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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAACAATGAGGTCACTGTTAGGCAGCTTGCTGAAATAATGATTCAG

Basic information

species Glycine max
transcript GLYMA11G19550.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 6
gtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAACAATGAGGTCACTGTTAGGCAGCTTGCTGAAATAATGATTCAG
|| ||| || | | | || | | | | | | ||| | ||| ||||| || || | |||| | ||| || ||||||| ||||| | |||||||| || || || ||||| || || ||||||||||| |||||||||||||| | |||||||| |||| ||
-----------------------------------gtatgttttctctgtttatctttacttcctttgctcttatgctagatttaccttgtt---agttgaactgaaatgtgt-actttatgtcaaaagGAAAATCCTGCTCGTGCCAATGGTCAAATCTTCAATGTCGGGAATCCTAACAATGAAGTCACTGTTAGGCAATTGGCTGAAATGATGACAGAG

upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 6
gtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAACAATGAGGTCACTGTTAGGCAGCTTGCTGAAATAATGATTCAG
||| ||| || | | | || | || || || | | | | | | |||| | ||||| | || ||||| || ||||||||||| ||||| ||||| || |||||||||||||| ||||||||||| ||||||||||||||||| ||||| |||| | ||
-----------------------------------gttagtggacc--atccttcctttcattatctgattccacatttagcttacttggaaaaaaaaaaggttgctgaatactatgatattttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG

upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 6
gtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgttgttgtcagctggtc----cactgagtgttatgacctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAACAATGAGGTCACTGTTAGGCAGCTTGCTGAAATAATGATTCAG
|| ||| || | | | |||| || || || | || | | | | |||| | |||||| || || ||||| || |||| |||||| ||||| ||||| || |||||||||||||| |||||||| | || |||| ||||||||| ||||| |||| | ||
-------------------------------------gtgagttgaccatcctttctttcattatatgattccacatttagtttacttggaaaaaaaaaaaacaggatgctgaatattatgatcttttctcagGATAATCCTGGCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCAAACAATGAAGCTACAGTTAAGCAGCTTGCAGAAATGATGACTGAG

upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S379_19V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaataca-gattcatgtgatattttttcatgttca-attattgttgttgtcagctggtccactgagtgttatgacctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAACAATGAGGTCACTGTTAGGCAGCTTGCTGAAATAATGATTCAG
||| | ||| | | | | | | | || |||| |||| || || || || || | || | | || | | | | | | || |||||||||||||| || |||||||||||||| || || || |||||||| |||| || || || | | |||||||||| | |||| | |
-------gtaagtcgcgatcact--ccaccaaaacacacatctctacagtccatgatttcactgattgattcagatcttggcatcatcactattaataac--gtatattaa-cggtgtcccc------cagGAAAACCCTGCTAGAGCCAATGGCCACATCTTCAACGTCGGCAACCCGCACAACGAAGTGACCATCCAGGAGCTTGCTGAGCTGATGACTGAT

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|120491113|gb|EH219280.1|EH219280
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|192329859|gb|FK023363.1|FK023363
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|207760735|gb|GD734058.1|GD734058
EST:     TCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: TCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|12688166|gb|BG154502.1|BG154502
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|6481482|gb|AW200753.1|AW200753
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|18039409|gb|BM307712.1|BM307712
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|21677203|gb|BQ629554.1|BQ629554
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|22540261|gb|BU090104.1|BU090104
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|19937163|gb|BQ081176.1|BQ081176
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|16105256|gb|BI892996.1|BI892996
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTATTGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|19934967|gb|BQ079997.1|BQ079997
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|27445843|gb|CA952966.1|CA952966
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|7693239|gb|AW761334.1|AW761334
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
EST: gi|14012078|gb|BG727009.1|BG727009
EST:     GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATT                         GAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC
genomic: GAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttcta ... ctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAACAATGAGGTCACTGTTAGGCAGCTTGCTGAAATAATGATTCAG
     aattattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacagGAAAACCCTGCCAGGGCCAATGGCCACATATTTAATGTGGGCAACCCTAACAATGAGGTCACTGTTAGGCAGCTTGCTGAAATAATGATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT