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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgaatcactgattctctgatcaatttgatggataggcttggttgtcacaatgtcagtatctttaacgtgtaaactgtccacttgttgctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG

Basic information

species Glycine max
transcript GLYMA03G38850.1
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
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttgaatcactgattctctgatcaatttgatggataggcttggttgtcacaatgtcagtatctttaacgtgtaaactgtccacttgttgctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTACACGGAATTTAAATTCCCACAGATTAAAGCGCATCCATGGCACAAG

- - - - - -ctgattc
- - - - - - - - - - - - - - ttgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - -caatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtccac