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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcattagctatatagatggtaaagaactgctgaaagaagttcttgaatttagtattatgatgaatttgacataaactcatatattgtgtatttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGTGGAAAAGTTGTTGCTGTGAGTGACATAACTGGAGCCATAAAGAACAGCA

Basic information

species Glycine max
transcript GLYMA16G04560.2
intron # 6
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 6
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 7
--agcattagctatatagatggtaaagaactgctgaaagaagttcttgaatttagtattatgatgaatttgacataaactcatatattgtgtatttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGTGGAAAAGTTGTTGCTGTGAGTGACATAACTGGAGCCATAAAGAACAGCA
|| | | || || | ||| | || | || | | ||| |||| | | ||| ||| | | || || | | || ||||| ||||| ||||| || || |||||||||||| | || ||| | | |||||||| |||||||||| |||||||| ||||||||||| ||||| ||||
atagaagaatggatgtaagggagaaaaacttgataaactcgataaataaatcatttatttataagctttttccatta-ttaatggatc-ttttttatcccagGGGTTTGGGAATGTGGGTTCTTGGGCTGCCCAACTCATCAGTGAACACGGTGGAAAGATTGTTGCTGTAAGTGACATCACTGGAGCCATTAAGAATAGCA
















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|7284551|gb|AW597139.1|AW597139
EST:     TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAG                         GGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
genomic: TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAGgtacttgttg ... atttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
EST: gi|192308765|gb|FG999790.1|FG999790
EST:     TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAG                         GGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
genomic: TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAGgtacttgttg ... atttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
EST: gi|12496130|gb|BG046909.1|BG046909
EST:     TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAG                         GGTTTTGAAAATGTACGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
genomic: TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAGgtacttgttg ... atttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
EST: gi|26058522|gb|CA801436.1|CA801436
EST:     TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAG                         GGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
genomic: TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAGgtacttgttg ... atttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
EST: gi|208192091|gb|GD992389.1|GD992389
EST:     TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAG                         GGTTTTGGAAATGTAGGGTCATGGGCTGCCCAAT
genomic: TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAGgtacttgttg ... atttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAAT
EST: gi|4396467|gb|AI495464.1|AI495464
EST:     TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAG                         GGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
genomic: TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAGgtacttgttg ... atttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
EST: gi|6070029|gb|AW099659.1|AW099659
EST:     TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAG                         GGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
genomic: TGCTTAATGAGTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAGgtacttgttg ... atttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
EST: gi|151413195|gb|EV283003.1|EV283003
EST:     GTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAG                         GGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT
genomic: GTATGGGAAGAGTGTATCTGGACAACGGTTTGTCATACAGgtacttgttg ... atttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatttagtattatgatgaatttgacataaactcatatattgtgtatttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGTGGAAAAGTTGTTGCTGTGAGTGACATAACTGGAGCCATAAAGAACAGCA
                   atttgac  putative branch site (score: 4)
 tatttcttc  putative PPT
 tattatgatgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcattagctatatagatggtaaagaactgctgaaagaagttcttgaatttagtattatgatgaatttgacataaactcatatattgtgtatttcttcagGGTTTTGGAAATGTAGGGTCATGGGCTGCCCAATTAATTAGTAATAAAGGTGGAAAAGTTGTTGCTGTGAGTGACATAACTGGAGCCATAAAGAACAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC