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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgctgaagtgatgataaatgtttgatcatggtttgctagtttactacaggtttaaacaaacattttttttgtttttgagatttttcttattttctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCTGTTCATCCAACTCATGGAGCCTTTTGGGGAATGGGTGTGGGCGTTGGTT

Basic information

species Glycine max
transcript GLYMA16G17640.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17640.2 (Glycine max), 3'ss of exon 1
lower sequence: AT4G19070.1 (Arabidopsis thaliana), 3'ss of exon 1
-tatgctgaagtgatgataaatgtttgat---catggtttgctagtttactacaggtttaaacaaacattttttttgtttttgagatttttcttattttctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCTGTTCATCCAACTCATGGAGCCTTTTGGGGAATGGGTGTGGGCGTTGGTT
 | |||    |   ||||  |  ||   |    |  |   | || |||| |   |||  |   ||||  || ||  |||||  | || |||   | |||  |||||  | ||||| || |||||  | ||| | || || |||| |||||| ||||| ||||| ||| ||||||| ||||||||||||||  | ||  ||||||
atgtgcattggatttgatttagtttcagtgggtactgaaagataatttagt-tgggtcaatgtaaac--ttattccgttttc-aaatctttaccaattttgcagGTCTTGATGATCATTAAAGGTATATTTCGGAGATATGAAAAATGGAATCCTGTGCATCCTACTTATGGAGCATTTTGGGGAATGGGGATTGGGATTGGTT

upper sequence: GLYMA16G17640.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0043g00140.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------------------------tatgctgaagtgatg---ataaatgtt--tgatcatggtttgctagtttactacaggtttaaacaaacattttttttgtttttgagatttt----tcttattt--tctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCTGTTCATCCAACTCATGGAGCCTTTTGGGGAATGGGTGTGGGCGTTGGTT
                                                                                    | |  |||  |       | | |||||  ||  |||||  | ||| | |  | |   |      |||  | ||| |     ||  ||| ||    || |||||  |  ||| | |||||||| |||||||| |||||| |||| || ||||||||||| ||||| ||||||||    |||||||||||||| |||||  | ||| ||||||
gtatggttcttggaactaatcactttttttttttatttgataggtaactaatcacttaatatgaacagacattatatgtgaagctttattgacatctcataaacagatgttattgtgcatgggat-ctattatgattctattccttttaaatttctttgtgaaaattctgatcttgttatcatatttggttgcagATCCTAATGATCATAAAAGGGTTGTTTAGAAGATATGAAAGATGGAATCCTGTGCATCCAACATCCGGAGCCTTTTGGGGCATGGGGATAGGCATTGGTT
















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|6481516|gb|AW200787.1|AW200787
EST:     AAATATTACTATGTGCTTGCATTAACTGATTGATTTACTCCAAAATTTAG                         GTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT
genomic: AAATATTACTATGTGCTTGCATTAACTGATTGATTTACTCCAAAATTTAGgtaatgtaat ... attttctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT
EST: gi|151398487|gb|EV268358.1|EV268358
EST:     AAATATTACTATGTGCTTGCATTAACTGATTGATTTACTCCAAAATTTAG                         GTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT
genomic: AAATATTACTATGTGCTTGCATTAACTGATTGATTTACTCCAAAATTTAGgtaatgtaat ... attttctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT
EST: gi|6481677|gb|AW200948.1|AW200948
EST:     AAATATTACTATGTGCTTGCATTAACTGATTGATTTACTCCAAAATTTAG                         GTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT
genomic: AAATATTACTATGTGCTTGCATTAACTGATTGATTTACTCCAAAATTTAGgtaatgtaat ... attttctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT
EST: gi|298163703|gb|HO012436.1|HO012436
EST:     AAATATTACTATGTGCTTGCATTAACTGATTGATTTACTCCAAAATTTAG                         GCTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT
genomic: AAATATTACTATGTGCTTGCATTAACTGATTGATTTACTCCAAAATTTAGgtaatgtaat ... attttctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT
EST: gi|298190599|gb|HO032720.1|HO032720
EST:     AAATATTACTATGTGCTCGCATTAACTGATTGATTTACTCCAAAATTTAG                         GTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT
genomic: AAATATTACTATGTGCTTGCATTAACTGATTGATTTACTCCAAAATTTAGgtaatgtaat ... attttctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacaggtttaaacaaacattttttttgtttttgagatttttcttattttctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCTGTTCATCCAACTCATGGAGCCTTTTGGGGAATGGGTGTGGGCGTTGGTT
                                     tttttcttattttctc  CT-rich tract
              aaacattttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgctgaagtgatgataaatgtttgatcatggtttgctagtttactacaggtttaaacaaacattttttttgtttttgagatttttcttattttctcagGTTCTAATGATTATAAAAGGATTGTTTGGAAGGTACGAAAGATGGAACCCTGTTCATCCAACTCATGGAGCCTTTTGGGGAATGGGTGTGGGCGTTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- tgctgaa
- - - - - tgatgat
- - - - - - - - - -atgtttg
- - - - - - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - -ctacagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa