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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgctgggtcttgtgtaacatggctcccttttgtaatagtgaaatggtgttgtgttccttaatgatatagtgatggttttctgtgaatgggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGCAACTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC

Basic information

species Glycine max
transcript GLYMA04G35730.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G35730.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv17s0000g08560.t01 (Vitis vinifera), 3'ss of exon 7
--tcttgctgggtcttgtgtaacatggctcccttttgtaatagtgaaatggtgttgtgttccttaatgatatagtgatggttttctgtgaatgggcc--tgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGCAACTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC
    ||  || |  |||  |   |    |   |  |||  |  || | |  |  |   ||||   |  || | |  |   | ||  |  | |||     ||||||| |||||||||||||||||||||||||| || ||||||||||| ||||| || ||||| |||||||| ||||||||||| |  |||||  |||||||||
ttctttagtgagagttgactccta-aatttgttgctgtctt--tgtattattcatcaattccgacaaaatttggcta-aatatttagaaattggattgatgcagGTCTCTTATATGATATTGCAAAGGGTATCCCCAGTTACCCACTCTGTGGGTAATTGTGTTAAGCGGGTGGTGGTCATTGTTACTTCTGTTCTCTTCTTCC

upper sequence: GLYMA04G35730.1 (Glycine max), 3'ss of exon 7
lower sequence: EDP02676 (Chlamydomonas reinhardtii), 3'ss of exon 8
tcttgctgggtcttgtgtaacatggctcccttttgtaatagtgaaatggtgttgtgttccttaatgatatagtgatggttttctgtgaatgggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGCAACTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC
 |  | |  | ||| |       |  |  |     |       |  |   |       ||  ||    |             |      || ||   ||||| || || |||||  |     | || || || || || |||  | | |||||||| |||||||||||||||||||| | |  ||| ||  | |||||||
acgggtttcgccttttccgttccgcttttcccgctttcccccaaccttcaggcactcaccccaaccccaacccacacccaccccacacttgcgcgcacagGTGTCGTACATGATCCTATCGCGCGTGTCGCCGGTGACGCACAGCATCGGCAACTGCGTGAAGCGGGTTGTGGTCATCGCGGCCTCGGTGCTGTTCTTCC

upper sequence: GLYMA04G35730.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 7
tcttgctgggtcttgtgtaacatggctcccttttgtaatagtgaaatggtgttgtgttccttaatgatatagtgatggt-tttctgtgaatgggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGCAACTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC
                                                     || | |  | |||  |   |   | | ||||||      |   ||||||| || || |||||||||||||||||||| || ||||| |||||||| || |||||||| ||||| ||  | || ||||| |  || |||||||||||  
-----------------------------------------------------gtttgctctgatgcaagtttagcgttgtttctgaaggacgatttgcagGTGTCCTACATGATATTGCAAAGGGTATCGCCGGTTACGCACTCCGTTGGAAACTGTGTCAAGCGCGTGATTGTGATTGTAACTTCAGTCATCTTCTTTA

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|31469095|gb|CD411123.1|CD411123
EST:     TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAA                         GTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
genomic: TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAAgtgagttttg ... gggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
EST: gi|10256147|gb|BE823913.1|BE823913
EST:     TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAA                         GTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
genomic: TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAAgtgagttttg ... gggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
EST: gi|10846064|gb|BF069053.1|BF069053
EST:     TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAA                         GTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
genomic: TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAAgtgagttttg ... gggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
EST: gi|8403936|gb|BE059570.1|BE059570
EST:     TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAA                         GTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
genomic: TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAAgtgagttttg ... gggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
EST: gi|192301535|gb|FG998443.1|FG998443
EST:     TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAA                         GTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
genomic: TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAAgtgagttttg ... gggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
EST: gi|16346350|gb|BI971945.1|BI971945
EST:     TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAA                         GTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
genomic: TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAAgtgagttttg ... gggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
EST: gi|58016526|gb|CX703268.1|CX703268
EST:     TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAA                         GTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC
genomic: TTTACATCAGATCTCTTCTTGCTGCACTCTGTTTCCATGCGTATCAACAAgtgagttttg ... gggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtgttgtgttccttaatgatatagtgatggttttctgtgaatgggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGCAACTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC
             ccttaat  putative branch site (score: 4)
               ttaatgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgctgggtcttgtgtaacatggctcccttttgtaatagtgaaatggtgttgtgttccttaatgatatagtgatggttttctgtgaatgggcctgcagGTTTCTTATATGATATTGCAAAGGGTATCACCTGTTACCCACTCCGTGGGCAACTGTGTGAAGCGGGTTGTGGTCATTGTGAGCTCTGTCATCTTCTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-cttgctg
- - - - - tcttgtg
- - - - - - - - - - - - -ctccctt
- - - - - - - - - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgtg