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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttttctcctagtatattgtaacttattttgttgccatatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA

Basic information

species Glycine max
transcript GLYMA08G42380.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
-------------------------------------------------------------ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttttctcctagtatattgtaacttattttgttgccatatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA
                                                             |   |||||  | || |||| |       |  |  ||   |  | | || ||| |||   || ||   | |   ||||           |||||   |||  || ||  | || |||||||| |||||||| ||||||||||| |||||||||||||||||||| || ||| | |||||||||   ||| ||||| | ||
gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattattctaacttataata-gatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatc--cagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA

upper sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 7
---ttcttctttcctcactttatcc--agttcggttgtttgagagaatgttattcgtttttctcctagtatattg-taacttattttgttgccatatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA
   ||   |  | ||    ||||    | ||  | |     |  |  |   | | ||  || | ||| |||     |  |  || || ||         ||| |||| || ||  | || |||||||||||||| || |||||||||||||| |||||||| |||||||| || ||| | || ||| ||  ||| |  ||||| ||
tacttgagcagttctggtgttatgttaacttttgataaaacatgggcttgaagttgtagttttactaatattgcactggcaaatctttttaat------tttccagCTATGTACCTTGCAAGAGGAAATCATGAAAGCAAGAGCATGAACAAAATATATGGCTTTGAGGGGGAAGTGAGGTCAAAGCTGGGTGAGAAGTTTGTTGA

upper sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------------------------ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttt----tctcctagtatattgtaacttat--tttgttgccatatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA
                                                    | ||| |    |||||        ||   || |||   |   | | ||  | ||     | |||   |  ||||||| |     |||     | | ||   | ||||||||||| ||||||||||||| ||||| || |||||||||||||| || |||||||||||||||||||| || || ||||||| ||||| ||| || ||
gtaagttctctaaaactttgttgtaataattctttgatgttcatgttttaattgcttttgctatcactggcaaggattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaaatcgccatttacacacctttgtactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA

upper sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 2
-ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttttctcctagtatattgtaacttattttgttgc-catatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA
 || ||   || ||  ||  | ||       |   | | | |||   |     |||| | ||  | ||   |  ||| ||   | |  || |  || |||||| |||||| |  | ||||||||||| ||||| ||||||||||||||||||||||||||||| || |||||  | || ||||||| |||||||||||| ||
tttgtttcctcttcctttgtttcatgctctctaagtaacaaaatcacaactaattttattctcatgtaacat--cttgttgactggttcaaaaaatcttcagCTATATATCTCTCTAGAGGAAATCACGAGAGCAAGAGCATGAACAAGATATATGGTTTTGAAGGGGAGGTCAGATCCAAGTTGAGTGAAACATTTGTGGA

upper sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S80_144V6.1 (Physcomitrella patens), 3'ss of exon 7
------ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttttctcctagtatattgtaacttattttgttgccatatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA
      ||||  |   || | |   |  |  || |  |  |||    |  | | ||  | | || |   | ||   |   ||  ||| ||| |   ||| |   ||   | ||  |  | ||||| |||||||| || |||||||||||||| |||||||||||||| || |||||   | ||||||| ||||| ||| |     |
tatatgttctgatgagcttattcagtgtatatcaggagactgatcacacttaactcactctacttcctctctaacctcgttttatttattgtc---tgaat---agGGCTGTACCTTTCTAGAGGTAATCATGAAAGCAAGAGCATGAACAAAATATATGGTTTTGAAGGGGAGGTTAACGCGAAGTTCAATGAGACAATGAATAA

upper sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S87_139V6.1 (Physcomitrella patens), 3'ss of exon 8
-ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttttctcctagtatattgtaacttattttgttgccatatgatttt-cagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA-
  |    | |  | | ||| |    ||  ||   |   |||| ||      ||   | |  |  ||   ||      || || |||   | |||||    ||   | ||  |  ||||||| |||||||| ||||||||||||||||| |||||||||||||| || || ||   | ||||||| ||||| || | || ||| 
agtaagttgtgatgagtttgtt-gtttttgtaaatcaggagactgagtcctgtcaatttttttataccctgcctaacatgtttttgt-gtgtgattgaatagGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGAC-TATGACGAA

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|207747150|gb|GD718343.1|GD718343
EST:     ATTGGAAGTTATCCTCACTTTGTTTGCATTTAAGTGCATGTCTCCATCAG                         CCATATATTTAGCCAGAGGAAATCATGAGAGCAAGAGCATGAACAAGATAT
genomic: ATTGGAAGTTATCCTCACTTTGTTTGCATTTAAGTGCATGTCTCCATCAGgtaaacccta ... tgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATAT
EST: gi|192332390|gb|FK026055.1|FK026055
EST:     ATTGGAAGTTATCCTCACTTTGTTTGCATTTAAGTGCATGTCTCCATCAG                         CCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAA
genomic: ATTGGAAGTTATCCTCACTTTGTTTGCATTTAAGTGCATGTCTCCATCAGgtaaacccta ... tgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcgtttttctcctagtatattgtaacttattttgttgccatatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA
                      ttgtaac  putative branch site (score: 2)
                                                ttttc  putative PPT
               tagtatattgtaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttttctcctagtatattgtaacttattttgttgccatatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA

- - - - -cctcact
- - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgcc