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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctaattgagtgttgataataattatagccttctgaaattacatagaatttctggatctgttgatttatgtatcatatattcttccttggttacttccagGACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGTTTGAGAGATGTAGATATTAAAAATTATATTAAAGTTGAGAAGGTCCCAG

Basic information

species Glycine max
transcript GLYMA09G28650.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28650.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 8
gctaattgagtgttgataataattatagccttctgaaattacatagaatttc---tggatctgtt-gatttatgtatcatatat--tcttccttggttacttccagGACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGTTTGAGAGATGTAGATATTAAAAATTATATTAAAGTTGAGAAGGTCCCAG
      | ||| ||  |  || | |     ||        ||| |   | ||   |   | ||||   |||||   | || |    ||||  |    ||    |||||| | |||||||||||||||||||||| |||||||||  | || |||||| || | || || ||||| || || ||||| ||||| |||||||| || |
-----gtaagtatttcttttattcaaga--tttgagtgccacacaacttctcggttaagtgtgttcagtttatagtttatctgacgtcttgttgtactatgctcagGACCTTGCTATTGATGCTACTACAACAGCAGGTGTTGACCTAGGTCAAGGTATGCGTGAAGTTGATATCAAGAAATATATCAAAGTGGAGAAGGTTCCTG

upper sequence: GLYMA09G28650.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 8
--gctaattgagtgttgataataattatagccttctgaaattacatagaatttctggatctgttgatttatgtatcatatattcttccttggttacttccagGACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGTTTGAGAGATGTAGATATTAAAAATTATATTAAAGTTGAGAAGGTCCCAG
  |  |||       |||| | ||| |        || |      ||| |  | |  | |  |   |||| ||||   |||       |||  |   | |||||| | |||||||||||||||||||||| |||||||||  |||| || ||| || | || || ||||| || || || ||||||||||| ||||| || |
aggacaatgccagaatgatta-aataaatttgaattggaggggggtagtacctattcaaccttgattttacgtatttgataactcgtgttg-ctgtattcagGACCTTGCTATTGATGCTACTACAACAGCAGGTGTTGACCTTGGTCAGGGTATGCGTGAAGTTGATATCAAGAAATACATTAAAGTTGAAAAGGTTCCTG
















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|193324828|gb|FK288068.1|FK288068
EST:     AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCT                         GACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGT
genomic: AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCTgtgagtatcc ... ttacttccagGACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGT
EST: gi|208176087|gb|GD974318.1|GD974318
EST:     AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCT                         GACTTAGCTATTGATGCTA
genomic: AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCTgtgagtatcc ... ttacttccagGACTTAGCTATTGATGCTA
EST: gi|209725416|gb|BW658278.1|BW658278
EST:     AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCT                         GACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGT
genomic: AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCTgtgagtatcc ... ttacttccagGACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGT
EST: gi|207717196|gb|GD697690.1|GD697690
EST:     AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCT                         GACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAA
genomic: AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCTgtgagtatcc ... ttacttccagGACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAA
EST: gi|207835101|gb|GD809130.1|GD809130
EST:     AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCT                         GACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGT
genomic: AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCTgtgagtatcc ... ttacttccagGACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGT
EST: gi|207832867|gb|GD804005.1|GD804005
EST:     AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCT                         GACTTAGCTATTGATAGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGG
genomic: AAAGCTGCATAGGTACCAAATTCACAGGTCAATTTGGGGATTTAATTGCTgtgagtatcc ... ttacttccagGACTTAGCTATTGAT-GCTACTACAACAGTAGGTGTTGAGATTGGCCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatttctggatctgttgatttatgtatcatatattcttccttggttacttccagGACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGTTTGAGAGATGTAGATATTAAAAATTATATTAAAGTTGAGAAGGTCCCAG
             tgttgat  putative branch site (score: 4)
                                             ttacttcc  putative PPT
               ttgatttatgtatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctaattgagtgttgataataattatagccttctgaaattacatagaatttctggatctgttgatttatgtatcatatattcttccttggttacttccagGACTTAGCTATTGATGCTACTACAACAGTAGGTGTTGAGATTGGCCAAGGTTTGAGAGATGTAGATATTAAAAATTATATTAAAGTTGAGAAGGTCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG