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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttatctaatcggtgttctattcttggtgctacatgacatggtgatgtatgaacaaggatgtgttgaccagtgacccattgcttgttattgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCTGGTGATGAGG

Basic information

species Glycine max
transcript GLYMA10G12350.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G12350.2 (Glycine max), 3'ss of exon 1
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 1
tgtttatctaatcggtgttctattcttggtgctacatgacatggtgatgtatgaacaaggatgtgttgaccagtgacccattgcttgt-tattgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCTGGTGATGAGG
 ||||    |||  ||    ||    | |   | | |       |  |   ||   |      |   |   |  || | | ||  ||  | ||  |   ||||||||||||| ||   ||||||||||| ||| || |||| ||| || ||  | ||||| ||||||||||| ||||||||||| |||   | ||||||| 
-gtttgatcaatttgtaccgtagctgttgcaattcttagttgttttcttggtggttagtagaattcagtgaaacgaactaatgaatgcgtctttgttgaagGTTCTTGGTGTTGAAGCAACAGCATCTCCACAAGAGATAAGGAAAGCGTATCATAAGTTAGCATTGAGGCTTCATCCTGATAAAAACAAGGATGATGAG-

upper sequence: GLYMA10G12350.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 1
------------tgtttatctaatcggtgttctattcttggtgctacatgacatggtgatgtatgaacaaggatgtgttgaccagtgacccattgcttgttattgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCTGGTGATGAGG
            |  ||   | |  | ||| || || ||  |  ||||  | |   |      || |  | ||  || |||  | | |||         || |  ||   |||||||||||||||| || || |||||||| |||||||| ||||| || ||||| |||||||||||| |||| ||||||||||| || |||||||||||| 
ccattctccctcttcttggtttactgatgtact-ttttttttattaca--ataaaatttcaagtggagcaagagatgctgaataataacc---------ttgtgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG-
















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|193486269|gb|FK449543.1|FK449543
EST:     TCGAATCCGATACCAACCCCTTCGATAAAAACGAAAACTCTCTCTATCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
genomic: TCGAATCCGATACCAACCCCTTCGATAAAAACGAAAACTCTCTCTATCAGgttatcttaa ... ttgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
EST: gi|207729869|gb|GD706421.1|GD706421
EST:     TCGAATCCGATACCAACCCCTTCGATAAAAACGAAAACTCTCTCTATCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
genomic: TCGAATCCGATACCAACCCCTTCGATAAAAACGAAAACTCTCTCTATCAGgttatcttaa ... ttgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
EST: gi|208257299|gb|GE056714.1|GE056714
EST:     TCGAATCCGATACCAACCCCTTCGATAAAAACGAAAACTCTCTCTATCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAG
genomic: TCGAATCCGATACCAACCCCTTCGATAAAAACGAAAACTCTCTCTATCAGgttatcttaa ... ttgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAG
EST: gi|207703247|gb|GD685305.1|GD685305
EST:     TCGAATCCGATACCAACCCCTTCGATAAAAACGAAAACTCTCTCTATCAG                         GTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC
genomic: TCGAATCCGATACCAACCCCTTCGATAAAAACGAAAACTCTCTCTATCAGgttatcttaa ... ttgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtatgaacaaggatgtgttgaccagtgacccattgcttgttattgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCTGGTGATGAGG
                  tgttgac  putative branch site (score: 3)
                                             ttgctctt  putative PPT
                                       ttgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttatctaatcggtgttctattcttggtgctacatgacatggtgatgtatgaacaaggatgtgttgaccagtgacccattgcttgttattgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCTGGTGATGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - tggtgct
- - - - - - - - - - - - - - - - -acatgac
- - - - - - - - - - - - - - - - - - - - - ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - -tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt