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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaattataactataagttactggttatatatggcatactcttgacatttatgcagatggtctaaatttgagcgtacatgattaaaaatgtaaaattctggtcataatttgttcgttgtactcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG

Basic information

species Glycine max
transcript GLYMA11G05340.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 5
gtgtgaattataactataagttactggttatatatggcatactcttgacatttatgcagatggtctaaatttg-agcgtacatgattaaaaatgtaaaattctggtcataatttgttcgttgtactcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG
          |   | |    | ||     ||||    |  || |  | |||   ||    |   ||  | || |   ||| ||  || | |   | |      || ||  ||| ||   |||  | |  || ||||||||||||| ||||| ||||| ||||| || || |||||||| ||||||||||||||||| |||
---------gtgtgtttgccctcctatgattataaaataacctatcaaaatt---gccatggccttacttctgtaaattacttgcgtatagaaagatagcaactgttatgctttatttactgt-ttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgaattataactataagttactggttatatatggcatactcttgacatttatgcagatggtctaaatttgagcgtacatgattaa-aaatgtaaaattctggtcataatttgttcgttgtactcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG
              ||  ||||||  ||   |  |||  |    ||     || | || ||    | || |  ||  |   | || || ||||||||  |||   |  | | | |   | | |  |       |||| |||||||| || || ||||||||||||||||| || ||||| |||||||| ||||| || |||
-------------gtaacagttac-agtggcagttggtgttaatttt---cttttacatattacttgaaatgcagtttgtcttatcaataaatgtaactttcaactactcaatgga--ggtttttttcccaacagATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAG

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgaattataactataagttactggttatatatggcatactcttgacatttatgcagatggtctaaatttgagcgtacatgattaaaaatgtaaaattctggtcataatttgttcgttgtactcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG
||| || |||  ||||     |  || |  |  ||     | |        | ||   |    |   | |||  |  |  ||  | |  |   |    || |  |||  ||   |   || |    || ||||||| |||||||| ||||| |||||||||||||||||||| ||||||||||||||||| || || |||
gtgagatttactactac----tgttgatcttgaat----catttgaagggctgattgtgccatttacattttttgtatttattttaattatcattttgttttactcagtatacttctattat----ttatgtagATCTTTCGCAAGGAACCATTCTTTTATGGTCATGACAATCATGATCAGCTTGTCAAGATTGCCAAG

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgtgaattataactataagttactggttatatatggcatactcttgacatttatgcagatggtctaaatttgagcgtacatgattaaaaatgtaaaattctggtcataatttgttcgttgtactcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG
||  | | | ||  | ||  ||     || |  |||  | | || |||     ||        ||  |   ||| |   || | ||  |||  | |    | ||  |  |||||||   |         ||||||| || ||||| || || || || ||||||||||||||  |||||||||||||||| || ||||||
gtaaggaatgta-ttctatattttgaattttgcatg-tacattcctgaagcccatt------atcccataatgaaccagca-ggttgcaaacctga----caggctaccatttgtttaat---------tgtagATTTTCCGCAAGGAGCCGTTTTTCTATGGTCATGACAATTATGATCAGCTTGTCAAGATCGCTAAG

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
gtgtgaattataactataagttactggttatatatggcatactcttgacatttatgcagatggtctaaatttgagcgtacatgattaaaaatgtaaaattctggtcataatttgttcgttgtactct----tttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG
                                                                                         | | |    | ||| ||||   |  ||  |    | |     ||   ||||||||||||||||||| ||||||||||| |||||||| || |||||||| || || || || |||
--------------------------------------------------------------------------------------gtgagtcttttgt-ctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG

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|207689746|gb|GD670949.1|GD670949
EST:     ATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG                         ATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT
genomic: ATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATGgtgtgaatta ... tcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT
EST: gi|208215776|gb|GE008544.1|GE008544
EST:     GAGCCTTGGCTGTCTATGTTTGCTGGAATG                         ATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT
genomic: GAGCCTTGGCTG-C-ATGTTTGCTGGAATGgtgtgaatta ... tcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT
EST: gi|10233590|gb|BE802478.1|BE802478
EST:     ATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG                         ATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT
genomic: ATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATGgtgtgaatta ... tcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT
EST: gi|38193563|gb|CF922769.1|CF922769
EST:     ATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG                         ATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT
genomic: ATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATGgtgtgaatta ... tcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT
EST: gi|20813341|gb|BQ297819.1|BQ297819
EST:     ATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG                         ATATTTCGCAAAGAACC
genomic: ATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATGgtgtgaatta ... tcttttgtagATATTTCGCAAAGAACC
EST: gi|214009784|gb|DB986911.1|DB986911
EST:     ATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG                         ATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT
genomic: ATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATGgtgtgaatta ... tcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgattaaaaatgtaaaattctggtcataatttgttcgttgtactcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG
                                          tactctttt  CT-rich tract
     ttaaaaatgtaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgaattataactataagttactggttatatatggcatactcttgacatttatgcagatggtctaaatttgagcgtacatgattaaaaatgtaaaattctggtcataatttgttcgttgtactcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT