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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtgtcaattgtcaaagctccacaccaacttataatttgttttgtgtattttacctgatgttggaatgttcgtaaaatctgtttttgttccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGCCTCAATTATTATGCATAGGCTGGATTTTGGAACAAGCTAT

Basic information

species Glycine max
transcript GLYMA20G38030.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
cagtgtcaattgtcaaagctccacaccaacttataatttgtttt-gtgtattttacctgatgttg-gaatgttcgtaaaatctgtttttgttccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGCCTCAATTATTATGCATAGGCTGGATTTTG-GAACAAGCTAT
                        |   |  |||  || || || |||  | | || | | | || | ||| |  |  |     |  |   |      | |||||||||||||||| || ||||||||||| |||||||| ||||| ||||||||||||||| | ||||| || || || |     ||||  | |||  ||  
----------------------gtatgcatatatctttcgtcttagtggttgtaactttaggatgtggatgat-atggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT-

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
cagtgtcaattgtcaaagctccacaccaacttataatttgtt-ttgtgtattttacctgatgttggaatgttcgtaaaatctgtttttgt-tccaaacgt--agGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGCCTCAATTATTATGCATAGGCTGGATTTTGGAACAAGCTAT-
  ||   ||  | || | |||   |   | ||    ||| |  ||||||| |||      | ||  || | | |     |||||| |||| |      ||  ||||||||||||| ||||| ||||||||||| || |||||||| || ||||||||||||||| | || || || || |   ||   | |   | ||   ||| 
--gtaaaaaa-gacagaactct-taatgatttgagctttatgattgtgtagtttggtctgttttttaa-ggtggggttctctgttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCAT-TTATT

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
cagtgtcaattgtcaaagctccacaccaacttataatttgttttgtgtattttacctgatgttggaatgttcgtaaaatctgttt--ttgttccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGCCTCAATTATTATGCATAGGCTGGATTTTGGAACAAGCTAT
 || ||    ||       |    || | |   || |     || ||   | ||||    |    | |  |  |   | ||||    ||| |   |    ||||||||||||||||||| || |||||||| |||||||| || || ||||||||| ||||| | ||||||||||||||||||     |   |||| |  ||
-agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcgga-ctgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT

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|192317514|gb|FK008966.1|FK008966
EST:     CTGTTTGTGTTGAGGCTGGCATGTTGGCTTTACGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTTTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|209727252|gb|BW663198.1|BW663198
EST:     ACGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: ACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|31460097|gb|CD402125.1|CD402125
EST:     CTGTTTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTTTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|208096865|gb|GD894196.1|GD894196
EST:     CTGTTTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTTTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|209718511|gb|BW662656.1|BW662656
EST:     CTGTTTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTTTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtattttacctgatgttggaatgttcgtaaaatctgtttttgttccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGCCTCAATTATTATGCATAGGCTGGATTTTGGAACAAGCTAT
        acctgat  putative branch site (score: 4)
                                 tctgtttttgttcc  putative PPT
                            taaaatctgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtgtcaattgtcaaagctccacaccaacttataatttgttttgtgtattttacctgatgttggaatgttcgtaaaatctgtttttgttccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGCCTCAATTATTATGCATAGGCTGGATTTTGGAACAAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT