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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttgaatttctgtgcttaatttttcacttttttggggggtttctctatgttgattaaagtttaaatagttccttgtattttggtctatcttttggaagGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCAGAGGAGCGTAAGT

Basic information

species Glycine max
transcript GLYMA12G34150.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G34150.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G27120.2 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------------------------------------ttcttgaatttctgtgcttaatttttcactt----ttttggggggtttctctatgttgattaaagtttaaatagttccttgtattttggtctatcttttgga---agGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCAGAGGAGCGTAAGT
                                                                                   || |   | || |    |     ||     |      ||||  |  |  |  || |   ||       |  |   |  ||   || || ||| | |||| |    |||||||||||||| |||| ||||||||| |  ||||||||||| | ||| ||||||||||||||  ||||||||| || || |||||||| ||||  ||||
gtgagatttttctatttattctactagaatttttggcaggattaaggatgagaaattctaggaatatcagttggtaagttacattgtgatagttttagattccgacttaaggatagagcattggcagaatattacatctcttttgggacg-actttcctgattaagttctgttctttttttttggtatagGCTGAGGAAGCTACACGCGAGTCAAGGAATACAAAACAAGATTGGTATGCAGAAATGCGGAGGAAGAAGGATGAAGAACGCGAGGCAGAAGAGCTGAAGT

upper sequence: GLYMA12G34150.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0177g00150.t01 (Vitis vinifera), 3'ss of exon 3
ttcttgaatttctgtgcttaatttttcacttttttggggggtttctctatgttgatt-aaagtttaaatagtt-----ccttgtattttggtctatcttttggaagGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCAGAGGAGCGTAAGT
      | |||   | | | ||  ||    ||||||      |||| |   ||| ||  ||| || | || ||     |  |   || || | | |  | | |||||| || ||||||||||| ||||||||||   ||||||||||  | ||| |||||| | |||||  ||||||||||||||| || ||| |||||||  || 
------agttttcctacatgatccttgtgatttttgttcttattcttttccttgttttgaagctttagtaatttgcaactctaagttctgatttgtaatcttgaagGCCGACGAAGCTGCACGTGAGTCAAGGCTAACAAAACAAGACAGATATGCAGAAACGAGGAGGAGGAAGGATGAGGAGCGCGAAGCAAAGGAGCGCCAGC
















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|298185187|gb|HO030400.1|HO030400
EST:     CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAG                         GCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA
genomic: CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAGgtattttttc ... cttttggaagGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA
EST: gi|209696572|gb|BW672857.1|BW672857
EST:     CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAG                         GCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA
genomic: CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAGgtattttttc ... cttttggaagGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA
EST: gi|298176686|gb|HO026807.1|HO026807
EST:     CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAG                         GCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA
genomic: CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAGgtattttttc ... cttttggaagGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA
EST: gi|209712107|gb|BW676724.1|BW676724
EST:     CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAG                         GCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA
genomic: CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAGgtattttttc ... cttttggaagGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA
EST: gi|213617939|gb|DB967301.1|DB967301
EST:     CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAG                         GCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA
genomic: CACCAAAGAAAAAGGAAACTAAAAAGCAAGAGAGGGAAGCACGGCGTCAGgtattttttc ... cttttggaagGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatgttgattaaagtttaaatagttccttgtattttggtctatcttttggaagGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCAGAGGAGCGTAAGT
    tgttgat  putative branch site (score: 4)
                                        tctatctttt  putative PPT
      ttgattaaagtttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttgaatttctgtgcttaatttttcacttttttggggggtttctctatgttgattaaagtttaaatagttccttgtattttggtctatcttttggaagGCTGAGGAAGCTGCACGAGAGTCAAGGCAGGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCAGAGGAGCGTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - tctgtgc
- - - - - - - - - - - - - - - - - tgggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttgta