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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatagcaagcctggcttctgtgtagtttcttctatcttctcttccttccttttgcttagttgatataccaatgtatgtgactgtttttctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCCTGGGGGCTTGACACCTATGCTTGGTGATCGAAAG

Basic information

species Glycine max
transcript GLYMA08G24660.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G24660.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
---aatatagcaagcctggcttctgtgtagtttcttctatcttctcttccttccttttgcttagttgatataccaatgtatgtgactgtttttctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCCTGGGGGCTTGACACCTATGCTTGGTGATCGAAAG
    | |||     | |   |    | |||||| |   |||             |   ||| ||||  | || | |   |  |   ||||    ||||  ||||||||| ||||| ||  | ||||| ||||| ||||||||||||||| |||||||  |||| ||||| |||||||||||  |||||
gtatacatatgcttcattattcagttttagtttttggaatcactgagatacaagtgacgctcagtttctttaacta-acacatatttgttacattatt--cagACAAACCAGTGATCCTCAGAGTGGGTTTGCGACTGTTGAGAAGGATGTTCCTGGAAGCTTAACACCAATGCTTGGTGACAGAAAG

upper sequence: GLYMA08G24660.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0078g00440.t01 (Vitis vinifera), 3'ss of exon 11
-aatatagcaagcctggcttctgtgtagtttcttctatcttctcttccttccttttgcttagttgatataccaatgtatgtgac-tgtttttctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCCTGGGGGCTTGACACCTATGCTTGGTGATCGAAAG
 ||| |    |   |||| | | |||    |  | |  |||  ||   ||  | |     | ||  | | |  ||   | | |  |||| |  |  |  ||| ||||||||||| || | |||||||||||| || |||||||||||| | |||||| |||| ||||| |||||||| ||| |||||
aaatcttaggattatggcctgt-tgttacataatttg-ctttcctgtattaatgtactcgaatttgtttgctcatccttttcatatgttctgttggttccagCCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCCTGGGAGCTTAACACCCATGCTTGGCGATAGAAAG
















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|151410856|gb|EV280671.1|EV280671
EST:     GCTCGTTTGCAGACACCCTATCTTGTTCTTAGTGGTCATGTTAAACCAGG                         ACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCC
genomic: GCTCGTTTGCAGACACCCTATCTTGTTCTTAGTGGTCATGTTAAACCAGGgtatgatttt ... ctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCC
EST: gi|298174867|gb|HO014784.1|HO014784
EST:     GCTCGTTTGCAGACACCCTATCTTGTTCTTAGTGGTCATGTTAAACCAGG                         ACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCC
genomic: GCTCGTTTGCAGACACCCTATCTTGTTCTTAGTGGTCATGTTAAACCAGGgtatgatttt ... ctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCC
EST: gi|192296695|gb|FG991263.1|FG991263
EST:     GCTCGTTTGCAGACACCCTATCTTGTTCTTAGTGGTCATGTTAAACCAGG                         ACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAG-ATCTTCC
genomic: GCTCGTTTGCAGACACCCTATCTTGTTCTTAGTGGTCATGTTAAACCAGGgtatgatttt ... ctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCC
EST: gi|16348613|gb|BI974208.1|BI974208
EST:     GCTCGTTTGCAGACACCCTATCTTGTTCTTAGTGGTCATGTTAAACCAGG                         ACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCC
genomic: GCTCGTTTGCAGACACCCTATCTTGTTCTTAGTGGTCATGTTAAACCAGGgtatgatttt ... ctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttccttttgcttagttgatataccaatgtatgtgactgtttttctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCCTGGGGGCTTGACACCTATGCTTGGTGATCGAAAG
              agttgat  putative branch site (score: 5)
                                     ctgtttttct  putative PPT
                                        tttttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatagcaagcctggcttctgtgtagtttcttctatcttctcttccttccttttgcttagttgatataccaatgtatgtgactgtttttctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCCTGGGGGCTTGACACCTATGCTTGGTGATCGAAAG

- - - gcaagcc
- - - - - - -tggcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactg