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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattggtcttttgtttatgtcctgcttttactgatttattataagctgctattgtgttttatttcacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA

Basic information

species Glycine max
transcript GLYMA10G29000.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 5
cattggtcttttgtttatgtcctgcttttactgatttattataagctgctattgtgttttatttcacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA
        ||||    | | | |  ||| |||| |||  | |||    || | ||   | | |  |||  |      ||||  || | | || |    ||  ||| ||||| || || || ||||| || ||||||||||| ||||| || |||||| | ||||||||||| ||||| ||||||||  | ||||| || |
-------gttttaaacaagacttcttttaactgcttttctgtaa----ctgtggtaactaactaaacatgt------ttatctttggctgttat----agACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGACGAGGAAGTTCTCACTGATGCATGCTGGGCCCTGTCATACTTATCTGACGGCA

upper sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 5
cattggtcttttgtttatgtcctgcttttactgatttattataagctgctattgtgttttatttcacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA
            ||    | |  |  ||   | |||  || |   |||  |  |||     || |  | |  | |  |||| |||||  | || |   ||  ||| ||||| || || || ||||| || ||||||||||| |||||||| |||||| | |||||||| || |||||  |||||||  | ||||| || |
------------gtcgtagacaagacttctttaattgctttt---ctgtaacagtg----gttactaaataaacatgttattctttgactgttac---agACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA

upper sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 5
--cattggtcttttgtttatgtcctgcttttactgatttattataagctgctattgtgttttatttcacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA
   | ||||||| ||   ||| | || |     |  |      ||| |||   |  | | |||||| |    |  |   |  |  |   |||| ||   |||   || ||||| ||||| || ||||  |||||||| || || || |||||||| || || ||||||||||||||||||||||| ||||||||||||||||
tgtaatggtcttatggc-atgccttgttgaatgttgtaggccgtaacctgtattgttatgttatttgattaatt-tttttcctcttgaattttgttgcacagACAAAGCCTGCTCTTCCAGCACTTGAGCGTCTTATTCACTCAAATGATGAAGAGGTGTTAACTGATGCATGTTGGGCACTGTCTTATCTTTCTGATGGTA

upper sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0183g00210.t01 (Vitis vinifera), 3'ss of exon 4
cattggtcttttgtttatgtcctgcttttactgatttattataagctgctattgtgttttattt--cacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA
    | ||        ||  |||  | ||  | |||| || | ||  | ||     ||||||      || |     ||    ||    |  ||||  | ||   || ||||| ||||| |||||||  |||||||| || ||||| |||||||| ||  | |||||||| |||||||||||||| || |||||||||||||
-tcagttcaaacagagattaccttttgttttttattttttctgaga-gttaacagattttatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCGTGTTGGGCACTGTCTTACCTTTCTGATGGTA

upper sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0183g00040.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------------------------------------cattggtcttttgtttatgtcctgctt--ttactgatttattataagctgctattgtgttttattt--cacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA
                                                               |        |  ||| |      | ||   | ||| ||| ||       | ||     ||||||      || |     ||    ||    |  ||||  | ||   || ||||| ||||| |||||||  |||||||| || ||||| |||||||| ||  | |||||||||||||||||| |||| || |||||||||||||
gttgaagattggacaaaggattataacatctgaacctcgctgaagttaccatagataaatggtccccttctatcagttcaaacagagattaccttctgttttttttctgagagttaacagattttatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCATGTTGGGCATTGTCTTACCTTTCTGATGGTA

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|19934371|gb|BQ079401.1|BQ079401
EST:     GGACACTTTCAAACTTCTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAG                         GTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAA
genomic: GGACACTTTCAAACTTCTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAGgtataaaaat ... ttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAA
EST: gi|254341052|gb|GR854780.1|GR854780
EST:     GGACACTTTCAAACTTCTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAG                         GTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAA
genomic: GGACACTTTCAAACTTCTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAGgtataaaaat ... ttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAA
EST: gi|19935944|gb|BQ080652.1|BQ080652
EST:     GGACACTTTCAAACTTCTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAG                         GTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAA
genomic: GGACACTTTCAAACTTCTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAGgtataaaaat ... ttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAA
EST: gi|10847521|gb|BF070194.1|BF070194
EST:     GGACACTTTCAAACTTTTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAG                         GTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATACATACGAACGATGAA
genomic: GGACACTTTCAAACTTCTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAGgtataaaaat ... ttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAA
EST: gi|19935942|gb|BQ080651.1|BQ080651
EST:     GGACACTTTCAAACTTCTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAG                         GTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAA
genomic: GGACACTTTCAAACTTCTGCAGGGGCAAGCCACAGCCTCCTTTTGATCAGgtataaaaat ... ttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctattgtgttttatttcacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA
                                ttatactttgtttttt  CT-rich tract
                           atacattatactttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattggtcttttgtttatgtcctgcttttactgatttattataagctgctattgtgttttatttcacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - -tcctgct
- - - - - - - - - - - - - - - - - - - - - aagctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catacat