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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctctctgcccacctgattcaatattaatgttagtactactataatactattattttgtgatgaattttggtttctgatttggttgcgtggttttttgtcctgttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTTGAGATTCCTGAAGAAACCTTTTTGAGATTTGTCCGCTTGGTCAAAAGTG

Basic information

species Glycine max
transcript GLYMA08G06660.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G06660.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G21320.1 (Arabidopsis thaliana), 3'ss of exon 2
gtctctctctgcccacctgattcaatattaatgttagtactactata--atactattattttgtgatgaattttggtttctgatttggttgcgtggttttttgtcctgttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTTGAGATTCCTGAAGAAACCTTTTTGAGATTTGTCCGCTTGGTCAAAAGTG
                         ||  ||| || |   | | |||  | |   ||  | |  ||  |   || | || |  |  ||||   | || ||||       || |  |||| || |||||||||||||||||||| |||||||| ||||     | ||||||  ||||||| |||||  || |  ||| ||| || ||| | || |  |
------------------------gtaaaaatctttgacattccataggaaatggttggtattggagaagaattaggtttttgtgaggttaaattgtgtttta------tggcgcagGAGTGTAAGCAGTTGGGGTTTGACACTATTGAGCTGAATGCAAATTTGCTTGAAGTTCCTGAGGAAACTCTTCTACGATATGTACGTTTGATTAAGAACG

upper sequence: GLYMA08G06660.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s1274g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtctctctctgcccacctgattcaatattaatgttagtactactataatactattattttgtgatgaatt-ttggtttctgatttggttgcgtggttttttgtcc-tgttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTTGAGATTCCTGAAGAAACCTTTTTGAGATTTGTCCGCTTGGTCAAAAGTG
                                ||  | || |  || ||   |||  ||| |  | |||| ||  |||  |   |  ||   |  ||| || |   | | |||  |||| || ||||| ||||| ||||||||||| ||||| |||||||| || || |  ||||| ||||||||  ||||||||||||| || ||| | || ||||
--------------------------------gtgggcacaaaaatcat-taattggtttttcttcaattatttatttgagcactaattcaattttttcttatatgtttcgtcgcagGAGTGTAAGCATTTGGGATTTGACACAATCGAGCTAAATGTGGGTTCACTAGGAATTCCAGAAGAAACTCTTTTGAGATTTGTGCGTTTGATTAAGAGTG
















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|151402962|gb|EV272775.1|EV272775
EST:     CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAG                         GAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
genomic: CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAGgtctctctct ... gttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
EST: gi|151394464|gb|EV264335.1|EV264335
EST:     CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAG                         GAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
genomic: CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAGgtctctctct ... gttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
EST: gi|151401140|gb|EV270954.1|EV270954
EST:     CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAG                         GAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
genomic: CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAGgtctctctct ... gttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
EST: gi|51336189|gb|CO980055.1|CO980055
EST:     CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAG                         GAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
genomic: CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAGgtctctctct ... gttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
EST: gi|298166286|gb|HO009257.1|HO009257
EST:     CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAG                         GAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
genomic: CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAGgtctctctct ... gttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
EST: gi|9258852|gb|BE346999.1|BE346999
EST:     CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAG                         GAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
genomic: CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAGgtctctctct ... gttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
EST: gi|213613975|gb|DB960954.1|DB960954
EST:     CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAG                         GAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
genomic: CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAGgtctctctct ... gttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
EST: gi|298163532|gb|HO012265.1|HO012265
EST:     CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAG                         GAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
genomic: CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAGgtctctctct ... gttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
EST: gi|151394843|gb|EV264714.1|EV264714
EST:     CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAG                         GAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT
genomic: CTGAGCACATGATTAGCAAAAGTCCATCAGGTTTCAAGGAATATGTAGAGgtctctctct ... gttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgaattttggtttctgatttggttgcgtggttttttgtcctgttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTTGAGATTCCTGAAGAAACCTTTTTGAGATTTGTCCGCTTGGTCAAAAGTG
               ttctgat  putative branch site (score: 3)
                                  ttttttgtcctgtt  putative PPT
                                  ttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctctctgcccacctgattcaatattaatgttagtactactataatactattattttgtgatgaattttggtttctgatttggttgcgtggttttttgtcctgttgtcatagGAATGCAAGCAGTTGGGGTTTGACACAATTGAGCTCAATGTGGGATCGCTTGAGATTCCTGAAGAAACCTTTTTGAGATTTGTCCGCTTGGTCAAAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA