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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaccattttgtttttccacgctttagttatcttcctgattgtcaagaaggaaacttggtgaagttatctgattttgtcattttctcactgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTA

Basic information

species Glycine max
transcript GLYMA13G43050.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43050.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g03410.t01 (Vitis vinifera), 3'ss of exon 4
-------tagaccattttgtttttccacgctttagttatcttcctgattgtcaagaaggaaacttggtgaagttatctgattttgtcattttctcactgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTA
        | | ||||  | ||||| | || |  | | |  |  || ||   ||  |  | |  |  | | |||       | | ||||| | |   ||   || |||||||||||||||||||||||||||  | || | |||||| |||||||||||| | ||||| || ||  | ||||| ||||| || | ||| ||||||||
gttacttcacatcattccgattttcaaagcatccggtttaattatgttttggaatgataacatctcattatgtt-------tgtctcattgtttt-ttgtgttttagCTCAAAGAGATTCCTCTGCTGGTGGAATCCAGACCAAGCATGAGGAAGAGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTA
















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|22928435|gb|BU545574.1|BU545574
EST:     GCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
genomic: GCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|192297031|gb|FG990317.1|FG990317
EST:     TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|302141315|gb|HO212191.1|HO212191
EST:     TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|192308530|gb|FK002426.1|FK002426
EST:     TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|7692407|gb|AW760514.1|AW760514
EST:     TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|5058123|gb|AI736599.1|AI736599
EST:     TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAACCTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|13312662|gb|BG406313.1|BG406313
EST:     CTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAA-AGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA
genomic: CTCTCTTCTGCTGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaggaaacttggtgaagttatctgattttgtcattttctcactgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTA
                                      ttctcac  putative branch site (score: 2)
                                    ttttctcact  CT-rich tract
                 aagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaccattttgtttttccacgctttagttatcttcctgattgtcaagaaggaaacttggtgaagttatctgattttgtcattttctcactgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGGGTTCACAACAAGCAGGAGGAAGAGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA