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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgcttattcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA

Basic information

species Glycine max
transcript GLYMA05G30830.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgcttattcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
                                                  | ||   | ||  ||| | |  | |  |||    ||       | |    |||| || | | || | |   | |   |   ||   ||| |    |   ||||||||||| ||  |||||||||||||||||||||||||||| ||||||||| | || || |||||||||||||| ||  ||||| | ||  ||| ||||
--------------------------------------------------gtaaacataact-ttactttgctctagctactccaatcttcctgaggctagcttgtttaaccat-taactctctctggttattg--tatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA

upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgcttattcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
                                                                                  ||  |  |    || | |    | |  | | | |   | |  |   |  |    |||| |       ||||||||||| ||| | ||  |||| || |||||||| |||| ||| || ||||| || ||||||||||| || || || ||||| || ||||||||||||
---------------------------------------------------------------------------------gtatcaatatctttgctttaaccacttttttttatctggtttcttgactctctcatattgtgaacataagGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA

upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgct-tattcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
                                                          |||||  |    | |||       ||   |  ||| |  | || | | || ||   |  |       |  |||  |    || |       |||||||||||| ||| ||||| |||| ||||| ||||| |||  |||||| ||||| ||  | |||||||||||||||||||| || |||||||| ||||||
---------------------------------------------------------gtacca--aacgctctttattct-ttatggtagaaaatagtttggtgtgtttatgactactgactcccttggcacctggaaatatat-----tagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA

upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgcttattcatctatgttatgatattaagcattt--aattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
                                                  | |||    |  |  |  | | |||   || ||    |||         |    ||| |||||     | | || || | |||  |||   ||||  |   ||||||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||| || || ||||||||||| || || |||||| | ||  | ||||||
--------------------------------------------------gtaac----aaaacaaacactttttttttatctc---tcag--------tttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA

upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 3
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgctt-attcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
                       ||||  |     ||  ||   ||  ||   |     |   | | | || | ||      |  ||| |    || |||| || |||| | ||  ||     |||      ||    |||||   ||||||||||||||||||  | ||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || ||||| |||||||||||||||
-----------------------gtaaggagcttctgcaaaggattatttttgaacagaagtttcact-ttttctggtaggtttcaataagctatggtctgttttattcttttaactt----catt-----ctttgcaatttt--gtcctagGTGGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgctt-attcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
                       ||||  |     ||  ||   ||  ||   |     |   | | | || | ||      |  ||| |    || |||| || |||| | ||  ||     |||      ||    |||||   ||||||||||||||||||  ||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || ||||| |||||||||||||||
-----------------------gtaaggagcttctgcaaaggattatttttgaacagaagtttcact-ttttctggtaggtttcaataagctatggtctgttttattcttttaactt----catt-----ctttgcaatttt--gtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

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|208189805|gb|GD987765.1|GD987765
EST:     GAGTGGTCAAAGCGGGCAATTCATGTGAGTGTCCGCAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GAGTGGTCAAAGCGGGCAATTCATGTGAGTGTCCGCAAACAGACCAAATGgtaagaatcc ... tccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|208299059|gb|GE100490.1|GE100490
EST:     GGTCAAAGTCGGGTCTAATTTCATGTGAGTGTCCGCAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GGTCAAAG-CGGG-C-AA-TTCATGTGAGTGTCCGCAAACAGACCAAATGgtaagaatcc ... tccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|208281624|gb|GE073772.1|GE073772
EST:     GGCAATTCATGTGAGTGTCCGCAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GGCAATTCATGTGAGTGTCCGCAAACAGACCAAATGgtaagaatcc ... tccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|208133221|gb|GD932162.1|GD932162
EST:     GCGGGCAATTCATGTGAGTGTCCGCAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GCGGGCAATTCATGTGAGTGTCCGCAAACAGACCAAATGgtaagaatcc ... tccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|193438151|gb|FK402170.1|FK402170
EST:     TGAGTGTCCGCAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: TGAGTGTCCGCAAACAGACCAAATGgtaagaatcc ... tccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|193304306|gb|FK270335.1|FK270335
EST:     GCGGGCAATTCATGTGAGTGTTCGCAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GCGGGCAATTCATGTGAGTGTCCGCAAACAGACCAAATGgtaagaatcc ... tccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|208187995|gb|GD986809.1|GD986809
EST:     GCGGGCAATTCATGTGAGTGTCCGCAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GCGGGCAATTCATGTGAGTGTCCGCAAACAGACCAAATGgtaagaatcc ... tccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|7639690|gb|AW734007.1|AW734007
EST:     GAGTGGTCAAAGCGGGCAATTCATGTGAGTGTCCGCAAACAGACCAAATG                         GTGGTATGCCAAGCG
genomic: GAGTGGTCAAAGCGGGCAATTCATGTGAGTGTCCGCAAACAGACCAAATGgtaagaatcc ... tccctcctagGTGGTATGCCAAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcttattcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
                                 atttaat  putative branch site (score: 4)
                                       ttattttccctcct  CT-rich tract
            atctatgttatgatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgcttattcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA

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