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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctatggtctaaagaaatttatcttaaattttaaaatataaatttgaattactatgtgacaattttatgagttgcaattatcattatgttgctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG

Basic information

species Glycine max
transcript GLYMA13G44000.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44000.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 4
cctatggtctaaagaaatttatcttaaattttaaaa---tataaatttgaattactatgtgacaattttat-gagttgcaattatc--attatg----ttgctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG
           ||  | ||  |  ||| ||| |      |     ||| | || ||     || ||| |||  |||||    ||||  |  |||    | ||  |||||||||||||||| ||||||||||| |||||||| || ||||| ||||| | ||||||||||   |||||
----------taatcatttctttataactttcagggctgtgcctttttaacttcctggaaaactattgtattaagttgtttatatcttaccatggacatggcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTGCTGTAAAAAAATTCAG
















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|17154054|gb|BM143987.1|BM143987
EST:     TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATG                         ATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
genomic: TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATGgtaagtaaca ... gctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
EST: gi|151403951|gb|EV273761.1|EV273761
EST:     TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATG                         ATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
genomic: TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATGgtaagtaaca ... gctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
EST: gi|58019023|gb|CX705765.1|CX705765
EST:     TCCCCAGTGTGGATTTAGTTCTTTTGCAGTTAGAGTGTTACAACAATATG                         ATGTTCCTTTAAGTGCTAGAAACA-TTTGGAAGATCCTGAACTGAAAAATG
genomic: TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATGgtaagtaaca ... gctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
EST: gi|58018776|gb|CX705518.1|CX705518
EST:     TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATG                         ATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
genomic: TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATGgtaagtaaca ... gctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
EST: gi|193689192|gb|FK631403.1|FK631403
EST:     TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATG                         ATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
genomic: TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATGgtaagtaaca ... gctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
EST: gi|31462442|gb|CD404470.1|CD404470
EST:     TCCACTGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATG                         ATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
genomic: TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATGgtaagtaaca ... gctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
EST: gi|12690674|gb|BG157010.1|BG157010
EST:     TCCACAGTGTGGATTTAGTTCTC-TGGAGTTAGAGTGTTACAACAATATG                         ATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG
genomic: TCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATGgtaagtaaca ... gctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattactatgtgacaattttatgagttgcaattatcattatgttgctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG
                              aattatcattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctatggtctaaagaaatttatcttaaattttaaaatataaatttgaattactatgtgacaattttatgagttgcaattatcattatgttgctattgcagATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - aaagaaa
- - - - - - - - - - - - - - - - -aaatataa
- - - - - - - - - - - - - - - - - - - - - - - - - -ctatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agttgca