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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaattcttctcaacattaatgttgcacagcatctcttgttggttaccacatacttttctttgctatccttgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAGCAGTCACTAAAAGGATACGAG

Basic information

species Glycine max
transcript GLYMA02G12930.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G12930.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 2
tcaaattcttctcaacattaatgttgcacagcatctcttgttgg-ttaccacatacttttctttgct-atccttgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAGCAGTCACTAAAAGGATACGAG------------
    |  ||   ||| ||   |         ||| |     |    |   | ||    || |  | | ||| ||  |    |||     |   |  || |||||||||||| || |  |||||||| |||||||||||||||||||| ||||||||||||||  ||||||||||||| || || ||||||            
--ggaggctgtgcaatatatttacatatgtacatttgaaactaaacttttatatggggttttaagtttatctttcctggtgttttggtatgaatgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAGGAAAGAGGCCTCTGAGCAGTCACTGAAGGGCTACGAGGCATGTTCACTT
















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|207840744|gb|GD810937.1|GD810937
EST:     TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|10843368|gb|BF067173.1|BF067173
EST:     TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|14011701|gb|BG726623.1|BG726623
EST:     TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|18690824|gb|BM519672.1|BM519672
EST:     TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|21887789|gb|BQ741002.1|BQ741002
EST:     TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|4306793|gb|AI443955.1|AI443955
EST:     TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|208081589|gb|GD882047.1|GD882047
EST:     TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|7924046|gb|AW830054.1|AW830054
EST:     TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
EST: gi|57574121|gb|CX547096.1|CX547096
EST:     TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGAT                         GAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG
genomic: TTGATTCCTTCTTCCGGATCAGCAGAAGCTAGCGTTTTCTACTACAAGATgtgagtcatg ... tttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccacatacttttctttgctatccttgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAGCAGTCACTAAAAGGATACGAG
                                            ttttgat  putative branch site (score: 4)
         cttttctttgctatcc  CT-rich tract
                                  tttattcttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaattcttctcaacattaatgttgcacagcatctcttgttggttaccacatacttttctttgctatccttgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAGCAGTCACTAAAAGGATACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - ctcaaca
- - - - - - - - - - - - tgcacag
- - - - - - - - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - - - - - - -ccacata