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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgaagtcgatgatgctattggcgtcccgtttgtggtttgcgttttgtgattctgtgtttactgacttggcttgttgccgttttcgtgtgctgtttagGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATATACGATGTGGTGCATGTCAAGTATTTTGATGAG

Basic information

species Glycine max
transcript GLYMA11G07910.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07910.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G51130.1 (Arabidopsis thaliana), 3'ss of exon 1
-----gattgaagtcgatgatgctattggcgtcccgtttgtggtttgcgttttgtgattctgtgtttactgacttggcttgttgccgttttcgtgtgctgtttagGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATATACGATGTGGTGCATGTCAAGTATTTTGATGAG
       |   ||   ||| || | || |  |     || |         | | | ||  |  | | |  ||   | ||  |    ||| | ||||  | || ||| ||||| || ||||||||||||||||| ||||||||||| ||||||||||| ||||| || ||||| || || |  || |||
tctttagtaatagcaaatgctg-tgttagttttttagttctttagcagactgtttcatcttccgatca--gaaccgactaatcaa-gttgttgtgttgt-ttcagGAATGCCGATTTGTGAAGCATTTGCTCAAATAGAGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG

upper sequence: GLYMA11G07910.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 1
gattgaagtcgatgatgctattggcgtcccgtttgtggtttgcgttttgtgattctgtgtttactgacttggc-ttgttgccgttt--tcgtgtgctgttt-agGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATATACGATGTGGTGCATGTCAAGTATTTTGATGAG
     |  ||||   || |       | ||  | |    |  | | ||||| || |   |||  | |   ||   |||      ||  |   ||  ||||| ||||||||| || |   |||| |||||||| |||||||| || |||||||| |||||||| || || |||||||||||||| |||
----aatatcgactctgtttgacaatttcctgtggcttctatcctattgtgcttattcattttttcatccggagctgtatttaattgatttggttttgtttcagGGATGCCGATCTCCAAAGCGTTTGCTCAAATAGAGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAG
















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|193410135|gb|FK372958.1|FK372958
EST:     CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCG                         GGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATAT
genomic: CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCGgtaattatta ... tgctgtttagGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATAT
EST: gi|193415174|gb|FK380092.1|FK380092
EST:     CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCG                         GGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATAT
genomic: CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCGgtaattatta ... tgctgtttagGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATAT
EST: gi|27426508|gb|CA938028.1|CA938028
EST:     CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCG                         GGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATAT
genomic: CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCGgtaattatta ... tgctgtttagGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATAT
EST: gi|23052777|gb|BU577268.1|BU577268
EST:     CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCG                         GGATGCCTATATGTGAAGCATTTGCTCAGATATTTTAGCAACCTAACATAT
genomic: CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCGgtaattatta ... tgctgtttagGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATAT
EST: gi|213595247|gb|DB963980.1|DB963980
EST:     CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCG                         GGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATAT
genomic: CATCGTTCTCGATCTCCGTCCCGGTCTCGGAATTGGACCCTTCTCCCTCGgtaattatta ... tgctgtttagGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgattctgtgtttactgacttggcttgttgccgttttcgtgtgctgtttagGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATATACGATGTGGTGCATGTCAAGTATTTTGATGAG
                tactgac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgaagtcgatgatgctattggcgtcccgtttgtggtttgcgttttgtgattctgtgtttactgacttggcttgttgccgttttcgtgtgctgtttagGGATGCCTATATGTGAAGCATTTGCTCAGATAGAGCAGCAACCTAACATATACGATGTGGTGCATGTCAAGTATTTTGATGAG

- - - - - - tgatgct
- - - - - - - - - - - -gcgtccc
- - - - - - - - - - - - - - - gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgtt