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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgctttattttttttacaattctttcttcttaaaatattaatataaatgaaataggcttcacatatttttagacatagttctcaaataacaagagatgggccctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTG

Basic information

species Glycine max
transcript GLYMA10G38590.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
gcatgctttattttttttacaattctttcttcttaaaatattaatataaatgaaataggcttcacatatttttagacatagttctcaaataacaagagatgggccctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTG
|    |  | |||  |  |||  | | | ||||  |  | |  |   | || ||||  |    | | | |||| |||| ||    ||| |   |              | || |||| |||||||| |||||||||||||| ||||||||||||||||| || |||||  | || || |||||||| ||||| ||||||||||||||||| ||||
gttcaccctttttagtcaacagatgtattttct--aggtttgcaaccagataaaattaggaggataaactttttgacaaag----caacttgta-------------tgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG

upper sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
-------------------gcatgctttattttttttacaattctttctt-cttaaaatattaatataaatgaaataggcttcacatatttttagacatagttctcaaataacaagagatgggccctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTG
                      ||   |  ||    |  ||  || |||| ||||||||   ||  |  ||       |    || | | |    ||| | |       ||||||  ||     | ||| |||||||||||||||| ||||||||||||||||| |||||||||||||| || |||||  |||| |||||||| |||||||||||||||||||||||||||||||
gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaat-gactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG

upper sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ34621 (Selaginella moellendorffii), 3'ss of exon 14
gcatgctttattttttttacaattctttcttcttaaaatattaatataaatgaaataggcttcacatatttttagacatagttctcaaataacaagagatgggccctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTG
                                                  |     | ||| |  |  || | ||  || |||| ||   | ||| |         | | |  |||| || ||||| ||||| |||||||| ||||| ||||| || || ||  ||||  ||||||| || || ||||||||||| || |||||||| |||||||
-------------------------------------------------gtacgggacgctaccgactttatgagcaatggttcaca--cagcaaaa---------ttgttgaagGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTG

upper sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ32824 (Selaginella moellendorffii), 3'ss of exon 14
gcatgctttattttttttacaattctttcttcttaaaatattaatataaatgaaataggcttcacatatttttagacatagttctcaaataacaagagatgggccctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTG
                                                  |     | ||| |  |  || | ||  || |  |||| | | ||| |         | | |  |||| || ||||| ||||| |||||||| ||||| ||||| || || ||  ||||  ||||||| || || ||||||||||| || |||||||| |||||||
-------------------------------------------------gtacgggacgctaccgactttatgagcgatgg--ctcacacagcaaaa---------ttgttgaagGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTG

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|22541844|gb|BU091687.1|BU091687
EST:     GCGGTGCTCTGGACCGTGTTGCTAAAAAATTGAACCTCCCTTTCTTTGAG                         GTCCCCACTGGTTGGAAATTNTTTGGGAATCTTATGGATGCTGGGAATTTG
genomic: GCGGTGCTCTGGACCGTGTTGCTAAAAAATTGAACCTCCCTTTCTTTGAGgcatgcttta ... ctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTG
EST: gi|15203242|gb|BI426010.1|BI426010
EST:     GCGGTGCTCTGGACCGTGTTGCTAAAAAATTGAACCTCCCTTTCTTTGAG                         GTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTG
genomic: GCGGTGCTCTGGACCGTGTTGCTAAAAAATTGAACCTCCCTTTCTTTGAGgcatgcttta ... ctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTG
EST: gi|120494261|gb|EH222428.1|EH222428
EST:     GCGGTGCTCTGGACCGTGTTGCTAAAAAATTGAACCTCCCTTTCTTTGAG                         GTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTG
genomic: GCGGTGCTCTGGACCGTGTTGCTAAAAAATTGAACCTCCCTTTCTTTGAGgcatgcttta ... ctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacatatttttagacatagttctcaaataacaagagatgggccctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTG
                          aaataac  putative branch site (score: 2)
     atatttttagacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgctttattttttttacaattctttcttcttaaaatattaatataaatgaaataggcttcacatatttttagacatagttctcaaataacaagagatgggccctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA