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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaaaattaaaattgaatcttgaagcgttgcgttaataatgttttgttttttaatattttttttataatttgtgtttgtgtgtttgttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTTTATGTTGAACCTGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG

Basic information

species Glycine max
transcript GLYMA09G06860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 2
gtattaaaattaaaattgaatcttgaagcgttgcgttaataatgttttgttttttaatattttt-tttataatttgtgtttgtgtgtttgttttttc------agCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTTTATGTTGAACCTGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG
                                    |||  || |||    |   ||||    |  ||  ||  |||  |||    | | |||| ||      || | |||||||||||   |||||| || || ||||||||||||||||| || |||||||| ||||||||||||||||||||||||||| | ||||||||
-----------------------------------gtaaacatttttatcctccaaatacaaatacttggaaactgtagttgatcttctcttttatccttgatagGAGAAGGAGTTGATCTCGTTGAAACGCGAGGCCAAGCTTAAGGGAGGTTTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG
















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|192302637|gb|FG994889.1|FG994889
EST:     ACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: ACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
EST: gi|7285803|gb|AW598290.1|AW598290
EST:     AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
EST: gi|298188869|gb|HO035562.1|HO035562
EST:     AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
EST: gi|298175439|gb|HO015072.1|HO015072
EST:     AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
EST: gi|192302636|gb|FG994888.1|FG994888
EST:     AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
EST: gi|209706672|gb|BW676168.1|BW676168
EST:     AGCTGATTTTTAACAGAGCCAAACAGTACTCAGAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
EST: gi|6072110|gb|AW101429.1|AW101429
EST:     CTGATTTTTTAACAGAAGCCATACAGTACTCACAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: CTGA-TTTTTAACAG-AGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
EST: gi|192307307|gb|FK001265.1|FK001265
EST:     AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
EST: gi|24205580|gb|BU964833.1|BU964833
EST:     AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
EST: gi|151401089|gb|EV270903.1|EV270903
EST:     AGCTGATTTTTAACAGAGCCAAACAGTACTCGAAGGAATACGACGAGCAG                         CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT
genomic: AGCTGATTTTTAACAGAGCCAAACAGTACTCAAAGGAATACGACGAGCAGgtattaaaat ... gttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgttttttaatattttttttataatttgtgtttgtgtgtttgttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTTTATGTTGAACCTGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG
        ttttaat  putative branch site (score: 3)
                                          tttgttttttc  putative PPT
      ttttttaatatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaaaattaaaattgaatcttgaagcgttgcgttaataatgttttgttttttaatattttttttataatttgtgtttgtgtgtttgttttttcagCAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTTTATGTTGAACCTGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC