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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA

Basic information

species Glycine max
transcript GLYMA20G39050.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaatt-ttaaatggtatttg-ttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
                  ||||||  |  | || |    ||  |||  ||  |   | |||  | | || |||  |   |||||  ||||    |     ||||  | ||  |||||||||| ||||||||||||||||||||||||||| |||| || || 
-------------gtgacattttagttccgtttctt---ttcgtatacaatgtcacttaatcttgtgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattt-taaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
        |||| | | ||| |   ||||  || ||| ||   ||  ||   ||| | |||| |  |  ||| |  | |||   ||| ||| |   || ||    | ||  |||||||||| ||||||||||| ||||||||||||||| ||||||| || 
-------gtgttaatt-tatctcctatttc-ttgtgcagt-gctacttatcctttcttaatgatggtatttagg-aagtat--gtttgttattc--tgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG

upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
aaaacaa-atgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
  || |   || || || | | | || ||   ||||    ||||  |      | ||   || ||||  || |   ||| |||| |||| |  |||   ||||  | ||| ||||||| || ||||||||||||||||||||||||||| |||| || || 
gtaatatcgtggttcctttttctcaagttc--ttat----ttaacctt----gtattgcttgttattaattgc---atttttgaattttca--tatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
aaaacaaatgtttactctattttaaatttggttatgcggtt-aatatctaaaatt-ttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
        | || | | | | |   || |   | | |  || | | | |   |   ||  |   |  | ||  |  ||| ||  ||||  || |  ||  ||  | | ||| ||||||| || ||||||||||||||||||||||| ||| |||| || || 
-------gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattcttt--agGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG

upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 4
aaaacaaatgtttactctattttaaat-ttggttatgcggtt-aatatctaaaatt-ttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
         ||||  | ||| | | || |    | | |  || | | | |   |   ||  |   |  | |   |  ||| ||  ||||  || |  ||  ||  | | ||| ||||||| || ||||||||||||||||| ||||||||| |||| || || 
---------gttt-ttttatctcatatgtcttctgtactctttagtgtttgttaccatttcacaatgatggaatctagataatgcatttgatattcttt--agGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGGAAAAGTCGGCTGAGGAAAAAG

upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattat----tgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
                 ||  || |  |  ||    |   ||  ||||     | | |    |||   | |  || ||  |    ||||  || |       |||| || || ||||||||||| |||||||||||||||||||||||  | ||||| ||||| 
-------------gtgatagattcatctctgtggatcaactagcatctgtgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG

upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 3'ss of exon 4
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
     | ||||  |      | || ||  | | |  | |||  |||  |       || |  || |   |   || ||  | || |||| ||      ||||||| || ||||||||||| || |||||||||||||| |||||  | ||||| ||||| 
--gtgacatgtccatctc--tgtagataagatca--ctgtttttattcag----ccaatttataatctctttttgtttccttatattttgatc--catagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG

upper sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
            |  | ||  | ||| |   ||  | |  ||  |||| ||  |  |    |||    ||       | ||| || |||   | |  |||||||| || ||||||||||| |||||||| || ||| ||||||| || ||||||||||||
-----------gtcatatagatcaaact-aattgcgtgtatatcatctcaa-ctgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA

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|192300889|gb|FG992949.1|FG992949
EST:     CTGTGGCTTCTGACTCCAGTGACAGATCAAAGGATAAATCAGATCAGAAG                         ACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTG
genomic: CTGTGGTTTCTGACTCCAGTGACAGATCAAAGGATAAATCAGATCAGAAGgtaaagtgta ... attattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA
                                        ttttaat  putative branch site (score: 3)
                 tatttgttacgtgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA