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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaattctgcacttgtttgacattgtaaactattgtagctttgctatgtgcacgccaattattttgagatgcttctgcattgttattcatgcagTTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGTCTATGCTATCTGTTATGTGATCAACCAGATCCTGCGCTACGAGATGCAA

Basic information

species Glycine max
transcript GLYMA14G00540.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G00540.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G35230.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------gtgcaattctgcacttgtttgacattgtaaactattgt-------agctttgctatgtgcacgccaattattttgagatgct----tctgcattgttattcatg-------------cagTTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGTCTATGCTATCTGTTATGTGATCAACCAGATCCTGCGCTACGAGATGCAA
                              | |   || | | | || |   ||| |    ||| ||       || ||||| |     |      |||| | || ||  |         || ||||   |               ||||| ||||| |||||||||||||| || |||||||| ||||   |||| |||||||||||  |  |||| |||||||||||| | || ||||| || ||||
gtcttgatttctggctacttcttcttacatttccgctcagtattagtatcggatttttggttatggttaaagccagatttgccaaaaaaattttgtttatctggatatagtagaactcatatggttacatacattgcttctgtggacagTTCATTGACGTTGGAACAATGGTATCTCCAACTGTATTTGGTCGGCGAAGTCTATGCTACTTACTATGCGATCAACCAGATGCAGCACTACGCGACGCAA

upper sequence: GLYMA14G00540.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g03270.t01 (Vitis vinifera), 3'ss of exon 8
---------gtgcaattctgcacttgtttgacattgtaaactattgtagctttgctatgtgcacgccaattattttgagatgcttctg-cattgttattcatgcagTTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGTCTATGCTATCTGTTATGTGATCAACCAGATCCTGCGCTACGAGATGCAA
          |   |||  |   |   ||||  | |  ||     |||||| ||  ||      |  | |   |||| | | ||| || | |||||  |   ||||||| | ||||| ||||| ||||| ||||||||||| | |||| |||||||||||||||||||| | ||||| ||||||||| |||| ||  |||||||||
atgcgcccattttgatttagagatctcttgaattgggcaaaggaagtagctgtgtcat------gatattctctttgtggtccttttggctttgtttctggagcagTTTGTAGATGTGGGAACCATGGTGTCCCCAACTGTTTATGCACGGCGCAGTCTATGCTATCTGCTGTGTGACCAACCAGATGCTGCCCTTAGAGATGCAA
















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|6724974|gb|AW309373.1|AW309373
EST:     ATGCATTCCGTGACAAGGACTTTAGGACAGCCATTGATAACTATTCCCAG                         TTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGT
genomic: ATGCATTCCGTGACAAGGACTTTAGGACAGCCATTGATAACTATTCCCAGgtgcaattct ... attcatgcagTTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGT
EST: gi|51341542|gb|CO982859.1|CO982859
EST:     ATGCATTCCGTGACAAGGACTTTAGGACAGCCATTGATAACTATTCCCAG                         TTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGT
genomic: ATGCATTCCGTGACAAGGACTTTAGGACAGCCATTGATAACTATTCCCAGgtgcaattct ... attcatgcagTTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGT
EST: gi|15814119|gb|BI786394.1|BI786394
EST:     ATGCATTCCGTGACAAGGACTTTAGGACAGCCATTGATAACTATTCCCAG                         TTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGT
genomic: ATGCATTCCGTGACAAGGACTTTAGGACAGCCATTGATAACTATTCCCAGgtgcaattct ... attcatgcagTTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctatgtgcacgccaattattttgagatgcttctgcattgttattcatgcagTTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGTCTATGCTATCTGTTATGTGATCAACCAGATCCTGCGCTACGAGATGCAA
                 aattattttgagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaattctgcacttgtttgacattgtaaactattgtagctttgctatgtgcacgccaattattttgagatgcttctgcattgttattcatgcagTTTATTGATGTTGGAACAATGGTCTCCCCAACTGTGTTTGCAAGGCGCAGTCTATGCTATCTGTTATGTGATCAACCAGATCCTGCGCTACGAGATGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG