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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttagcattgatttatatacttccattttttttggtaacgtgttagtgatcattggtgtcatcctgttgcttctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAG

Basic information

species Glycine max
transcript GLYMA08G11740.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G11740.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g63090.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------------------------------gtttagcat-tgatttatatacttccattttttttggtaacgtgtta---gtgatcattggtgtcatcctgttgcttctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAG
                                                                  | | |   | | |    || ||| |  ||| |   |  |  |  ||    |  |||| |||| | |    |||   |   ||  ||||| ||||| || || ||||| |||||||| |||||||||||||| ||||| ||||| || ||||| || || ||||| || |||||||||
gtggttttccttcttgatgatctgtttcaatgctctttagccaattttatacgttttctgttatctgctgaaagtattaggagtagactgcattttgtcaagtcagagcattgcatgacatcactggtctaacttggttttgttcattttcagGGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG

upper sequence: GLYMA08G11740.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G118586_T01 (Zea mays), 3'ss of exon 6
---------gtttagcat-tgatttatatacttccattttttttgg------taacgtgttagtgatc--attggtgtcatcctgttgcttctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAG
          |||| ||  | ||  | |||  | | | |   ||        |||  ||||   ||    | ||||| ||   | |  ||| ||||  ||||| ||||| || || ||||| |||||||| ||||| |||||||| ||||| |||||||| ||||| || || || |||||||||||||||
agagctcagctttaccaagttatcaacataactgcttatcccttcagaaatctaaattgttcacgactgaactggtggcaaattatgccttatgttt-cagGGCTATGATATCAGTTTCCTGATAACAAACTACCATTGTGAGGACATGCATAAGCACAAGCTCATAGATTTCATCGTGCAATTTATGGAG

upper sequence: GLYMA08G11740.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14147.2 (Arabidopsis thaliana), 3'ss of exon 7
-gtttagcattgatttatatacttccattttttttggtaacgtgttagtgatcattggtgtcatcc--------tgttgcttctgttgg---------cagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAG----
   || || ||   |  | ||||    | ||     | |  |||| |  ||||  |    | || |        || |   | ||||||         ||||| |||||||| ||||| ||||||||||| |||||||| || ||||||||||| || || || ||||| || ||| | || |||||||||    
gccttggctttagatggtttactgtt-tattcccctgcattgtgtgaacgatccattcccttattcccttcaattggtttctttgttggtgttttgaacagGGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAGGCAA

upper sequence: GLYMA08G11740.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14147.1 (Arabidopsis thaliana), 3'ss of exon 7
-gtttagcattgatttatatacttccattttttttggtaacgtgttagtgatcattggtgtcatcc--------tgttgcttctgttgg---------cagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAG
   || || ||   |  | ||||    | ||     | |  |||| |  ||||  |    | || |        || |   | ||||||         ||||| |||||||| ||||| ||||||||||| |||||||| || ||||||||||| || || || ||||| || ||| | || |||||||||
gccttggctttagatggtttactgtt-tattcccctgcattgtgtgaacgatccattcccttattcccttcaattggtttctttgttggtgttttgaacagGGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAG

upper sequence: GLYMA08G11740.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 6
-----------gtttagcattgatttatatacttccatt--ttttttggtaacgtgttagtgatcattgg----tgtcatcctgttgcttctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAG
            || |    |   || | |||||  |    |||  || |  |   ||  || | | |      |||    ||| || |||  || |||||| |||||||||||||| ||||||||||| || ||||||||||| ||||| || ||||| || ||||| ||||| |||||||||||||||
aagtcatagctcttgaattctttcttttttacttagaacagtttcctgtttgcaaatttttgcttagtttcatttgtttctctggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG

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|192307232|gb|FK001232.1|FK001232
EST:     TCTCAATGAGAGCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAG                         GGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGC
genomic: TCTCAATGAGAGCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAGgtttagcatt ... ctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGC
EST: gi|192307233|gb|FK001233.1|FK001233
EST:     TCTCAATGAGAGCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAG                         GGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAG
genomic: TCTCAATGAGAGCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAGgtttagcatt ... ctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAG
EST: gi|192325005|gb|FK016146.1|FK016146
EST:     TCTCAATGAGAGCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAG                         GGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAG
genomic: TCTCAATGAGAGCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAGgtttagcatt ... ctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAG
EST: gi|15287594|gb|BI471485.1|BI471485
EST:     TCTCAATGAGAGCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAG                         GGATATGACATTAGCTTCCTTATA
genomic: TCTCAATGAGAGCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAGgtttagcatt ... ctgttggcagGGATATGACATTAGCTTCCTTATA
EST: gi|298176414|gb|HO026649.1|HO026649
EST:     GCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAG                         GGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAC
genomic: GCCGAGGCTTTCCAAGTACTGAGGAGAAAGCCTGTTCAGgtttagcatt ... ctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttggtaacgtgttagtgatcattggtgtcatcctgttgcttctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAG
     tggtaac  putative branch site (score: 2)
                                       ttgcttct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttagcattgatttatatacttccattttttttggtaacgtgttagtgatcattggtgtcatcctgttgcttctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC