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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taactaaacagggatcatatattctgccttttacattatgttggctttgtttgtcatgttcttcttcacattataggatgatctaacatggatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGC

Basic information

species Glycine max
transcript GLYMA10G34370.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G34370.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 7
---taactaaac--agggatcatatattctgccttttacattatgttggctttgtttgtcatgttcttcttcacattataggatgatctaacatg-gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGC
   ||   |     | || |  |  ||| || |   | || ||     | |     | |  ||  | | ||||| || ||       || |  |   || | ||||||||||||||||||||||| |||||  ||  ||||||||||| || ||||||||||||||||| ||||||   ||||||||||| || |||||||| |||
ttttactcatgttaaagggttgttgattttgtc---tgcactaca---gttccacatatagtgcacattttcactttgtacagcagactgatgtataatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGC
















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|120532166|gb|EH260299.1|EH260299
EST:     GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAG                         GGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
genomic: GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAGgtttgtgtta ... gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
EST: gi|17022153|gb|BM093187.1|BM093187
EST:     GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAG                         GGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
genomic: GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAGgtttgtgtta ... gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
EST: gi|9899914|gb|BE608882.1|BE608882
EST:     GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCGGAGATAAG                         GGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGTTGTAGTTAGCAA
genomic: GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAGgtttgtgtta ... gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
EST: gi|9564018|gb|BE473527.1|BE473527
EST:     G-A-ATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAG                         GGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
genomic: GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAGgtttgtgtta ... gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
EST: gi|193710242|gb|FK642940.1|FK642940
EST:     GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCGGAGATAAG                         GGACTTTGATGCATTTGATCTACGGAGGCGGCTCCCAGTTGTAGTTAGCAA
genomic: GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAGgtttgtgtta ... gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
EST: gi|209709966|gb|BW681009.1|BW681009
EST:     GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAG                         GGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
genomic: GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAGgtttgtgtta ... gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA
EST: gi|6916528|gb|AW398058.1|AW398058
EST:     GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCGGAGATAAG                         GGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGTTGTAGTTAGCAA
genomic: GAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAGgtttgtgtta ... gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttgtcatgttcttcttcacattataggatgatctaacatggatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGC
                                   atctaac  putative branch site (score: 2)
                      acattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taactaaacagggatcatatattctgccttttacattatgttggctttgtttgtcatgttcttcttcacattataggatgatctaacatggatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- -ctaaaca
- - - - - - - - - - - -ctgcctt
- - - - - - - - - - - - - - - - - - - tgttggc
- - - - - - - - - - - - - - - - - - - - - - - ttgtttg