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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcctactattttaatcttatgagattgctgtatagtgggtcatgatttctcctaaattattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT

Basic information

species Glycine max
transcript GLYMA07G03930.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------gttcctactattttaatcttatgagatt-gctgtatagtgggtca--tgatttctcctaa--------attattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
                                                |     | |    ||  |||   |||  || || |  ||  ||   ||| ||  | | |        |   |    |||    |  |||| ||||||||||| ||| ||||||||||||| |||||| |||| ||||||||||| || |||||||| || |||
gtacaatactcaacagctgaaattgaataaataaataaaatcatggcatcatggcaaagagaaaattaaaggatgagcagtgtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT

upper sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------------gttcctactattttaatcttatgagattgc-tgtatagtgggtcatgattt---ctcctaaattattcc------caatgatatt-----cagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
                                             ||| || ||  | |    || |   ||||| |  || | | || |    ||   | ||  || |||| |      || |  ||||      |||| ||||||||||| ||| ||||||| ||||| |||||  |||| ||||||||||| |||||||| || || || 
gtatctgttacgcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaccgttgctccttatctgtatttcttgaattgcatccatcg-gtgttacacctttaacaccagaagtattacaccttacacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTCTGTGAGGTGGAGACG

upper sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 6
------------gttcctactat----tttaatcttatgagattgctgtatagtgggtc---atgatttctcctaaa--ttattccca-atgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
            || | || |||     ||||| ||  |      |      | |  |     |  ||  |  || |  |||| |    ||  | |  |||| ||||||||||| ||| ||||||| ||||| |||||  |||| ||||||||||| || ||||| || || |||
tgttttagttttgtacatattatgcaacttaattttccgcagcaacgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT

upper sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
----gttcctactattttaatcttatgagatt----gctgtatagtgggtcatgatttctcctaaattattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
    || ||| ||   |   ||||| || | |       || || ||  | || |||   |  ||  |||        |  |||||||||||||||| || ||| |||||||||||||||||||| |  |||||||||||||||| |||||||||||||||
gcatgtacct-ctgaatacctcttacgaaaattaacatggtttattgttttatcattctactaaagatatctgttgaaac-ttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT

upper sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 6
-----gttcctactattttaatctta--tgagattgctgtatagtgggtcatgat-ttctcctaaattattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
     | || |  |||||   ||||     | | |  |||    |   || | || ||||  |||  | || ||||   | || |||||||||| || || ||| |||| ||||||||||||||| |  ||||||| ||||| ||||||||||||||||||
gcatggatctt--tatttacctcttgatcaaaacttatgtccgttttatctttatgttctaataagctttttccaa---tttttagGGTAACATCGCCAGGTGGCTGAAAAAAGAAGGTGATAAAGTTGCTCCTGGGGAAGTACTCTGTGAAGTTGAAACT

upper sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 7
gttcctactattttaatcttatgagattgc------tgtatagtgggtcatgatttctcctaaattattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
|    | |  || | |   ||||||| | |      ||   | |      |  | |     ||  | ||    || | || |||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||| |||
gcatgtgcctttctgaagctatgagaatacaaaccatgctcaatttactgttttatgattgaatgttttgtttatcaaatgcagGGTAACATTGCGAGGTGGTTGAAGAAAGAGGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAGACT

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|27809080|gb|CB063502.1|CB063502
EST:     CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAG                         GGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGT
genomic: CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAGgttcctacta ... tgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGT
EST: gi|213616567|gb|DB965737.1|DB965737
EST:     CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAG                         GGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGT
genomic: CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAGgttcctacta ... tgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGT
EST: gi|19269403|gb|BM885659.1|BM885659
EST:     CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAG                         GGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGT
genomic: CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAGgttcctacta ... tgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGT
EST: gi|209714755|gb|BW654105.1|BW654105
EST:     CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAG                         GGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGT
genomic: CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAGgttcctacta ... tgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattgctgtatagtgggtcatgatttctcctaaattattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
                            tcctaaa  putative branch site (score: 2)
                               taaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcctactattttaatcttatgagattgctgtatagtgggtcatgatttctcctaaattattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG