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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAGGTCGTGGCAGCTCCGGCGAGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgtttggtactacgttgtttgctgtcggatccagttgttgatgtgttcggattagggtttggttccatgctttcgatctgtttcggatcatgttc...

Basic information

species Glycine max
transcript GLYMA08G20830.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 1
--GATGAGGTCGTGGCAGCTCCGGCGAGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgtttggtactacgttgtttgctgtcggatccagttgttgatgtgttcggattagggtttggttccatgctttcgatctgtttcggatcatgttc--
  |  |  | || ||| ||  | ||    |  |||||||||| |||||||   ||| ||||||| |||||||||||  ||||||||||||| || ||||||||| |      |      ||     | | |  |    | |     |  | ||      |  | | ||  ||  | |    |    | |  ||      |||  
GCGGAGGCGGCGAGGCGGCCGCAGCCG--CAGCCGCAGCCGCGGGAGTGGCGGTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtgagaacgcgccgacccgcccccttccgctgctcgccgcgtgcgtcgcgtggctcgtgagatctgcctcggtccgg--ggcgggatgtgggagggtttcga

upper sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 1
GATGAGGTCGTGGCAGCTCCGGCGAGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgtttggtactacgttgtttgctgtcggatccagttgttgatgtgttcggattagggtttggttccatgc--tttcgatctgtttcgg-----atcatgttc-
|||||   ||  ||  |  | |||  ||| |||| ||  ||||||||||||||||| ||||| ||||| || ||  |||| || |||||||| |||||||||| ||||| | |      || |  |  || ||||||     ||| || ||     |||||||||||||    |   ||| |||||||||| |     || | |||  
GATGACACCGCAGCTCCCTCCGCGCCTCCTCCGCCGCAACTGGAGTGGAAATTCTCTCAGGTATTCGGCGAGCGGGCGGCCGGCGAGGAAGTGCAGGAAGgta-ttgttggct------ttttgcggcgttggatccgccaattgttgcgtg-aatttagggtttggttttgcgtagttttgatctgtttctggatcgattaggtttt

upper sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 1
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 5'ss of exon 1
GATGAGGTCGTGGCAGCTCCGGCGAGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgta----attgtttggtactacgttgtttgctgtcggatccagttgttgatgt-gttcggattagggtttggttccatgctttcgatctgtttcggatcatgttc
|  |     |  ||  || |  |    |||  ||   |||||||||||||||| || |||||||||||||| ||| |    ||||| ||||| || |||||||    || | | |    | |||||   |     |  |  |     ||| || || |||  |  ||| ||| |   |  || |  | | |||| | ||  |   
GGGGCCCCGGATGCCACTTCTTCTGCGCCATTGCCTGCGCTGGAGTGGAAATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAGgtatgttatggatcgcagttgcgttggggggaagagtgtgtatcccgtgaggtagtgcggggt--ggtgtggat---tatttcccttgtttttcagttctcgaga

upper sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 1
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 5'ss of exon 1
GATGAGGTCGTGGCAGCTCCGGCGAGTCCACC---GCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgtttggtactacgttgtttgctgt-cggatcc-agttgttgatgtgttcggattagggtttggttccatgctttcgatctgtttcggatcatgttc-----
     | ||  ||     ||   ||| |  ||   ||  ||||| ||||||||||||||||| || ||||| |||||| | |||||||| |||||||| ||||||    ||    |  || ||| |||| |   | ||||  || | |||||   | |  ||    |||  |||     ||   |  ||||| |  ||    |||     
--CCCGCTCCCGG-GTTGCCAATGAGCCAGCCTTTGCCTCCGCTTGAGTGGAAATTCTCGCAAGTGTTCGGAGAACGTGCTGCGGGGGAAGAAGTTCAAGAAGgtg-cggtcacattttatgttttttgtttcactgatcggagctcttgat-catcc--atcgctgtt--gttgtg-actcgtggactgttgcttattgcattccactt

upper sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 1
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 1
GATGAGGTCGTGGCAGCTCCGGCGAGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgtttggtactacgttgtttgctgtcggatccagttgttgatgtgttcggattagggtttggttccatgctttcgatctgtt--tcggatcatgttc-
      |     |   ||   ||    |||  ||   || |||||||||||||||||||||||||||| || ||| |    || |||||||| || ||||||| | |||  | |   ||| || || ||   | |   | ||||          |||   | |||       |   |  |  ||| |    ||||  | | | 
CCCACTGCTACTGGTTCTGTTGCTGCGCCATTGCCCGCGTTGGAGTGGAAATTCTCGCAGGTTTTCGGCGAGCGTGCCATCGGAGAGGAAGTGCAAGAAGgta-tggttctggat--cgtcgtatgttggtagtttaggatgttcggagaagaagatcgtgttttccgcgagttagtgggggctggtgtctggattgtttcct

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|208177685|gb|GD974838.1|GD974838
EST:     CGGCGGGGGAGGAAGTTCAGGAAG                         TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
genomic: CGGCGGGGGAGGAAGTTCAGGAAGgtaattgttt ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
EST: gi|193304649|gb|FK272694.1|FK272694
EST:     CGGCCGGGGAGGAAGTTCAGGAAG                         TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
genomic: CGGCGGGGGAGGAAGTTCAGGAAGgtaattgttt ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
EST: gi|193647235|gb|FK588402.1|FK588402
EST:     CGGGGGAGGAAGTTCAGGAAG                         TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTAATCATCTTGCTA
genomic: CGGGGGAGGAAGTTCAGGAAGgtaattgttt ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
EST: gi|208151571|gb|GD950412.1|GD950412
EST:     GGAGGAAGTTCAGGAAG                         TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
genomic: GGAGGAAGTTCAGGAAGgtaattgttt ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
EST: gi|308099093|gb|HO760934.1|HO760934
EST:     GGCGGGGGAGGAAGTTCAGGAAG                         TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
genomic: GGCGGGGGAGGAAGTTCAGGAAGgtaattgttt ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
EST: gi|208306047|gb|GE104896.1|GE104896
EST:     CGGCGGGGGAGGAAGTTCAGGAAG                         TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
genomic: CGGCGGGGGAGGAAGTTCAGGAAGgtaattgttt ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGAGGTCGTGGCAGCTCCGGCGAGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgtttggtactacgttgtttgctgtcggatccagttgttgatgtgttcggattagggtttggttccatgctttcgatctgtttcggatcatgttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA