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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatttagtgaggaacttggtagaatgtgtgcttatgggtgtttgtttccaagccagattttgtcaaaggaatcaataatcataacttgtttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGAT

Basic information

species Glycine max
transcript GLYMA08G07670.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07670.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0028g00460.t01 (Vitis vinifera), 3'ss of exon 1
gaatttagtgaggaacttggtagaatgtgtgcttatgggtgtttgtttccaagccagattttgtcaaaggaatcaataatcataacttgttta-ttctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGAT
   | || | |      | |   | |  | |        | ||  || |     |   |||  | ||     | ||  |||  |   ||  || || | |||| |||||  | || ||||||   || ||||| || ||||| |||||||| || ||||| ||||| |||||||||||| |||| |||||||
-gttgtactcatccttcttgagaattaagagtgagaaattattcattccttcaacttgtttcctaaatttcctaaaagatctcattatgcctaatttttagGTACAACTCTTTCGGATTCAATTCAGAGTACCAGAATATGGTTGGACAACACAAAAGGTCTTCCACTTGATGAATTTTATTGTAAATGGAT

upper sequence: GLYMA08G07670.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23006 (Selaginella moellendorffii), 3'ss of exon 1
gaatttagtgaggaacttggtagaatgtgtgcttatgggtgtttgtttccaagccagattttgtcaaaggaatc---aataatcataacttgtttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGAT
                                 |||||   |  |  |      | | | || || |  || ||      |||| |  |   ||   || ||| | |||||  | || ||  | |   | || || |||||||| ||||| ||||||||||| ||||||||| |||||||  |||| |||||| 
--------------------------------gtatgga-atccgactagttttctggtcttttctattgattcttggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG

upper sequence: GLYMA08G07670.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
gaatttagtgaggaacttggtagaatgtgtgcttatgggtgtttgtttccaagccagattttgtcaaaggaatc---aataatcataacttgtttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGAT
                                 |||||      | |     |   | | || || |  || ||      |||| |  |   ||   || ||| | |||||  | || ||  | |   | || || |||||||| ||||| ||||||||||| ||||||||| |||||||  |||| |||||| 
--------------------------------gtatggaatccggctagtttgtt-ggtcttttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG

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|192307419|gb|FK000761.1|FK000761
EST:     CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTG                         GTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
genomic: CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTGgttggtattc ... ttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
EST: gi|11275013|gb|BF325337.1|BF325337
EST:     CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTG                         GTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
genomic: CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTGgttggtattc ... ttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
EST: gi|163926925|gb|EH038506.1|EH038506
EST:     CCTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTG                         GTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
genomic: CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTGgttggtattc ... ttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
EST: gi|213601479|gb|DB970409.1|DB970409
EST:     CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTG                         GTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
genomic: CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTGgttggtattc ... ttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
EST: gi|151393599|gb|EV263474.1|EV263474
EST:     CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTG                         GTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
genomic: CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTGgttggtattc ... ttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
EST: gi|298185371|gb|HO030584.1|HO030584
EST:     CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTG                         GTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
genomic: CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTGgttggtattc ... ttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
EST: gi|298173449|gb|HO016785.1|HO016785
EST:     CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTG                         GTGTAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG
genomic: CTTACTATGCCCTTTGTGCCGCTTATACGTTGGTCTCCTTTGTTGCCCTGgttggtattc ... ttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccaagccagattttgtcaaaggaatcaataatcataacttgtttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGAT
                                  tcataac  putative branch site (score: 2)
                                            tttattctc  putative PPT
                             aataatcataacttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatttagtgaggaacttggtagaatgtgtgcttatgggtgtttgtttccaagccagattttgtcaaaggaatcaataatcataacttgtttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGAT

- - - - - - - - - - - - -tgtgtgc
- - - - - - - - - - - - - - - - - atgggtg