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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcccctgaaagctctaccattctttctttgaactataatatctgttttccggtctaagttggcttattcttgactaaactttattattttcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGAGAAGAATGTCCTACCCTCATCAACAAATCCCACACGTCCTTATACACAT

Basic information

species Glycine max
transcript GLYMA11G37250.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 13
lower sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 15
ttcccctgaaagctctaccattctttctttgaactata-atatctgttttc--cggtctaagttggcttattcttgactaaactttattattttcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGAGAAGAATGTCCTACCCTCATCAACAAATCCCACACGTCCTTATACACAT
 |    ||  |     ||| |||| |  ||  | | |  ||||  ||||       | ||| | ||  |   ||    || | |||| |   || |    |||||||||||| |||||||| ||||||||||| || || ||||||||||| | ||| |||||  ||||||| ||||||||||| || || || | |||    
-ttttgtgttatacagacccttctattgttatattgtggatattcgtttatgatactgtaaatgggactga-ctaagttataatttactgccttgt-aaacagTGAAGGAGCAGGTGGTGGTCATGCTCCAGACATTATCAAAGTATGTGGAGTGAAAAATGTGTTACCCTCTTCAACAAATCCAACTCGGCCATTTACTTTG

upper sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
ttcccctgaaagctctaccattctttctttgaactataatatctgttttccggtctaagttggcttattcttgactaaactttattattttcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGAGAAGAATGTCCTACCCTCATCAACAAATCCCACACGTCCTTATACACAT
|     ||    || |    |       || | || | |||| ||||    | |   |  || |   ||  | |  |   | |     | |  ||| ||||||||| |||||||| || ||||||||||| ||||| ||||| ||||| |  || |||||  | ||||| ||||||||||| || || || | |||    
tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG

upper sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G67550.1 (Arabidopsis thaliana), 3'ss of exon 12
-----ttcccctgaaagctctaccattctttctttgaactataatatctgttttccggtctaagttggcttattcttgactaaactttatt------attttcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGAGAAGAATGTCCTACCCTCATCAACAAATCCCACACGTCCTTATACACAT
     |   | |   | ||||  ||| |     |   |   |    ||  |  |   || | |       ||||   |    |  ||| ||      ||  |  ||| ||||||||| ||||||||||| ||||| ||||||||||| | ||| ||||| | ||| ||||| || || |||||||| || || ||||| || |||||  | 
gttcatcagcttctcacctct-tcatgcacctctcagatgcttccttcactgcttatgtttgaagcaaaatattgaagtgctatttttgtttgttaaatcattctggacagTGAAGGTGCTGGTGGTGGACATGCACCAGATATCATTAGAGTTTGTGGAGTGAAAAATGTACTCCCGTCATCAACCAACCCAACACGGCCATATACGAAA

upper sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
-------ttcccctgaaagctctaccattctttctttgaactataatatctgttttccggtctaagttggcttattcttgac-taaactttattattttcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGAGAAGAATGTCCTACCCTCATCAACAAATCCCACACGTCCTTATACACAT
        |   ||||||    ||  ||   |||| |   || | | || |   || |  |     ||| |  | | ||||   | |  |   ||| || ||| |||||||||| ||||||||||| ||||||||||||||||| ||||||||||||| ||| ||||| ||||||||||| ||||| || ||||| ||||  ||    
ttttctaattttctgaaaa---taagatagattctatagccttttacattttggtttcttt-----ttgtcacacttttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC

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|151405862|gb|EV275677.1|EV275677
EST:     GAACATACAATTGCTGCATTTAAAGGAAGAACTACTCATACTTACCACAG                         TGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
genomic: GAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAGgtattgttta ... tcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
EST: gi|16278014|gb|BI942681.1|BI942681
EST:     GAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAG                         TGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
genomic: GAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAGgtattgttta ... tcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
EST: gi|151402941|gb|EV272754.1|EV272754
EST:     GAACATACAATTGCTGCATTTAAAGGAAGAACTACTCATACTTACCACAG                         TGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
genomic: GAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAGgtattgttta ... tcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
EST: gi|208294142|gb|GE092631.1|GE092631
EST:     GAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAG                         TGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
genomic: GAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAGgtattgttta ... tcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
EST: gi|151394452|gb|EV264323.1|EV264323
EST:     GAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAG                         TGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
genomic: GAACATACAATTGCTGCATTTAAAGGAAGAACTATTCATACTTACCACAGgtattgttta ... tcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
EST: gi|33388630|gb|CA851837.1|CA851837
EST:     GCTGCATTTAAAGGAAGAACTATTCATACTTACCACAG                         TGAAGGAGCTGGNGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA
genomic: GCTGCATTTAAAGGAAGAACTATTCATACTTACCACAGgtattgttta ... tcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccggtctaagttggcttattcttgactaaactttattattttcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGAGAAGAATGTCCTACCCTCATCAACAAATCCCACACGTCCTTATACACAT
                           gactaaa  putative branch site (score: 2)
                                  ctttattattttctt  CT-rich tract
                   ttattcttgactaaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcccctgaaagctctaccattctttctttgaactataatatctgttttccggtctaagttggcttattcttgactaaactttattattttcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGAGAAGAATGTCCTACCCTCATCAACAAATCCCACACGTCCTTATACACAT

ttcccct
- - - - - - ctctacc