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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgacatctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAG

Basic information

species Glycine max
transcript GLYMA15G02640.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 9
atcgacatctttcatttctgactttgtttgggggatttcttcttgtat--gttataaatt-cttaaagcttcatctcatttcactaatgacttgttttgt-cagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAG
    || | | |   |||||    || ||     | | | | |  |||  ||  || | | ||| ||   ||||   | | |  |  |   ||  ||| | ||||| ||||| || || |||||||||||||| |||||||||||||| |||||||| ||||| ||||| |||
--aaacttttatatattctgcagctgattctaatactacgtatcatataagtggtatactgcttgaaatgtcatt--agtccgttgctccttttctttcttcagTTATGGGATATAAACATGGATTCAGGCCCAGTTGCAACTTTCCAAGTTCATGAATATTTAAGACCTAAG

upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 9
atcgacatctttcattt-ctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAG
   ||  | |   |||| |||      |   || | | | ||  || | | | | | |||       ||    |||| | | |  |  | | || |  ||| | ||||| ||||| ||| | || || || |||||||| |||||||||||||||||||| || ||||||
ggtgatttatactattttctgtagccatagaggtgttatttttctgca-gctgttacttcgatgtttttgtgttcatataaattttttccttttgttccagCTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAG

upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 9
atcgacatctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaa-gcttcatctcatttca-ctaatgact--tgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAG
        |||| |      |     ||| || | | |   ||| | || || | ||  |||   |||  |  | |||| |  |||    |  |||||   |||||||||||  | || |||||||||||||| ||||||||||| ||||||||||| || ||  | || |||
----tagactttgaggatcaaggaacttttggtgctctgcccttttgtgataaatatgtttatctgctagaaataattttagttaaccgtttttgtttctccagTTGTGGGATCTAAACATGGATTCAGGCCCAGTTGCAACTTTTCAGGTTCATGAATACTTACGTCCTAAG

upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
---------------atcgacatctttcatttctgactttgtttgggggatttc--ttcttgtatgttataaattcttaaagcttcatctcatttcac-taatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAG
                |   |||| |||| |  |||  |    | |  | | ||  |   ||  |   ||   ||| |  |   | | || |   ||  | |||  ||   | | ||||| |||||||| || |||||  |||| || || |||||||||||||||||||| ||||||| ||| |||
gtccatattttcactgttttcatcattcaata-tgatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacat-gccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG

upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 9
atcgacatcttt-catttct--gactttgtttgggggatttcttcttgtatgtta---taaattcttaaagct-tcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAG
    |  ||||| |||  |   || ||  | ||    |||| |  || |   |||   ||    ||| ||    |||    | ||   |  | ||||| ||| |||||| ||||||||||||||||| |||||||| ||| |||| |||||||||||||| ||||| ||||| |||
----aggtctttgcatcacaaggaattgatatgtactatttgtctttctggcttaagttagggccttgaactaatcactggaatttgtt--ttacttgcttt-tcagTTATGGGACATTAATATGGACTCAGGCCCAGTTTCAACCTTCCAGGTTCATGAATATTTAAGACCTAAG

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|208032405|gb|GD828160.1|GD828160
EST:     TTGGGAAGGATGGAAGATACATACTAAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTACAAAGGCCCCGTTGCAACTTTCCAGGTT
genomic: TTGGGAAGGATGGAAGATACATACTAAGTCGTGATTACATGACTTTAAAGgtttggaatt ... gttttgtcagTTGTGGGACATTAATATGGATT-CA--GGCCCCGTTGCAACTTTCCAGGTT
EST: gi|193343412|gb|FK308190.1|FK308190
EST:     TTGGGAAGGATGGAAGATACATACTAAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCTAACTTTTCCTTAGGT
genomic: TTGGGAAGGATGGAAGATACATACTAAGTCGTGATTACATGACTTTAAAGgtttggaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGC-AAC-TTTCC--AGGT
EST: gi|11274020|gb|BF324388.1|BF324388
EST:     TTGGGAAGGATGGAAGATACATACTAAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCC
genomic: TTGGGAAGGATGGAAGATACATACTAAGTCGTGATTACATGACTTTAAAGgtttggaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAG
                                 cactaat  putative branch site (score: 2)
                                          cttgtttt  putative PPT
     tataaattcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcgacatctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAG

- - - - - - - -ttctgac
- - - - - - - - - - - - - - -gggggat
- - - - - - - - - - - - - - - - - - - - - -tgtatgt