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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttcaattttcactttttattcttcctcgtgtcattttgtgcaagtagattttgtttctggtgatgggaagtaaaatgctctatatctgcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCTGTGCTGGACGAACCGG

Basic information

species Glycine max
transcript GLYMA09G39150.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
attttcaattttcactttttattcttcctcgtgtcattttgtgcaagtagattttgtttctggtgatgggaagtaaaatg--ctctatatctgcatttt-cagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCTGTGCTGGACGAACCGG
                  | |       |     ||       |||   | |        | |||      | | |||||   | | | |  | ||||| ||||| |||||  | ||||| ||||| || ||||| | |||||| ||||||||||| || |||||||| |||||||||||  |    |   | || | |   |
-----------------gtcagagaagataacaacaga--acacaaactgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG

upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 13
attttcaattttcactttttattcttcctcgtgtcattttgtgcaagtagattt---tgtttctggtgatgggaagtaaaatgctctata-----tctgcattttc-agGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCTGTGCTGGACGAACCGG
|     |||| |||        | ||          ||  |||||||||   ||   ||||| | ||||      ||  | | ||| | |     |     ||||| |||| || ||| |||| ||||||||||||||||| |||||||| ||||| |||||||| |||||||| |||||||||||||||||||  || || ||||| |
acccaaaattgtcaggaagaggttttt---------ttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagatttaatgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG
















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|6095032|gb|AW119699.1|AW119699
EST:     CATCTGGATTACGCGGTGGTCTTGTGAAACTACAG                         GAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
genomic: CATCTGGATTACGCGGTGGTCTTGTGAAACTACAGgtgacatttt ... gcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
EST: gi|192302659|gb|FG994897.1|FG994897
EST:     AGAAGCTTGGATATGTATCTGGATTACGCGGTGGTCTTGTGAAACTACAG                         GAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
genomic: AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAGgtgacatttt ... gcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
EST: gi|7029492|gb|AW459275.1|AW459275
EST:     AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG                         GAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
genomic: AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAGgtgacatttt ... gcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
EST: gi|5175463|gb|AI759796.1|AI759796
EST:     AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG                         GAGGAGAATCTGTCAGCTATGAATA
genomic: AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAGgtgacatttt ... gcattttcagGAGGAGAATCTGTCAGCTATGAATA
EST: gi|7690863|gb|AW759000.1|AW759000
EST:     AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG                         GAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
genomic: AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAGgtgacatttt ... gcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
EST: gi|19270564|gb|BM886820.1|BM886820
EST:     AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG                         GAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
genomic: AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAGgtgacatttt ... gcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
EST: gi|5175455|gb|AI759788.1|AI759788
EST:     AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG                         GAGGAGAATCTGTCAGCTATGAATA
genomic: AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAGgtgacatttt ... gcattttcagGAGGAGAATCTGTCAGCTATGAATA
EST: gi|214005851|gb|DB988692.1|DB988692
EST:     AGAAGCTTTGATATGCATCTGGATTACGCGGTGTTCTTGTGAAACTACAG                         GAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
genomic: AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAGgtgacatttt ... gcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
EST: gi|22933929|gb|BU551068.1|BU551068
EST:     AGAAGCNNNGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG                         GAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC
genomic: AGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAGgtgacatttt ... gcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagattttgtttctggtgatgggaagtaaaatgctctatatctgcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCTGTGCTGGACGAACCGG
                                              cattttc  CT-rich tract
     attttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttcaattttcactttttattcttcctcgtgtcattttgtgcaagtagattttgtttctggtgatgggaagtaaaatgctctatatctgcattttcagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCTGTGCTGGACGAACCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - -cttcctc
- - - - - - - - - - - - - - - - - - - - -tgcaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgctc