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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatactgtgtaccttctataattgttcaaatgactatataaatctactttgtcattgctgctttttatttattttttcccactttgtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTA

Basic information

species Glycine max
transcript GLYMA09G38550.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtatatactgtgtaccttctataattgttcaaatgactatataaatctactttgtcattgctgctttttatttattttttcccactttgtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTA
    |||| |||||   |     | || |  |||   | ||||| ||  | ||        | |||  | |  | |  |    ||  ||| |   | | |||| || || || || || || || |||||| | ||||||||||||||||| || |||||||||||||| ||| ||||||| |||||||| || || || ||
gtgggtatctactggcaaaacaatttagtacttctttttactatcta--tgtagaaaactgtagcttttctcaactagtgacctc--actgttactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTA

upper sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatatactgtgtaccttctataattgttcaaatgactatataaatctactttgtcattgctgcttttt-atttattttttcccactttgtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTA
         || ||   |||  |  | |   ||  |   |  |  | |      |  | |||   |  | || |||  | |   |  ||   ||| |||| |||||||| || || || ||||||||||| |||||||| |||||||| || |||||||||||||| ||| ||||||| |||||||| ||||| |||||
---------gtatatactcttaagctttatgaaacatcgtgaatctttcagcgttagtagctatatactgatatatactattttatctttccttatcagGTGTAAGAAATGCCGCACAAAGGAAGCTTTTCGATGAGCTCGGTATTGTAGCAGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGCATGCTTTA

upper sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ31498 (Selaginella moellendorffii), 3'ss of exon 4
gtatatactgtgtaccttctataattgttcaaatgactatataaatctactttgtcattgctgctttttatttattttttcccactt-tgtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTA
                                 | |  |      | | ||| |  | ||||  |  | | | |      | |||      |    |||||||||||||||| || || ||||||||||| |||||||| ||||| |  || |  ||    || || ||    |||||     |||| || || || ||
--------------------------------gtaaacaagcttgttttcttagctagtgct--tcctcactcacacacacacacacacacacccacagGAGTAAGAAACGCTGCGCAAAGGAAGCTTTTTGATGAGCTCGGTATCGCAGCAGCCGACTCCCCGGTGGACGCCTTCACTTTTCTGGGCCGGATCCTCTA

upper sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ38651 (Selaginella moellendorffii), 3'ss of exon 4
gtatatactgtgtaccttctataattgttcaaatgactatataaatctactttg-tcattgctgctttttatttattttttcccactt-tgtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTA
                   || |   | |    |   ||  ||   || | |   ||| |  | |     |   |      | |||      |    |||||||||||||||| || || ||||||||||| |||||||| ||||| |  || |  ||    || || ||    |||||     |||| || || || ||
------------------gtaaacaagcttgttttcttagctagtgctccctcactcactcatacacac-acacacacacacacacccacacacgcacagGAGTAAGAAACGCTGCGCAAAGGAAGCTTTTTGATGAGCTCGGTATCGCAGCAGCCGACTCCCCGGTGGACGCCTTCACTTTTCTGGGCCGGATCCTCTA

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|6848648|gb|AW350938.1|AW350938
EST:     GTGAATCTGAGCTTATTGATGAGAATGCNNNNN                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: GTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|17022222|gb|BM093256.1|BM093256
EST:     TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|193552359|gb|FK508990.1|FK508990
EST:     GAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: GAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|26268343|gb|CA819406.1|CA819406
EST:     TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|13563422|gb|BG551651.1|BG551651
EST:     TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|38191106|gb|CF920312.1|CF920312
EST:     TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|31468516|gb|CD410544.1|CD410544
EST:     TCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|9259122|gb|BE347269.1|BE347269
EST:     TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|24206105|gb|BU965358.1|BU965358
EST:     TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|8283037|gb|BE020598.1|BE020598
EST:     TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|208234389|gb|GE033292.1|GE033292
EST:     TAGCCATCCTCTGTACCGTGAGTCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAG
EST: gi|15813110|gb|BI785385.1|BI785385
EST:     TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|19938293|gb|BQ081652.1|BQ081652
EST:     TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctactttgtcattgctgctttttatttattttttcccactttgtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTA
                    ctttttatttattttt  CT-rich tract
                  tgctttttatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatactgtgtaccttctataattgttcaaatgactatataaatctactttgtcattgctgctttttatttattttttcccactttgtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG