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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgaatagctgctgcactctctgttttgattcttgttgttgttattgttttaattgataactgagcatttgtgtggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC

Basic information

species Glycine max
transcript GLYMA04G05580.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 3
--------------------tcttgaatagctgctgca----ctctctgttttgattcttgttgttgttattgttttaattgataactgagcatttgtgtggatg-ttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
                    |   |||    |   | |    |  | |||||    | |||   ||  ||||   || || | ||  ||  | ||  ||||  || |||  | | || |    |||||| || ||||| ||||| ||||| ||||| || ||||| || || |||||||| |||||||| || ||||| ||||| ||||| ||||||||||| ||
gtatctatgcttacggtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcg-tatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA04G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 3
tcttgaatagctgct-gcactctctgttttgattcttgttgttgttattgttt-taattgataact-------gagcatttgtgtggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
    | ||   ||||     | | ||| | |   ||||     | |||  ||| | ||| ||  ||       || ||||         ||  |  |  || |    ||||||||||||||| ||||| ||||| ||||| || || || || ||||| ||||| |||||||| ||||| || || || ||||| ||||| ||||| ||
----gtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC

upper sequence: GLYMA04G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 3
tcttgaatagctgctgcactctctgttttgattcttgttgttgttattgttttaattgataac-tgagcatttgtgtggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
    | ||   ||  | |  ||       | |   | ||||  ||  ||| |||  | | ||| | | |   || |||    || | ||  |||| ||   ||||||||||||| ||||| ||||| ||||| || || || || ||||| ||||| |||||||| ||||| || || || ||||| ||||| ||||| ||
----gtatgtgtgtaggaa-cttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgc---ttctgttttttcttag-

upper sequence: GLYMA04G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------tcttgaatagctgctgcact-ctctgttttgattcttgttgttgttattgtttta-attgataac--tgagcatttgtgtggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
                                        | |  || | | |||      | ||| ||   | |||||  | | |  | ||   | || ||    | | ||      |    ||| | ||| || | |  |||||| |||||||| ||||| ||||| ||||| || ||| |||| ||||||||||| |||||||| || |||||||| ||||||||||||||||| || ||
gtaagtgaagtatttcctttgagaacacattctatacataccttcattgtttctgtctagttttgtattttcttttgtttgtttcaaagcttagtactgttactcttaaacaacctcatattggttttgttatttatcattagGTTTCGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATTATTCCATTCTGCAAGGGTCTTGATGTGATCCAGCAAGCTCAATCTGGAACTGGAAAGACCGC

upper sequence: GLYMA04G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.1 (Arabidopsis thaliana), 3'ss of exon 3
-----tcttgaatagctgctgca----ctctctgttttgattcttgttgttgttattgttttaattgataactgagcatttgtgtggatg-ttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
     |   |||    |   | |    |  | |||||    | |||   ||  ||||   || || | ||  ||  | ||  ||||  || |||  | | || |    |||||| || ||||| ||||| ||||| ||||| || ||||| || || |||||||| |||||||| || ||||| ||||| ||||| ||||||||||| ||
gtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcg-tatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA04G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g01000.t01 (Vitis vinifera), 3'ss of exon 2
----tcttgaatagctgctgcactctctgttttgattcttgttgttgttattgttttaattgataactgagcatttgtgtggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
    || | |||  ||||   | | | | || | |||  |||| |          || || || || |||  |  ||   |   | | ||    ||||  | ||||||||||||||||||||||||||| ||||| || |||||||| |||  ||||||||||||||| |||||||||||||| ||||||||||||||||| ||
tgcatcataaatcactgcctga-tttttattgttatttatgttttga--gccaccttcatggaaaaatgaaaagctgaaagttggatctaac-tttcttggtagGTTTTGAGAAGCCCTCTGCAATTCAGCAAAGAGGTATTGTTCCCTTCATCAAGGGGCTTGATGTAATTCAGCAAGCACAGTCTGGAACTGGAAAAACAGC

upper sequence: GLYMA04G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S136_29V6.4 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------tcttgaatagctgct--------gcactctctgttttgattcttgttgttgttattgttt--------taattgataac--tgag---catttgtgtggatgttgtattact--tctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
                                                              | | | |  || ||        ||| | | |   | |   |   || |  | || ||||        ||  | |||||  || |   ||||  |       |  | ||  |  | |  | ||||||||||||||| ||||| ||||||||  | || ||||| || ||   |||||| || ||||||||||||||||||||||| || ||||| || |||||
gtaaggtcttcacctaatttcattgatattctaatcgaatgcaattcatttattcatttatacataagttactcctccttgggcgcatttttttagtaggcacgcattatcttcatagtttccttccaataggttataacattgcgatccattcctactagcttaattttgttaatttttgcagGTTTTGAGAAGCCATCTGCTATTCAACAGCGTGGTATTGTACCCTTTACCAAGGGCCTCGATGTTATTCAGCAAGCACAATCAGGGACTGGCAAGACTGC

upper sequence: GLYMA04G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 3
tcttgaatagctgctgcactctctgttttgattcttgttgttgttattgttttaattgataactgagcatttgtgtggatgttgtattactt---ctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
  ||| ||   |  ||    || |||  || |  | |||         |    ||||||        |   ||     || |  |  |  ||   |||   ||||||||||||||| ||||| || |||||  | || || ||||| |||  |||||| |||||||| ||||| ||||| || ||||||||||| || || ||
--ttgcatgttttgtgggtgct-tgtggtgttcgtagtttcctaccgagaaccaattgaaccgcactctgctgctctaatctcattctggttgacctgtacagGTTTTGAGAAGCCATCTGCTATCCAACAGCGTGGAATCGTTCCCTTCACCAAGGGTCTTGATGTCATTCAACAAGCCCAGTCTGGAACTGGCAAGACAGC

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|192332026|gb|FK026320.1|FK026320
EST:     TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATG                         GTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
genomic: TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATGgtatgttcat ... ttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
EST: gi|209718869|gb|BW669056.1|BW669056
EST:     TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATG                         GTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
genomic: TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATGgtatgttcat ... ttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
EST: gi|213610635|gb|DB961110.1|DB961110
EST:     TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATG                         GTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
genomic: TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATGgtatgttcat ... ttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
EST: gi|209717675|gb|BW671519.1|BW671519
EST:     TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATG                         GTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
genomic: TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATGgtatgttcat ... ttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
EST: gi|254319672|gb|GR830804.1|GR830804
EST:     TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATG                         GTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
genomic: TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATGgtatgttcat ... ttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
EST: gi|209707836|gb|BW683732.1|BW683732
EST:     TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATG                         GTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
genomic: TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATGgtatgttcat ... ttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
EST: gi|298185063|gb|HO030276.1|HO030276
EST:     TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATG                         GTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
genomic: TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATGgtatgttcat ... ttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttttaattgataactgagcatttgtgtggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
           tgataac  putative branch site (score: 2)
                                         ttacttct  putative PPT
     tttaattgataact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgaatagctgctgcactctctgttttgattcttgttgttgttattgttttaattgataactgagcatttgtgtggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - -tagctgc
- - - - - - - - cactctc
- - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgta