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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttcatagttctgctgctattttcgtattggtgaaaatcttagcaatattagttggcatgtattaaacttaaagatgctattggttattttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAAGAGACAATGATTGCGGGAGCCCCTTTTGTTCTTCCTCTTGCTCACAAAC

Basic information

species Glycine max
transcript GLYMA16G10880.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G10880.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
-tttcttcatagttctgctgctattttcgtattggtgaaaatcttagcaatattagttggcatgtattaaacttaaagatgctattggttattttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAAGAGACAATGATTGCGGGAGCCCCTTTTGTTCTTCCTCTTGCTCACAAAC
 | | ||  ||  |      |||  |    || |   || ||  |    |  | |    |  || |  |   ||    ||   |  | || |||  | ||||| |||||||| || |||||||| || ||||| || || |||||||||||||||||  ||||||| ||||  || | |||  | ||||| ||| | || |
gtctatttctaagtacaggtctacatctaaatcgacaaatattatcagtaggtgataacgtttggacgaggttttttaat-tgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC
















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|120491370|gb|EH219537.1|EH219537
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|13562679|gb|BG550899.1|BG550899
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|22522877|gb|BU081688.1|BU081688
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|20812913|gb|BQ297391.1|BQ297391
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|7028945|gb|AW458728.1|AW458728
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|120495789|gb|EH223956.1|EH223956
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|12689187|gb|BG155523.1|BG155523
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGGAGCACGGGAA-GACAT
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCA-GGGAAAGACAT
EST: gi|120529139|gb|EH257273.1|EH257273
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|120531755|gb|EH259888.1|EH259888
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|10844582|gb|BF067838.1|BF067838
EST:     CCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|10844694|gb|BF070942.1|BF070942
EST:     GCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: GCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|6914782|gb|AW396312.1|AW396312
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|22523177|gb|BU081988.1|BU081988
EST:     GCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: GCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|6134837|gb|AW133230.1|AW133230
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCATGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|9205303|gb|BE331527.1|BE331527
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCANGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
EST: gi|20813349|gb|BQ297827.1|BQ297827
EST:     CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAG                         CCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA
genomic: CTGATGCCACCACTGTAGTTACAGGCATAGTTGGTTGTGCAGGATTAAAGgtaacacaaa ... ttttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatattagttggcatgtattaaacttaaagatgctattggttattttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAAGAGACAATGATTGCGGGAGCCCCTTTTGTTCTTCCTCTTGCTCACAAAC
                                          ttattttcttc  CT-rich tract
               atgtattaaacttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttcatagttctgctgctattttcgtattggtgaaaatcttagcaatattagttggcatgtattaaacttaaagatgctattggttattttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAAGAGACAATGATTGCGGGAGCCCCTTTTGTTCTTCCTCTTGCTCACAAAC

- - - - - - -ctgctgc
- - - - - - - - - - - - - - -attggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgcta