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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcccttactctatcatttttaaatttgtgcatcatttagatttcattttgtggcactatttatatacactaaaaaatgtatggtttccgtttggtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTCAAAACTCAGAGCTCATCCCTTGAAACCTGTTATCCATTGAGGTGAAATA

Basic information

species Glycine max
transcript GLYMA15G40590.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40590.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0039g00240.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtcccttactctatcatttttaaatttgtgca-tcatttagatttcattttgtggcactatttatatacactaaaaaatgtatggtttccgtttggtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTCAAAACTCAGAGCTCATCCCTTGAAACCTGTTATCCATTGAGGTGAAATA
                    |  ||   ||  | || | | |  || ||||  ||||      | |   | |  ||| || || | |  ||  | || | |  |||||||||  ||||||| |||||||||||||| ||||||||||| || ||| | || ||||| ||||| |||||| | || ||||| |  ||||||   | ||  
-------------------gtaattgctttcttccacttaatgtgaattcaccttgttatctcact---acatgctataatat-tgtttttaacattggattcttgcagAAGCATTGTTGGGGAACTAGATGAAGAGCTGGATTCTAGCCTTGATCTATCGAAACTGAGAGCACATCCCCTCAAGCCTGTCACTCATTGACTGGGAAAG
















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|22927651|gb|BU544790.1|BU544790
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|192300038|gb|FG992191.1|FG992191
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTTTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|193496721|gb|FK460305.1|FK460305
EST:     GGTGTACAACAACATGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|208303248|gb|GE101069.1|GE101069
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|151399825|gb|EV269696.1|EV269696
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|298199205|gb|HO042568.1|HO042568
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|192300037|gb|FG992190.1|FG992190
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|7285928|gb|AW598415.1|AW598415
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|151395293|gb|EV265164.1|EV265164
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|192310890|gb|FG998894.1|FG998894
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
EST: gi|192310889|gb|FG998893.1|FG998893
EST:     GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT                         AAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC
genomic: GGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACATgtatgtccct ... gtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggcactatttatatacactaaaaaatgtatggtttccgtttggtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTCAAAACTCAGAGCTCATCCCTTGAAACCTGTTATCCATTGAGGTGAAATA
                  cactaaa  putative branch site (score: 2)
      actatttatatacact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcccttactctatcatttttaaatttgtgcatcatttagatttcattttgtggcactatttatatacactaaaaaatgtatggtttccgtttggtcattgcagAAGTGTTGTTGGTGAACTAGATGAAGAACTGGATTCTAGTCTGGATTTGTCAAAACTCAGAGCTCATCCCTTGAAACCTGTTATCCATTGAGGTGAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA