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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatatatgctcttatgtttcactcaattaaaaagctaaaggttcaaatttgcatattccattcagtttgattaggtggctaatttggtttttatttcttagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGATATTGAAGGTGCTCAAAGAAGCAGAGTGGGAGCCTAGTTTATATTGGAGG

Basic information

species Glycine max
transcript GLYMA07G18200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G18200.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g02260.t01 (Vitis vinifera), 3'ss of exon 5
---gtaagtatatatgctcttatgtttcactcaattaaaaagctaaaggttcaaatttgcatattccattcagtttgattaggtggctaatttggtttttatttct-tagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGATATTGAAGGTGCTCAAAGAAGCAGAGTGGGAGCCTAGTTTATATTGGAGG
    |    | |||| || | ||  || |     |||||||   |||||   |||     ||  |   || ||        |  | || || ||  ||  || | |  || || || || ||| | |||| ||| || |||||| |||||   || |||||| ||||||||||| ||||||| ||||||||||| ||| || | |||| |
tttatcctcaaatattctatcattgttaat---gttaaaaacgaaaaggaaaaaaaaaatatgctttgtttagc-------gaggactgatctgtgttgaatgtgtgcagGGACGGCATCCATTTGTCAAGTGAAGGGAGCAAGGTAGTAGTGAAGGAGATACTGAAGGTGCTCGAAGAAGCTGAGTGGGAGCCCAGTCTACACTGGAAG
















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|37996897|gb|CF808486.1|CF808486
EST:     CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCAT                         TGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
genomic: CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCATgtaagtatat ... tatttcttagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
EST: gi|38192353|gb|CF921559.1|CF921559
EST:     CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCAT                         TGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
genomic: CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCATgtaagtatat ... tatttcttagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
EST: gi|254330810|gb|GR842075.1|GR842075
EST:     CTATGGTCTGCTATTCAGAAAA-GGATAACTGGAGAGATGTTTGCTTCAT                         TGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
genomic: CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCATgtaagtatat ... tatttcttagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
EST: gi|38193612|gb|CF922818.1|CF922818
EST:     CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCAT                         TGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
genomic: CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCATgtaagtatat ... tatttcttagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
EST: gi|38191127|gb|CF920333.1|CF920333
EST:     CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCAT                         TGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
genomic: CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCATgtaagtatat ... tatttcttagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
EST: gi|254330811|gb|GR842076.1|GR842076
EST:     CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCAT                         TGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT
genomic: CTATGGTCTGCTATTCAGAAAAAGGATAACTGGAGAGATGTTTGCTTCATgtaagtatat ... tatttcttagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgcatattccattcagtttgattaggtggctaatttggtttttatttcttagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGATATTGAAGGTGCTCAAAGAAGCAGAGTGGGAGCCTAGTTTATATTGGAGG
                              ggctaat  putative branch site (score: 3)
                                         tttttatttctt  putative PPT
                                 taatttggtttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatatatgctcttatgtttcactcaattaaaaagctaaaggttcaaatttgcatattccattcagtttgattaggtggctaatttggtttttatttcttagTGATGGAATTCATCTTTCAACTGAGGGAAGCAAGATAGTAACAAAAGAGATATTGAAGGTGCTCAAAGAAGCAGAGTGGGAGCCTAGTTTATATTGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG