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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcttacaatatccaataaattgatttcactttgtgcccctccctcttttccggcagaatgtttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT

Basic information

species Glycine max
transcript GLYMA15G09090.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 6
catcttacaatatccaataaattgatttcact--ttgtgcccctccctcttttccggcagaatgtttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT
  |   |  ||| |   |    |   ||| ||  || ||    | | || |||  |  |   |      |    | |  | || |   |  | |  || |||||    |||||| | || ||||||||||| || || || |  ||||||||||| || || ||||||||||| || |||||||||| ||||||||| || |
-cttggattataactgttggcctctcttccctagttctgttatttcttcatttt-gctattttaacaaatagattgatgatctccttgtactattccaccagGTTCCTGGTGAACCGAACATATCATACATTTGCTCTCGCTATTATCGTGCTCCTGAGCTCATATTTGGTGCAACCGAGTATACAACTTCAATTGACATAT

upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 6
catcttacaatatccaataaattgatttcactttgtgcccctccctcttttccggcaga---atgtttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT
 |  | ||  ||    ||   ||    | |  |||  | | |  ||  | | | | | |    || | |   |  |||  |  | |  ||  ||  |  |||| |    |||||| | || ||||| |||||||| || || | ||||||||| || || || ||||||||||| || ||||||||||||||||| || || |
-acttgactgtaattcatgtgttataataa--ttggactctttacttgtataccgtaaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT

upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 6
catcttacaatatccaataaattgatttcactttgtgcccctccctcttttccggcagaatgt-ttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT
 |  | ||  ||    ||   || ||  || || |   |  | | | | | | |      | | | |   | ||||  |  | || || |||| |  |||| |    |||||| | || ||||| |||||||| || || |  |||||||||||||| || |||||||| || || |||||||||| |||||| || || |
gaattgactgtaattcatgtgtt-ataacaattagattctttacttgtatgctgtatttttttatccacatactaatcagttccatatgttgttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT

upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 5
----catcttacaatatccaataaattgatttcactttgtgcccctccctcttttccggcagaatgtttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT
     |  ||   | ||   ||||| | |||  |||| ||  |  |   | ||||| |  |   |||   ||  | |   ||  |   | |||||  |||   ||| ||||||||||| || || || ||||| || ||||||||||| ||||| || || || |||||||||||||| ||||| |||| ||| |||||||| |
gtaagactttgtgacat---ataaactcattcgactt-gtagcggttgttgttttctgtgatcttgtcatttactgttgaaattt---acttttgcttca---gGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCT

upper sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 6
catcttacaatatccaata---aattgatttcactttgtgcccctccctcttttccggcagaatgtttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT
  | | |   ||  || ||   | | |     |  |  |  |      | | || |      || |||| |||| | || |   | ||      | ||||||||| ||||||||||| || ||||||||||||||||| || ||||| || || || ||||| |||||||| ||||||||||||||||  ||||||||||| |
tctttcatggtagtcagtactcagtaggaagaaagtctttgcttgttttttctttctatgatatctttcatgttttcacca---tgaatccaattttcatcagGTTAAAGGTGAAGCAAACATATCATACATATGTTCTCGTTTCTACCGAGCACCTGAACTCATATTTGGGGCCACAGAGTATACAACCTCAATTGATATAT

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|7042489|gb|AW472383.1|AW472383
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTTGAAGTGCAGAAGTTCTA                         GTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCT
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtaggtctta ... gtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCT
EST: gi|27446207|gb|CA953330.1|CA953330
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA                         GTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCT
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtaggtctta ... gtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCT
EST: gi|208208469|gb|GE008460.1|GE008460
EST:     CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA                         GTAAAAGGTGAAGCTAATATATCATACTTATGTTCACGATTCTATCGTGCT
genomic: CTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTAgtaggtctta ... gtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttccggcagaatgtttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT
                        ttctaac  putative branch site (score: 1)
                                         ttttgtctc  putative PPT
                                   ttcaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcttacaatatccaataaattgatttcactttgtgcccctccctcttttccggcagaatgtttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT

- - - - - - -ccaataaa
- - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accttca