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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtgcttttttcccgatcaaatgagttgttcatcaacaatgtcgaatttgttttagcaaaagttaccaatagttttatatggtaggggaagaaaacattttatagaagctgtttttttagtgtttattctgaattttatgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGTTGAGGCAGATCCACTGGCTCAGTCGGATGACCTCTTGAAAGTTTATAAC

Basic information

species Glycine max
transcript GLYMA08G19780.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19780.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0034g01370.t01 (Vitis vinifera), 3'ss of exon 7
gtggtgcttttttcccgatcaaatgagttgttcatcaacaatgtcgaatttgttttagcaaaagttaccaatagttttatatggtaggggaagaaaacattttatagaagctgtttttttagtgtttattctgaatttta--tgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGTTGAGGCAGATCCACTGGCTCAGTCGGATGACCTCTTGAAAGTTTATAAC
                                               |  | ||  | |  |  |    ||  | || | || | |      | |||| |  | |   | ||   ||  |  |    | |      |  |  |||||| | ||||| ||||||||||| ||||| || | ||  || ||||| || || ||||||||||||||||| ||||| ||  |||||||||| |  || |||
-----------------------------------------------acatcttacatcttacatctataactgattaaaattgcattatctgtaaacttcctttgctaccttccttagtgattaaaaatgcttgctggacgtgcagGATTTTGAATGTTCAATTAGGGGAGACATCAAGGCTGGCTTGGCTCGGGGTGGAGGCAGATCCACTGGCCCAGTCAGACAACCTCTTGAAGGCGTACAAC
















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|192303440|gb|FG995678.1|FG995678
EST:     ACCCATTTTGACGTCATTGGAGTTGCCTTGTTCTTCAGCACAGCATTCAG                         GGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
genomic: ACCCATTTTGACGTCATTGGAGTTGCCTTGTTCTTCAGCACAGCATTCAGgtggtgcttt ... ttttatgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
EST: gi|193613487|gb|FK565547.1|FK565547
EST:     ACCCATTTTGACGTCATTGGAGTTGCCTTGTTCTTCAGCACAGCATTCAG                         GGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
genomic: ACCCATTTTGACGTCATTGGAGTTGCCTTGTTCTTCAGCACAGCATTCAGgtggtgcttt ... ttttatgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
EST: gi|22933540|gb|BU550679.1|BU550679
EST:     AGTTGCCTTGTTCTTCAGCACAGCATTCAG                         GGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
genomic: AGTTGCCTTGTTCTTCAGCACAGCATTCAGgtggtgcttt ... ttttatgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
EST: gi|13481224|gb|BG510567.1|BG510567
EST:     ACCCATTTTGACGTCATTGGAGTTGCCTTGTTCTTCAGCACAGCATTCAG                         GGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
genomic: ACCCATTTTGACGTCATTGGAGTTGCCTTGTTCTTCAGCACAGCATTCAGgtggtgcttt ... ttttatgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
EST: gi|26268061|gb|CA819124.1|CA819124
EST:     ACCCATTTTGACGTCATTGGAGTTGCCTTGTTCTTCAGCACAGCATTCAG                         GGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
genomic: ACCCATTTTGACGTCATTGGAGTTGCCTTGTTCTTCAGCACAGCATTCAGgtggtgcttt ... ttttatgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT
EST: gi|22928058|gb|BU545197.1|BU545197
EST:     AGTTGCCTTGTTCTTCAGCACAGCATTCAG                         GGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCNNNGAGT
genomic: AGTTGCCTTGTTCTTCAGCACAGCATTCAGgtggtgcttt ... ttttatgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaaacattttatagaagctgtttttttagtgtttattctgaattttatgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGTTGAGGCAGATCCACTGGCTCAGTCGGATGACCTCTTGAAAGTTTATAAC
                       tttttttagtgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtgcttttttcccgatcaaatgagttgttcatcaacaatgtcgaatttgttttagcaaaagttaccaatagttttatatggtaggggaagaaaacattttatagaagctgtttttttagtgtttattctgaattttatgcagGGTCTTGAACGTTCAATTAGGAGAGACCTCTAAGCGTGCCTGGCTTGGAGTTGAGGCAGATCCACTGGCTCAGTCGGATGACCTCTTGAAAGTTTATAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT