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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagaactttggcttttgttgtaattttctttttctttttaaatctttaccctgtgtggacgtcttcgtgctttatttatgaattatctttctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATTCAGATATTTTGCTTGAATCATCGGATCAAAAGGACATAG

Basic information

species Glycine max
transcript GLYMA19G44420.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G44420.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G46420.1 (Arabidopsis thaliana), 3'ss of exon 7
------------------------ttgagaactttggcttttgttgtaattttctttttctttttaaatctttaccctgt--gtggacgtcttcgtgctttatttatgaattatcttt--ctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATTCAGATATTTTGCTTGAATCATCGGATCAAAAGGACATAG
                        ||| ||  ||| |||          | |    |   ||  || ||  |     |    ||| ||  | | |    ||   ||| ||| ||||||  || ||||||| |||| ||| ||||||||||||| ||||| || ||| |||  ||||||||||| ||||| ||||| ||  | || ||| |||||||||
gtaagctctttttatcaaatgccattgcgag-tttagctcgaaaaactttataacatacgttggtagatgctccatgtacaggtgtactccatagaatgttgcatatcaatgatcttttactttgcagATTTAGGGGCTTTAGGAAACTATCCCGGTTCTCCTTTTCTGCCATCTGATTCAGAGATTTTACTTGACTCTCCCGAACAAGAGGACATAG

upper sequence: GLYMA19G44420.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G46420.2 (Arabidopsis thaliana), 3'ss of exon 7
------------------------ttgagaactttggcttttgttgtaattttctttttctttttaaatctttaccctgt--gtggacgtcttcgtgctttatttatgaattatcttt--ctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATTCAGATATTTTGCTTGAATCATCGGATCAAAAGGACATAG----------
                        ||| ||  ||| |||          | |    |   ||  || ||  |     |    ||| ||  | | |    ||   ||| ||| ||||||  || ||||||| |||| ||| ||||||||||||| ||||| || ||| |||  ||||||||||| ||||| ||||| ||  | || ||| |||||||||          
gtaagctctttttatcaaatgccattgcgag-tttagctcgaaaaactttataacatacgttggtagatgctccatgtacaggtgtactccatagaatgttgcatatcaatgatcttttactttgcagATTTAGGGGCTTTAGGAAACTATCCCGGTTCTCCTTTTCTGCCATCTGATTCAGAGATTTTACTTGACTCTCCCGAACAAGAGGACATAGGTAAACATTA

upper sequence: GLYMA19G44420.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0046g00990.t01 (Vitis vinifera), 3'ss of exon 7
ttgagaactttggcttttgttgtaattttctttttcttt---ttaaatctttaccctgtgtggacgtcttcgtgctttatttatgaattatct--ttctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATTCAGATATTTTGCTTGAATCATCGGATCAAAAGGACATAG
 ||||||    ||  | || | ||    |  |  |   |   |||  |  | | ||  | ||  |  | || || |||  | ||   |  |    |  | |||||||||||||||| | |||||||| || ||||| || ||| ||   ||||||||||| ||||||||||| ||  |||| ||| |||| ||||
-tgagaa----ggtatatggtatatcactgctgctgcatggattattttgtaatccattatgagcaacctcatgttttgataatttgtggtgaaatcgtttgcagATCTAGGAGCTTTGGGAAACTACCCCGGTTCTCCCTTTCTGGGTTCTGATTCAGACATTTTGCTTGATTCTCCGGAGCAAGAGGATATAG

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|120531303|gb|EH259436.1|EH259436
EST:     GTGGAATTTTAGTCTATCTGACTTAACAGCAGATTTGTCAAACTTGGGAG                         ATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATT
genomic: GTGGAATTTTAGTCTATCTGACTTAACAGCAGATTTGTCAAACTTGGGAGgtaaattcgt ... ttctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATT
EST: gi|151400669|gb|EV270483.1|EV270483
EST:     GTGGAATTTTAGTCTATCTGACTTAACAGCAGATTTGTCAAACTTGGGAG                         ATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATT
genomic: GTGGAATTTTAGTCTATCTGACTTAACAGCAGATTTGTCAAACTTGGGAGgtaaattcgt ... ttctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATT
EST: gi|208288823|gb|GE086628.1|GE086628
EST:     GTGGAATTTTAGTCTATCTGACTTAACAGCAGATTTGTCAAACTCGGGAG                         ATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATT
genomic: GTGGAATTTTAGTCTATCTGACTTAACAGCAGATTTGTCAAACTTGGGAGgtaaattcgt ... ttctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATT
EST: gi|208277120|gb|GE080791.1|GE080791
EST:     GTGGAATTTTAGTCTATCTGACTTAACAGCAGATTTGTCAAACTTGGGAG                         ATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATT
genomic: GTGGAATTTTAGTCTATCTGACTTAACAGCAGATTTGTCAAACTTGGGAGgtaaattcgt ... ttctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttaccctgtgtggacgtcttcgtgctttatttatgaattatctttctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATTCAGATATTTTGCTTGAATCATCGGATCAAAAGGACATAG
                                       ttatctttct  CT-rich tract
                           tttatttatgaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagaactttggcttttgttgtaattttctttttctttttaaatctttaccctgtgtggacgtcttcgtgctttatttatgaattatctttctatgcagATCTAGGAGCTCTAGGAAACTATCCTGGTTCACCATTTATGCAGTCTGATTCAGATATTTTGCTTGAATCATCGGATCAAAAGGACATAG

- - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcgtgc