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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcctttgacttgtacaggagtaatttagattgtattttgatttgttcatagtcgtatttatcagttctctcttaaccaacaaagatacatttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTTGGAGATGGATCAACAAGTCTGTTTTTTCAGTTG

Basic information

species Glycine max
transcript GLYMA06G14590.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G14590.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 3'ss of exon 7
tgcctttgacttgtacaggagtaattta--gattgtattttgatttgttcatagtcgtatttatcagttctctcttaaccaacaaagatacat----ttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTTGGAGATGGATCAACAAGTCTGTTTTTTCAGTTG
   | ||  |   |   | |||   | |  | ||   ||||  ||| ||     |    || | ||  | ||    ||  |       | | |     ||||| ||||||||| ||||||| ||||||||  | || || ||||||||||| || |||||| | ||| | ||||| ||||| || |||||||| || || ||||||
---ccttatcagat---gaagtgcctcaatgcttagcttttcctttttttccccttaatttgagcaagtatcaagaaatgacagctttttcctggttctgttttagGTTTGAGCGAGAACGGACTTGCCCCCTGTGTAGAGCATTGGTAAAGCCTGCTGATATTCGGTCATTTGGTGATGGTTCTACAAGTCTTTTCTTCCAGTTG

upper sequence: GLYMA06G14590.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G061980_T01 (Zea mays), 3'ss of exon 7
tgcctttgacttgtacaggagtaatttagattgtattttgatttgttcatagtcgtatttatcagttctctcttaaccaacaaagat-acatttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTTGGAGATGGATCAACAAGTCTGTTTTTTCAGTTG
 |    |  ||        | |  |||  |||   |||     || || |  |      || ||         | ||  |     || |   |  ||  ||||| ||| |||| || |||||||| || ||||| |||||||||||||| |||||| | ||| | ||||| ||||| || |||||||| || || ||||||
-ggtagtatctcaatgcttaattgtttgcattacttttgcccgtgatcctcctatctaataacaaacgagaagtgactgattgctattatgctgtttctagGTTCGAGCGAGAGCGGACTTGCCCCTTGTGCAGAGCATTGGTAAAACCTGCTGATATCCGGTCATTTGGTGATGGTTCTACAAGTCTATTCTTCCAGTTG
















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|254348117|gb|GR851796.1|GR851796
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|37994656|gb|CF806311.1|CF806311
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|207794526|gb|GD767175.1|GD767175
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|208150334|gb|GD947383.1|GD947383
EST:     TGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: TGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|208205470|gb|GE004915.1|GE004915
EST:     TTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: TTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|207698331|gb|GD680584.1|GD680584
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|193350610|gb|FK317530.1|FK317530
EST:     TATTGTTGAGCTGTAAAACACATGTTCTGTGAGGAGTGTGTATCTAAATG                         GTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: TATTGTTGAGCTGT-AAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|51342137|gb|CO983398.1|CO983398
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatagtcgtatttatcagttctctcttaaccaacaaagatacatttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTTGGAGATGGATCAACAAGTCTGTTTTTTCAGTTG
                         tcttaac  putative branch site (score: 2)
                                             tttgtttc  putative PPT
          tatttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcctttgacttgtacaggagtaatttagattgtattttgatttgttcatagtcgtatttatcagttctctcttaaccaacaaagatacatttgtttcagGTTTGAGAGAGAACGAACTTGCCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTTGGAGATGGATCAACAAGTCTGTTTTTTCAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - tgacttg
- - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacaa