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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggtgtttagttttgggcttcattttattgatataccactgcatcatcttgatttattagctagcagattaattattcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG

Basic information

species Glycine max
transcript GLYMA02G46380.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 6
-------aatggtgtttagttttgggcttcattttattgatataccactgcatcatcttgatttattagctagcagattaattattcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG
       | | ||||||| || ||   |   || ||   ||     | | ||   | |  ||    |   |  |   ||||||||| |  ||  || ||     |||||||| |||||||| || || || || || || |||||||||||||| || || || |||||||| |||||||| || |||||||| ||||| || ||||
gtacctcattagtgtttacttctgcattat-ttgtaccaatgacatatttcagtttttgtatgctgtgattt-cgttttaattatttatattacacatt-----cagGCAATTGATCATATCATCAATTCAGCTGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTG

upper sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
---aatggtgtttagttttgggcttcattttattgatataccactgc-atcatcttgatttattagctagcagattaattattcagttttaacctttgt-tgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG
   |||  |||||  | ||   ||  || ||   || |||  | | |  ||   |   | |  | || | || ||   ||| |  |    |   ||| | | |||||||| ||||| || ||||| || || || || || |||||||||||||||||||| |||||||| |||||||||||||| || || |||||||| ||||
aacaataatgtttgttatt---ctctatctttgaga-atatgaatactgtcgaatccgtatgctggcaaacaaatctcttaatt-gcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG

upper sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G097226_T02 (Zea mays), 3'ss of exon 6
aatggtgtttagttttgggcttcatt-ttattgatataccactgcatcatcttgatttattagctagcagattaattattcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG
| | || | |    |     |||    ||| ||  || |  |    ||| | |    ||||   |   | |  |  |    | | |  ||  |   | ||||| || |||||||| || || || || || || ||||| || ||||| ||||| || |||||||| |||||||| ||||||||||| || || || ||||
agtagtttctgtactgatttttccccattaatgtcatccaccaaattcaacattccatattt-ttgtgaaaaaacctgagtaatctatactgtatcttcagGCTATTGATCATATCATCAATTCAGCTGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTG

upper sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 6
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
aatggtgtttagttttgg---gcttcattttatt---gatataccactgcatcat--cttgatttattagctagcagattaattattcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG
       |  |||| | |    ||| || || ||   || ||   | ||||  |    |  | |||||  | |     |    || |   |  ||| |||  || |||||||| |||||||| || || || || ||||| ||||| |||||||||||||| || |||  ||| || || ||||||||||||||||||||||| ||||
-------tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttcttt-cagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG

upper sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
aatggtgtttagttttgggc-ttcattttattgatataccactgcatcatcttgatttattagctagcagattaattattcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG
  | |  |    |  ||  | ||   ||| ||  |     |||   |  | || |||| ||   |      ||  ||| ||    |      ||||| |||||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| || ||||||||||| ||||| || ||||| || ||||| || ||||
-gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG

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|8826851|gb|BE210581.1|BE210581
EST:     ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAG                         GCGCTAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
genomic: ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAGgttggagttt ... tttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
EST: gi|4292147|gb|AI441863.1|AI441863
EST:     ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAG                         GCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTG
genomic: ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAGgttggagttt ... tttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTG
EST: gi|192295237|gb|FG986956.1|FG986956
EST:     ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAG                         GCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
genomic: ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAGgttggagttt ... tttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
EST: gi|298167466|gb|HO012729.1|HO012729
EST:     ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAG                         GCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
genomic: ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAGgttggagttt ... tttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
EST: gi|213594578|gb|DB957997.1|DB957997
EST:     ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAG                         GCAATAGATCATATTATTAACTCTGCCGCANAATCAAACTACATGTCTGCT
genomic: ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAGgttggagttt ... tttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
EST: gi|207780409|gb|GD752218.1|GD752218
EST:     ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAG                         GCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
genomic: ATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAGgttggagttt ... tttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcttgatttattagctagcagattaattattcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG
                                     ttttaac  putative branch site (score: 2)
                                           cctttgtt  CT-rich tract
                      agattaattattcagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatggtgtttagttttgggcttcattttattgatataccactgcatcatcttgatttattagctagcagattaattattcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
aatggtg
- - - - - - - - -ggcttca
- - - - - - - - - - - - - - - - - - - cactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctagca