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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgaatcactgattctctgatcaatttgatggataggcttggttgtcacaatgtcagtatctttaacgtgtaaactgtccacttgttgctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG

Basic information

species Glycine max
transcript GLYMA03G38850.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 9
-tgtttgaatcactgattctctgatcaat-ttgatggataggcttggttgtcacaatgtcagtatct--ttaacgtgtaaactgtccacttgttgctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG
   ||  |||   || ||   | ||  ||  | ||   |   | ||  |    |  ||| |  |||   |  |  ||  || | |    | |||| ||| | ||||| |||| |||||||||||||| || || || |||||||| || ||||| || || || |||||||| || |||||||| || ||||||||||||
tcattccaatt--tggttga-taatagatactcattcttcctcctgtctaattct-tgtaatcatccagtccatttgccaaatctaatatggttgtttttgcagGTTTTGGGCACTCCAACAAGGGAGGAAATTAAATGCATGAACCCCAACTATACAGAGTTCAAATTCCCCCAAATTAAAGCTCACCCATGGCACAAG

upper sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------------------tgtttgaatcactgattctctgatcaatttgatggatag-gcttggttgtcacaatgtcagta------tctttaacgtgtaaactgtccacttgttgct--ttgg----------tagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG
                                                                             |||||||    ||  |  |     ||  |  | | | |  |||| | |     |||| |||       ||  ||   || | |      |||| | | |  ||||          |||||  |||| || || ||| | || |||||||||||||||||||| ||||||||||| || || || || || ||||| || ||||| |||||||||
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------tgtttgaatcactgattctctgatcaatttgatggataggcttggttgtcacaatgtcagtat-ctttaacgtgtaaactgtccact------tgttgctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG
                        |||  |    |  |  |  |     ||| ||| |  |  || |||      ||| |  || || |   |||| |       | |      |  |  | ||| ||||  ||||||| || ||  | || |||||||||||||||||||| ||||||||||| || || || || || || || || || || |||||||| 
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactg-ttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA

upper sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------------------------------tgtttgaa--tcactgattctctgatcaatttgatggatag-gcttggttgtcacaatgtcagtatctttaa-cgtgtaaactgtccacttgttgctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG
                                                                                        | ||| ||  |    | | ||||  |   || |   | |   ||   | |  | |||      ||   |  | | | | |   | |   | ||    |||  ||||  | || || || ||| | || |||||||||||||||||||| ||||||||||| || || || || || ||||| || || || |||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG

upper sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
tgtttgaatcactgattctctgatcaatttgatggataggcttggttgtcacaatgtcagtatctttaacgtgtaaac--tgtccacttgttgctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG
                            |        |  |||| |  |     | || || | |||  || ||      ||  ||    ||||||| | ||||  | || ||||| ||  | || || || || ||||||||||| ||||||||||| ||||| ||||| ||||||||||||||||| |||||||||
---------------------------gtacgcatgcattcttgctcttttt--tttctgttttttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
tgtttgaatcactgattctctgatcaatttgatggataggcttg-gttgtcacaatgtcagtatctttaacgtgtaaac--tgtccacttgttgctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG
                                    || || ||  || |  |  | |   |   |||  || ||      ||  ||    ||||||| | ||||  | || ||||| ||  |||| || || || ||||||||||| ||||||||||| ||||| ||||| ||||||||||||||||| |||||||||
-----------------------------------gtacgcatgcattcttgctctcttttttctttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 8
tgtttgaatcactgattctctgatcaatttgatggataggcttggttgtcacaatgtcagtatctt-taacgtgtaaactgtccacttgttg--ctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG
                                            |||| | |  |||   |  ||| |   |  |   |  ||     ||||  |||  | ||||||| ||||| || ||  | || ||||| ||||| |||||||| |||||||||||||| || ||||| || || || || ||||| |||||||||
--------------------------------------------gttggctcgttgtttttgccttatggtggctgggcgctcataaagttggacttgcgcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAG

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|192296807|gb|FG993105.1|FG993105
EST:     CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAC
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAC
EST: gi|17519874|gb|BM188916.1|BM188916
EST:     CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGG
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGG
EST: gi|15285595|gb|BI469486.1|BI469486
EST:     CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAC
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAC
EST: gi|21888144|gb|BQ741366.1|BQ741366
EST:     CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAC
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAC
EST: gi|22931093|gb|BU548232.1|BU548232
EST:     AGTTGATCAGCTTGTTGAGATCATCAAN                         NNNCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAC
genomic: AGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAC
EST: gi|208199154|gb|GD999479.1|GD999479
EST:     CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTG
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcacaatgtcagtatctttaacgtgtaaactgtccacttgttgctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG
                  ctttaac  putative branch site (score: 3)
                                           ttgcttt  putative PPT
               tatctttaa  TA-rich tract