upper sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 5'ss of exon 13
TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttgaaacttgtagtg------actatgatactgcttcctattttacacatcattcacaaggcattttctgtctttctcag--------
 |||||||| || || || ||||||||||| ||||||||||| || ||||||||||||||||| || || |||||||||||||||||||||||| ||||||||    | |   || | |        | |    |  ||  | |||||| | |  |||| ||  |   | ||||  | |   | |         
GGACGTGATCCTACAGTTGATTGACAAGGCAGGAGATTTTGTCAGTGATGACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGACCTACAGgtgatcatcatctttcttgcatgattcattggattggtgtcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcag

upper sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 13
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 5'ss of exon 13
TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgt-----------gtgtttgaaacttgtagtgactatgatactgcttcctattttacacatcattcacaaggcattttctgtctttctcag-------------------------------------------------------
||| || ||  | ||  | ||||| ||||| || ||||||||||| ||||| |||||||  || |||||||| |||||||| |||||||| ||  |||||||           |||||| |      || ||| |     ||| |    | ||||| |  | |  |   ||   | ||  | ||   | |                                                        
TGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaataagtgttttacgtacatattgaattgcgcacttcggtttctttta-aagttaacctagagaagtgtttgggctgaattaactaatacaattattccgttgttatgtttattttcttgaactctttggatacgtag

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|193557084|gb|FK512727.1|FK512727
EST:     ACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAG                         CCTTATGCTGCAGCAAAAGCTCGAGAATATCTTGACAAACCTGCTATACAT
genomic: ACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttga ... tctttctcagCCTTATGCTGCAGCAAAAGCTCGAGAATATCTTGACAAACCTGCTATACAT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttgaaacttgtagtgactatgatactgcttcctattttacacatcattcacaaggcattttctgtctttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA