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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttctttaaagagatttcttctacacaagtgaattcctttttgataacttaaatgacaatttccccccttttttgtgatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGCGAATATATTGTGAAGAAGATCCCAATCC

Basic information

species Glycine max
transcript GLYMA08G18240.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 6
-------gtaagttt-tctttaaagagatttcttctacacaagtgaattcctttt----tgataacttaaatgac--aatttccccccttttttgtgatttg-ccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGCGAATATATTGTGAAGAAGATCCCAATCC
        | ||| |  ||||   |     ||   |||  |     ||  || ||       |  |||   |  |    | |  ||| | |||  | |||||  ||||||||  | ||||| |||||||| || || ||||| || || ||| |||| || || ||||||||| | |||||||| ||||||||||| ||||| ||||
gtcaatactcagtgtgcctttgcggcaccatccaatacttatcaccatctctcttgttacagtgtcttctctttcttggtctgacccttctttgctcatttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 6
-gtaagttttctt----taaagagatttcttctacacaagtgaattcctt--tttgataacttaaatg----acaatttcccccc------ttttttgtgatttgc--cagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGCGAATATATTGTGAAGAAGATCCCAATCC
  || ||||||||       |  ||| | || ||      | | ||| |   || | |||  ||| |     | || ||    |       | |||       ||   |||   ||||||||||||| ||| ||  | || ||| | ||||||||  |||| || || |||||||| |||||||| || ||||| ||||||||||||||||
gttaggttttcttatctcttaaggatctgttgtagcattctcatttcgtcacttggttaagctaagtattgaagaacttggttctaaaatttctttcacatcctgttgcagAACACTGTTGCTGATGCTGCTCCGATCGTCCCTGTCTCAGCACAACTGAAATACAACATTGATGTGGTGTGCGAGTACATTGTCAAGAAGATCCCAATCC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 6
gtaagttttctttaaagagatttcttctacacaagtgaattcctttttgataacttaaa-tgacaatttccccccttt--tttgtgatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGCGAATATATTGTGAAGAAGATCCCAATCC
|| | || ||||  |  | |||   |  |  ||  ||  ||     ||   || ||| | |||  | ||       |    ||    | | ||||||||||||||| ||||||||||| |||||||| ||||| || ||  ||||||||||||||||||||||||| || ||||| ||||| |||||||| || |
gtga-ttctcttagatcacattaaatgaaagcatatg--ttatggcttaccaatttacactgatgaattgtattgctgaacttactctctaccagGGAACTGTTGCAGATGGTGCACCTGTAGTACCAATTTCTGCGCAACTGAAGTATAATATTGATGTTGTGTGTGAGTATATCGTGAAAAAGATCCCCATTC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttttctttaaagagatttcttctacacaagtgaattcctttttgataacttaaatgacaatttccccccttttttgtgatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGCGAATATATTGTGAAGAAGATCCCAATCC
||| |||| |||  |  | | |  ||  |   |  ||  |   | |    | |||| ||||| | | |    |     ||||  | | ||||||||||||||| |||||||||||||| ||||| ||||| || ||| ||||||||||||||||||||||||| |||||||||||||| |||||||| || |
gta-gtttccttagaccacactagttgaatttatatgt-tatgtgtcaatttacttcaatga-attgtattgctgaacttgtactataccagGGAACTGTTGCAGATGGTGCACCAGTGGTACCAATTTCTGCGCAGCTGAAGTATAATATTGATGTTGTGTGTGAATATATTGTGAAAAAGATCCCCATTC

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|254316161|gb|GR825970.1|GR825970
EST:     AAGAAAATGTCGCAATCAATCAGCATGAGGCAATTTCAAAGTTTATACAA                         GGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAG
genomic: AAGAAAATGTCGCAATCAATCAGCATGAGGCAATTTCAAAGTTTATACAAgtaagttttc ... gatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAG
EST: gi|192321216|gb|FK014306.1|FK014306
EST:     AAGAAAATGTCGCAATCAATCAGCATGAGGCAATTTCAAAGTTTATACAA                         GGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAG
genomic: AAGAAAATGTCGCAATCAATCAGCATGAGGCAATTTCAAAGTTTATACAAgtaagttttc ... gatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAG
EST: gi|9259268|gb|BE347476.1|BE347476
EST:     AAGAAAATGTCGCAATCAATCAGCATGAGGCAATTTCAAAGTTTATACAA                         GGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAG
genomic: AAGAAAATGTCGCAATCAATCAGCATGAGGCAATTTCAAAGTTTATACAAgtaagttttc ... gatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAG
EST: gi|207752019|gb|GD722136.1|GD722136
EST:     AAAGTTTTATACAA                         GGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACCAGTTTG
genomic: AAAG-TTTATACAAgtaagttttc ... gatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCA-CAG-TTG
EST: gi|18692825|gb|BM521673.1|BM521673
EST:     AAGAAAATGTCGCAATCAATCAGCATGAGGCAATTTCAAAGTTTATACAA                         GGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAG
genomic: AAGAAAATGTCGCAATCAATCAGCATGAGGCAATTTCAAAGTTTATACAAgtaagttttc ... gatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcctttttgataacttaaatgacaatttccccccttttttgtgatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGCGAATATATTGTGAAGAAGATCCCAATCC
          tgataac  putative branch site (score: 2)
                            tttccccccttttttg  putative PPT
      tttttgataacttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttctttaaagagatttcttctacacaagtgaattcctttttgataacttaaatgacaatttccccccttttttgtgatttgccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGCGAATATATTGTGAAGAAGATCCCAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG