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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattataaccagcactaagtaaaaggctactttaagattatttatggtgaatttatatctatgattgcagttggcttggaaactcctatagcatgtttcactaaagatattattaacaagcactctaatttcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAGGGGCAGTTTGTACGTCAACATGATCATCCTGTCGCTGAGGCTGGTGGTG

Basic information

species Glycine max
transcript GLYMA07G05530.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05530.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G179024_T01 (Zea mays), 3'ss of exon 7
gtattataaccagcactaagtaaaaggctactttaagattatttatggtgaatttatatctatgattgcagttggcttggaaactcctatagcatgtttcactaaagatattattaacaagcactctaatttcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAGGGGCAGTTTGTACGTCAACATGATCATCCTGTCGCTGAGGCTGGTGGTG--
                                             |    || | |  |      ||  | || | |  ||   |  |||  ||  |   |    |  | | ||| ||      | ||   || | |  |||||||||| || |||||||||  ||| ||||||||||| || ||||| ||||| |||||||| |||||| || ||        |   || ||| | |     
--------------------------------------------gtaagcaactaa-gtgcgcatttttatttcgatccga--tttttatgccacctacta--ggacctgtgattcacgc---ttttacaatcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATC--CAAGGAAGCTAGGGTCCAG

upper sequence: GLYMA07G05530.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G367834_T01 (Zea mays), 3'ss of exon 7
gtattataaccagcactaagtaaaaggctactttaagattatttatggtgaatttatatctatgattgcagttggcttggaaactcctatagcatgtttcactaa-agatattattaacaagcactctaatttcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAGGGGCAGTTTGTACGTCAACATGATCATCCTGTCGCTGAGGCTGGTGGTG
                                             |  |  | | || |  |   || || |    |   |  |||     |  |   | ||||  | || | ||| |      || |   ||| | |  ||||||| || || |||||||||  ||| ||||||||||| || ||||| ||||| |||||||| |||||| || ||        |   || ||| |     
--------------------------------------------gtaatcgactgat-tgcacattttcattccaatccaattctc----ggtgtcacttactaggacatgtgatttatgc---ctttgcattcatttgcagGTTCGGTACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTCCGTCAAGATCATAGCATC--CAAGGAAGCTAG-----

upper sequence: GLYMA07G05530.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv15s0048g02540.t01 (Vitis vinifera), 3'ss of exon 8
gtattataaccagcactaagtaaaaggctactttaagattatttatggtgaatttatatctatgatt-gcagttggcttggaaactcctatagcatgtttcactaaagatattattaacaagcactctaa--tttcttg-tatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAGGGGCAGTTTGTACGTCAACATGATCATCCTGTCGCTGAGGCTGGTGGTG---
                                          |||   || ||| || || | | || || | | ||    ||     ||||  | | | || | ||| | ||   |      | |  ||  ||||||   | |||||||||| |||||| ||||||| || ||||||||||| || || ||||| || ||||||||   || ||| |  ||  ||| | ||    | | || ||   
-----------------------------------------gttagcttggattcatctccaagttttgctgatagcgccaaa---tttatacaaggataca-tgaagttgttccaattgtttaatgcaagttttcttaacacagGTTCGATACCAAAGCAGGAAAAGGCTTGCAGAGCAGCGTCCCCGAGTGAAAGGACAGTTTGT---TCGACAAGTGCAGACTGACACTCCAACCGCTGATGGGT

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|254344405|gb|GR855383.1|GR855383
EST:     TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAG                         GTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG
genomic: TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAGgtattataac ... tcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG
EST: gi|23063602|gb|BU578576.1|BU578576
EST:     TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAG                         GTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG
genomic: TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAGgtattataac ... tcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG
EST: gi|22933025|gb|BU550164.1|BU550164
EST:     TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAG                         GTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG
genomic: TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAGgtattataac ... tcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG
EST: gi|208149147|gb|GD945947.1|GD945947
EST:     TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAG                         GTTCGATATCAA
genomic: TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAGgtattataac ... tcttgtatagGTTCGATATCAA
EST: gi|22931476|gb|BU548615.1|BU548615
EST:     TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAG                         GTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG
genomic: TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAGgtattataac ... tcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG
EST: gi|16995690|gb|BM085062.1|BM085062
EST:     TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAG                         GTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG
genomic: TGCTAGTGAAGTTTCGACTGAAGCGGAAAGAGAGATGCTTCGAGAAAAAGgtattataac ... tcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatagcatgtttcactaaagatattattaacaagcactctaatttcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAGGGGCAGTTTGTACGTCAACATGATCATCCTGTCGCTGAGGCTGGTGGTG
                                           tttcttgt  CT-rich tract
          tttcactaaagatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattataaccagcactaagtaaaaggctactttaagattatttatggtgaatttatatctatgattgcagttggcttggaaactcctatagcatgtttcactaaagatattattaacaagcactctaatttcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAGGGGCAGTTTGTACGTCAACATGATCATCCTGTCGCTGAGGCTGGTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG