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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatataagcaatattctaaagttgaattatataataaggaaaatgtctaaagctaatttgttcttttataattttattcatcttttggtatggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG

Basic information

species Glycine max
transcript GLYMA16G04560.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 7
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 6
tgatataagcaatattctaaagttgaattatataataaggaaaatgtctaaagctaatttgttcttttataattttattcatcttttggtatggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG
            | || || ||||   |     || ||    ||| | |    |||   || | |  | |||      ||    |||||| || || | ||||||||||||| ||||| || |||||||| ||  | ||||  ||||||||||||||||| || || ||||| |||
-----------gtcttttatagtttcttgtctcaaaaatattaatctattct-ctatcatgatttcctctaaac---ctctggctttggtctgtttta-gGGAAAATGCAAACGAAATAAAAGCCAAATTCATCATTGAAGGTGCTAATCACCCAACTGATCCTGAGGCTGACGAG

upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 8
tgatataagcaatattctaaagttgaattatataataaggaaaatgtc-taaagctaatttgttct-tttataattt--tattcatcttttggtatggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG
     |  ||| |     ||| | |      ||  || |    |  || | | ||| | |  |    || |||| |   | ||  |||||||||  | ||| |||||||||||||||||||| || |||||||||||| | |||||||| || || || || ||||| ||||| ||||||
----ttgggcattgcaacaaaatagtcaaccatcctaggttttagctcatgatgcttaatcataagattcataactaaatgttgttcttttggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG
















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|192308765|gb|FG999790.1|FG999790
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAG-CCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|12496130|gb|BG046909.1|BG046909
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGCGGGTGTCATCAATAG                         GGACAATGCAAATGATATCAACGCCATATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|21994949|gb|BQ786477.1|BQ786477
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|26058522|gb|CA801436.1|CA801436
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|22541194|gb|BU091037.1|BU091037
EST:     GAAGATTGTGATGTTCTATTCCCAGCATCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|8404383|gb|BE060017.1|BE060017
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|6070029|gb|AW099659.1|AW099659
EST:     GAAGATTGTGATGTTCTATTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATC
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATC
EST: gi|8403457|gb|BE059091.1|BE059091
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|8827932|gb|BE211662.1|BE211662
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|192308766|gb|FG999791.1|FG999791
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|151413195|gb|EV283003.1|EV283003
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
EST: gi|8402782|gb|BE058416.1|BE058416
EST:     GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAG                         GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA
genomic: GAAGATTGTGATGTTCTAGTCCCAGCAGCTCTTGGGGGTGTCATCAATAGgtgattttcc ... atggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctaaagctaatttgttcttttataattttattcatcttttggtatggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG
      agctaat  putative branch site (score: 3)
         taatttgttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatataagcaatattctaaagttgaattatataataaggaaaatgtctaaagctaatttgttcttttataattttattcatcttttggtatggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT