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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctctgtgtgtgcgtgtgtattcccaccagaatggaacgtctttttgataaattcctttcagttgctttattgtttgttttaccttctgtatcatttggaaatcccaatttcttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTGACACTGCCTTGAAG

Basic information

species Glycine max
transcript GLYMA08G06010.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G06010.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g02210.t01 (Vitis vinifera), 3'ss of exon 4
gtactctctgtgtgtgcgtgtgtattcccaccagaatggaacgtctttttgataaattcctttcagttgctttattgtttgttttaccttctgtatcatttggaaatcccaatttcttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTGACACTGCCTTGAAG
||| | | | | |        ||  ||  |   ||||     ||  |||| ||    |   |||||||   || ||    | |    |   || |    |  |      |    | || | | |||||||  ||||| | ||  ||||||||||||||||||| || |||||||||||  | || || |||
gtaatatgttt-taaattcaagttgtcttagttgaatctctagttgttttcattg--tatattcagtt--cttgttacccgatcattcccttggaaatctgagttgcttcttccttttttatccagCTAGTGTCTATGTTAAGCTGAAGAAACCAAATGCTGCAATCCGTGATGCTGATGCAGCTTTAAAG
















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|192298877|gb|FG987622.1|FG987622
EST:     AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAG                         CTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
genomic: AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAGgtactctctg ... ttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
EST: gi|308222667|gb|HO760642.1|HO760642
EST:     AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAG                         CTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
genomic: AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAGgtactctctg ... ttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
EST: gi|254343946|gb|GR857702.1|GR857702
EST:     AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAG                         CTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
genomic: AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAGgtactctctg ... ttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
EST: gi|192299227|gb|FG990710.1|FG990710
EST:     AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAG                         CTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
genomic: AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAGgtactctctg ... ttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
EST: gi|254315121|gb|GR830114.1|GR830114
EST:     AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAG                         CTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
genomic: AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAGgtactctctg ... ttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
EST: gi|254324847|gb|GR834272.1|GR834272
EST:     AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAG                         CTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
genomic: AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAGgtactctctg ... ttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
EST: gi|298196303|gb|HO044694.1|HO044694
EST:     AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTCTATGCTACTAGAG                         CTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
genomic: AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAGgtactctctg ... ttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
EST: gi|18730076|gb|BM525667.1|BM525667
EST:     AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAG                         CTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG
genomic: AGAAGCCATTTTGTTGAATCCGCAATCAGCTATACTTTATGCTACTAGAGgtactctctg ... ttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgtttgttttaccttctgtatcatttggaaatcccaatttcttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTGACACTGCCTTGAAG
                                         tttcttgttttc  CT-rich tract
      tttgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactctctgtgtgtgcgtgtgtattcccaccagaatggaacgtctttttgataaattcctttcagttgctttattgtttgttttaccttctgtatcatttggaaatcccaatttcttgttttcagCTAGCATCTATATGAAATTGAAGAAACCAAATGCTGCTATACGTGATGCTGACACTGCCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG