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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctcaaacttctcattcagtccaaattctcccatcatttccagctctataacttgatggaaaattatgatatcttacaaattgacatgtatatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCTGAAGTTGAACTCCCAATTGTGATCGATCAATTCTACTGTGACAAAAGAA

Basic information

species Glycine max
transcript GLYMA08G39340.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G39340.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0127g00400.t01 (Vitis vinifera), 3'ss of exon 7
gtctcaaacttctcattcagtccaaatt---ctcccatcatttccagctctataacttgatggaaaattatgatat-cttacaaattgaca---tgtatatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCTGAAGTTGAACTCCCAATTGTGATCGATCAATTCTACTGTGACAAAAGAA
      ||| | | | ||  ||| | ||   || ||| ||  | || || ||| |||  |||  | | ||    ||  |||||  ||  ||   | || ||||||||||||| || || || || || ||||| || ||||| || || |||||||||||||| |||||||||||||| || ||||||||||| ||||||||  | |
-----gaacctttaactcgatccgacttttacttccaacaccttcatct-tattactc-atgctagactaatgcatatttacatgttaccaaattttacatctgcagGGTGGCTCTGGGTCAGTGCAGGGAGTACTGTTCTCCAACATTCAAGTTTCTGAAGTGGAACTCCCAATTGTTATTGATCAATTCTATTGTGACAAGGGGA
















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|9901271|gb|BE610239.1|BE610239
EST:     CAAAAGATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: CAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|193567401|gb|FK522842.1|FK522842
EST:     GCACAACACAATG-ATGGTGTCAGAATCAAAACATGGCAG                         GGTGGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTC
genomic: GCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGT-GGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTC
EST: gi|193562738|gb|FK520725.1|FK520725
EST:     TGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: TGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|208111596|gb|GD909650.1|GD909650
EST:     AACACAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: AACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|207805189|gb|GD780686.1|GD780686
EST:     TGTCAACATGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGNGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: TGTCAACATGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|15204567|gb|BI427335.1|BI427335
EST:     ATGTCAACATGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: ATGTCAACATGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|193414592|gb|FK379300.1|FK379300
EST:     ATGTCAACATGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: ATGTCAACATGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|193307654|gb|FK270654.1|FK270654
EST:     TGTCAACATGCTACAACACAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATA
genomic: TGTCAACATGC-ACAACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATA
EST: gi|208150171|gb|GD947346.1|GD947346
EST:     ATGTCAACATGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: ATGTCAACATGCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|193568946|gb|FK526151.1|FK526151
EST:     CAACACAATGAATGGTGTCAGAATCAAAAACAATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTC
genomic: CAACACAATGAATGGTGTCAGAATC-AAAAC-ATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTC
EST: gi|193468145|gb|FK430906.1|FK430906
EST:     GCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: GCACAACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|193471265|gb|FK438158.1|FK438158
EST:     CAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: CAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|193726409|gb|FK656125.1|FK656125
EST:     GCACAACACAATGAATGGTGTCAGAATCAAAAACAATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTC
genomic: GCACAACACAATGAATGGTGTCAGAATC-AAAAC-ATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTC
EST: gi|17400641|gb|BM177423.1|BM177423
EST:     AACACAATGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: AACACAATGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
EST: gi|208305174|gb|GE102273.1|GE102273
EST:     ATGCACAACTACTAATTGAATGGTGTCAGAATCAAAACATGGCAG                         GGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT
genomic: ATGCACAAC-AC-AA-TGAATGGTGTCAGAATCAAAACATGGCAGgtaaaatatg ... atatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctataacttgatggaaaattatgatatcttacaaattgacatgtatatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCTGAAGTTGAACTCCCAATTGTGATCGATCAATTCTACTGTGACAAAAGAA
                                  aattgac  putative branch site (score: 3)
               aaaattatgatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcaaacttctcattcagtccaaattctcccatcatttccagctctataacttgatggaaaattatgatatcttacaaattgacatgtatatctgcagGGTGGATCAGGTTCTGTACAAGGAGTGCTATTCTCAAATATACAAGTTTCTGAAGTTGAACTCCCAATTGTGATCGATCAATTCTACTGTGACAAAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA