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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccataatttgactactcaagatatatatttggtttatcaagatggtcttggacttcttagtactcatgttatgatgttgaattatggttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAGCAGAAAGGAATTCATGTTAGTGCTTGGTCAGCTCTTGGTGCTTATAAGA

Basic information

species Glycine max
transcript GLYMA16G34570.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G34570.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g02480.1 (Oryza sativa), 3'ss of exon 2
---gtaccataatttgactactcaagatatatatttggtttatcaagatggtcttggactt-cttagtactcatgtt-atgatgttgaattatggttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAGCAGAAAGGAATTCATGTTAGTGCTTGGTCAGCTCTTGGTGCTTATAAGA
    |||  |  |||  ||| ||    | |  |     |||  ||| |||  | | || |   ||| || |  |||| | |   ||  || |      || ||||| ||  || |||| |  || | ||||   ||| | ||||||||||||||| |||||||||||||  |  |||| |  ||  || | ||||   |    |
catatacatttttttctctattctctttgtccaaaacattt--caacatgtacattgattaatttattaatattgttcacgggattacatga--acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAGGAGAAAGGAATTCAGCTCTGTGCCTACTCTCCTTTAGGTGGAAAGGGTA

upper sequence: GLYMA16G34570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0077g02150.t01 (Vitis vinifera), 3'ss of exon 2
gtaccataatttgactactcaagatatatatttggtttatcaagatggtcttggacttcttagtactcatgttatgatgttgaattatggttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAGCAGAAAGGAATTCATGTTAGTGCTTGGTCAGCTCTTGGTGCTTATAAGA
               || | ||        | ||      ||  || | |  |  ||  ||  |       | ||||  ||||   | |  | |||||||||||||||||| || | ||||| || | |||||| || ||||| |||| | |||| || |||||||| ||||| |||||  | || || ||  |     
--------------gtattaaaacagggggtgtgccgaggcataataggca-gagctagttcatgagttgatgatgaaattga---acgcgtgtttcagGTGGAAATGAACGCAGCATGGCAACAGGCGAAACTGAGAGAGTTTTGCAGGGAGAAGGGGATTCATGTGAGTGCATGGTCTCCCCTGGGAGCAAACGGAG
















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|31458692|gb|CD400720.1|CD400720
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|8670144|gb|BE191251.1|BE191251
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|298188911|gb|HO035604.1|HO035604
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|192297040|gb|FG991991.1|FG991991
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAAC
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAAC
EST: gi|192317399|gb|FK011245.1|FK011245
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|22524326|gb|BU083137.1|BU083137
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|10237616|gb|BE806504.1|BE806504
EST:     CTCACTAGACTCTTGAAAATNA-CCACCATTCCTGCTGC-GATCAATCAG                         GTGGAAATGAACCCATCTTTGCAGCAAGG
genomic: CTCACTAAACTCTTGGAAAT-AGCCACCATTCCTCCTGCAG-TCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGG
EST: gi|192294071|gb|FG986160.1|FG986160
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACT
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACT
EST: gi|9259759|gb|BE347906.1|BE347906
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAATGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|7588574|gb|AW704367.1|AW704367
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|151401281|gb|EV271095.1|EV271095
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCGG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|8670470|gb|BE191577.1|BE191577
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCACGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|51343795|gb|CO984528.1|CO984528
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTNNGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|151412385|gb|EV282197.1|EV282197
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGGAGTTCTGCAA
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGG-AGTTCTGCAA
EST: gi|192298024|gb|FG991304.1|FG991304
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|298190090|gb|HO032211.1|HO032211
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATC
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATC
EST: gi|213615012|gb|DB957050.1|DB957050
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCA
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCA
EST: gi|13787352|gb|BG649944.1|BG649944
EST:     AACTCACTAAACTCTTTGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|7692988|gb|AW761087.1|AW761087
EST:     AACTCACTAAACTCTTGGAGATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGG
EST: gi|6069723|gb|AW099347.1|AW099347
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|193525752|gb|FK481159.1|FK481159
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCAT
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCAT
EST: gi|120532091|gb|EH260224.1|EH260224
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|151412793|gb|EV282605.1|EV282605
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|192296175|gb|FG991545.1|FG991545
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|208186966|gb|GD985066.1|GD985066
EST:     CTTCACTTAAACTCTTGGAAANAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: C-TCAC-TAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
EST: gi|208113616|gb|GD912949.1|GD912949
EST:     AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAG                         GTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG
genomic: AACTCACTAAACTCTTGGAAATAGCCACCATTCCTCCTGCAGTCAATCAGgtaccataat ... gttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtcttggacttcttagtactcatgttatgatgttgaattatggttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAGCAGAAAGGAATTCATGTTAGTGCTTGGTCAGCTCTTGGTGCTTATAAGA
                                              ttttttc  CT-rich tract
                                      aattatggtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccataatttgactactcaagatatatatttggtttatcaagatggtcttggacttcttagtactcatgttatgatgttgaattatggttttttcagGTGGAAATGAACCCATCTTGGCAGCAAGGGAAACTCAGGGAGTTCTGCAAGCAGAAAGGAATTCATGTTAGTGCTTGGTCAGCTCTTGGTGCTTATAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC