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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttttatagtttgatgaaagtagaacgtctttttctaaaaacggaatagcatttttggtgccttttttttagattctaatgggtattataacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGGCTCATGTCTATCCCAGATGACGGGACCACTGCAAG

Basic information

species Glycine max
transcript GLYMA02G03990.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03990.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G23730.1 (Arabidopsis thaliana), 3'ss of exon 6
tatttttatagtttgatgaaag---tagaacgtctttttctaaaaacgg--aatagcatttttggtgccttttttttagattctaatgggtattataacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGGCTCATGTCTATCCCAGATGACGGGACCACTGCAAG---
  ||  | |    |  |   |    || || |    |  ||||||  |   |  |  |   |   ||    || |  | | | |||||     | | | |   |||||||||| ||| | |||||||||||||| || ||||| || |||||||| |||||| | ||   |||| |     |  |  | |    
-gttgatgtgacctagttctaaccctaaaaaggaggtccctaaaagtgttcaccaaaaaaataattgagccttgtagataatgtaatg----ctgtcattatcagGTGGAGAACATTCTTGTTATTGGACACAGCTGTTGTGGTGGAATAAAGGGACTCATGGCCATTGAAGATAATACAGCTCCCACTAAGAC

upper sequence: GLYMA02G03990.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0127g00720.t01 (Vitis vinifera), 3'ss of exon 6
tatttttatagtttgatgaaa-gtagaacgtcttttt--ctaaaaacggaatagcatttttggt--gccttttttttagattctaatg-----ggtattataacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGGCTCATGTCTATCCCAGATGACGGGACCACTGCAAG
          | |   | ||    | | | |||||    |  ||| |    |  | |||||  |  | ||||| ||  ||  ||   |      |||  ||    |  ||||||||||||||||||| ||||||||||| || |||||||| ||||||||||||||||||||||||||||| ||||||||||| ||
----------gatgagtaaaccacaaagcatctttggaacacaaatcattttcccttttttacttcgtcttttcttgggaaactggagttaaaagtaggatgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG
















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|298175511|gb|HO018222.1|HO018222
EST:     AGTATTCAGGAGCAGGGGCTGCCATAGAATATGCAGTGTTGCATTTAAAG                         GTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGG
genomic: AGTATTCAGGAGCAGGGGCTGCCATAGAATATGCAGTGTTGCATTTAAAGgtaattgttt ... taacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGG
EST: gi|298195403|gb|HO039234.1|HO039234
EST:     AGTATTCAGGAGCAGGGGCTGCCATAAAATATGCAGTGTTGCATTTAAAG                         GTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGG
genomic: AGTATTCAGGAGCAGGGGCTGCCATAGAATATGCAGTGTTGCATTTAAAGgtaattgttt ... taacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGG
EST: gi|23064138|gb|BU578911.1|BU578911
EST:     AGTATTCAGGAGCAGGGGCTGCCATAGAATATGCAGTGTTGCATTTAAAG                         GTGGAGAATATTG
genomic: AGTATTCAGGAGCAGGGGCTGCCATAGAATATGCAGTGTTGCATTTAAAGgtaattgttt ... taacttgaagGTGGAGAATATTG
EST: gi|20813541|gb|BQ298019.1|BQ298019
EST:     AGTATTCAGGAGCAGGGGCTGCCATAGAATATGCAGTGTTGCATTTAAAG                         GTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGG
genomic: AGTATTCAGGAGCAGGGGCTGCCATAGAATATGCAGTGTTGCATTTAAAGgtaattgttt ... taacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGG
EST: gi|20813542|gb|BQ298020.1|BQ298020
EST:     AGTATTCAGGAGCAGGGGCTGCCATAGAATATGCAGTGTTGCATTTAAAG                         GTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGG
genomic: AGTATTCAGGAGCAGGGGCTGCCATAGAATATGCAGTGTTGCATTTAAAGgtaattgttt ... taacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatagcatttttggtgccttttttttagattctaatgggtattataacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGGCTCATGTCTATCCCAGATGACGGGACCACTGCAAG
                                          ttataac  putative branch site (score: 2)
                   ttttttttagattcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttttatagtttgatgaaagtagaacgtctttttctaaaaacggaatagcatttttggtgccttttttttagattctaatgggtattataacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGGCTCATGTCTATCCCAGATGACGGGACCACTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG