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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcacggtataaaataattttgtatggttatccaattaaaaaaaataaaaattagttatgagtagcgaaaattaatatgtttgccggaatctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGGACAAAGATGGTGATTGGATGCTTGTTGGAGATGTCCCTTGGGA

Basic information

species Glycine max
transcript GLYMA08G22190.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22190.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g05150.t01 (Vitis vinifera), 3'ss of exon 1
-ctcacggtataaaataattttgtatggttatccaattaaaaaaaataaaaattagttatgagtagcgaaaattaatatgtttgccgga-atctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGGACAAAGATGGTGATTGGATGCTTGTTGGAGATGTCCCTTGGGA
  | |  ||||      |  || |||| | ||| || |  |       |  |  |       | ||  | || ||||   ||||    | || ||||  |||  || || |||||| ||||||| | ||| ||  |  ||||||| ||||||||||||||||| || ||||||||||| |||||||| ||||||||
gatgagcgtatttttcgagatt-tatgataatcaaaatctatggctccaccacaaaacccttgaag-aagaactaattcttttgttaaatatgtgttggcagGTGAAGCATTGAAAGATGCAGATAGTTCAGAGTATATTCCCATATATGAGGACAAAGATGGGGACTGGATGCTTGTAGGAGATGTTCCTTGGGA
















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|19270241|gb|BM886497.1|BM886497
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|13480056|gb|BG509399.1|BG509399
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|19348246|gb|BM892778.1|BM892778
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|20811483|gb|BQ295961.1|BQ295961
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|13125813|gb|BG316383.1|BG316383
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|7028314|gb|AW458097.1|AW458097
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAGTTCTGAACACGTTCCCATGTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|27426495|gb|CA938015.1|CA938015
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGGGGTGAAAAATGCAGACAAT
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAAT
EST: gi|27426652|gb|CA938172.1|CA938172
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|27427401|gb|CA938921.1|CA938921
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|13480101|gb|BG509434.1|BG509434
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|4284079|gb|AI440736.1|AI440736
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|7691324|gb|AW759517.1|AW759517
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
EST: gi|27445862|gb|CA952985.1|CA952985
EST:     CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGG                         TGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG
genomic: CTCAGATTTAGCTTTGGCTTTGGACAAGCTCTTTGGTTGCTATGGAATGGgtcagttccg ... ctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaattagttatgagtagcgaaaattaatatgtttgccggaatctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGGACAAAGATGGTGATTGGATGCTTGTTGGAGATGTCCCTTGGGA
                        aattaat  putative branch site (score: 3)
                                            tctgttc  putative PPT
                      aaaattaatatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcacggtataaaataattttgtatggttatccaattaaaaaaaataaaaattagttatgagtagcgaaaattaatatgtttgccggaatctgttcacagTGGAGGCGTTGAAAAATGCAGACAATTCTGAACACGTTCCCATTTATGAGGACAAAGATGGTGATTGGATGCTTGTTGGAGATGTCCCTTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - aaaataa
- - - - - - - - - - tgtatgg
- - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc