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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggacaccctgtagccttttctgccttttcctgtgattgcccttttacacttgagcttactttactctggaagattctgaggtaaatcaactcttacagTGCTACAGGTATAGTCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTCGGTTGAAGCAAGGTCAGAGTCAAAAGGCTATTTTGAGGAAACTGTGACA

Basic information

species Glycine max
transcript GLYMA19G40520.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G40520.2 (Glycine max), 3'ss of exon 15
lower sequence: Vv07s0005g01650.t01 (Vitis vinifera), 3'ss of exon 23
ctggacaccctgtagccttttctg----ccttttcctgtgattgcccttttacacttgagcttactttactctggaagattctgaggtaaatcaactc--ttacagTGCTACAGGTATAGTCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTCGGTTGAAGCAAGGTCAGAGTCAAAAGGCTATTTTGAGGAAACTGTGACA
    |||   |    |  || |||      |   ||||   ||     |  |    |   |||| |  |  |||  |||  || || |   |||||    || |||||||||||||| ||||||  | |||||||| || || |||| ||  ||||| ||||||||  | ||||| || |||||||||| ||||||||| || || 
----acaaatttgtactgttcctgaaaatgtcaacctgcagttcttactgcatctgtttccttattggagcctg--agaacctaagatggttcaacctctttgcagTGCTACAGGTACAGTCACCTTGTTGTCTGGCCAGCCAAAAGAAGGCGTTTCAGTTGAAGCCCGATCAGACTCCAAAGGCTATTATGAGGAAACAGTAACC
















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|14990753|gb|BI316426.1|BI316426
EST:     GCAGGGGAGTTCAAAGAAGTAGTTTTCCGGGCCACACGTGTAGCCTACAG                         TGCTACAGGTATAGTCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTC
genomic: GCAGGGGAGTTCAAAGAAGTAGTTTTCCGGGCCACACGTGTAGCCTACAGgttttatttc ... actcttacagTGCTACAGGTATAGTCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTC
EST: gi|15815183|gb|BI787458.1|BI787458
EST:     GCAGGGGAGTTCAAAGAAGTAGTTTTCCGGGCCACACGTGTAGCCTACAG                         TGCTACAGGTATT-TCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTC
genomic: GCAGGGGAGTTCAAAGAAGTAGTTTTCCGGGCCACACGTGTAGCCTACAGgttttatttc ... actcttacagTGCTACAGGTATAGTCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTC
EST: gi|22931640|gb|BU548779.1|BU548779
EST:     GCAGGGGAGTTCAAAGAAGTAGTTTTCCGGGCCACACGTGTAGCCTACAG                         TGCTACAGGTATAGTCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTC
genomic: GCAGGGGAGTTCAAAGAAGTAGTTTTCCGGGCCACACGTGTAGCCTACAGgttttatttc ... actcttacagTGCTACAGGTATAGTCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacacttgagcttactttactctggaagattctgaggtaaatcaactcttacagTGCTACAGGTATAGTCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTCGGTTGAAGCAAGGTCAGAGTCAAAAGGCTATTTTGAGGAAACTGTGACA
         agcttac  putative branch site (score: 3)
                                              ctcttac  putative PPT
            ttacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggacaccctgtagccttttctgccttttcctgtgattgcccttttacacttgagcttactttactctggaagattctgaggtaaatcaactcttacagTGCTACAGGTATAGTCACTCTCTTGTCTGGTCAACCCAAAGGAGAAGTTTCGGTTGAAGCAAGGTCAGAGTCAAAAGGCTATTTTGAGGAAACTGTGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- -gacaccc
- - - - - - - gcctttt
- - - - - - - - - - -ctgcctt
- - - - - - - - - - - - - - - cctgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattctg