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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactctaggcattcatacatatggaacttgatcccagatttaataggataggtgattcttcaatgttatctaacatgttatggttgaaaattatgtgcagAATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAGTGGGCTGATTTCAATGTTGATGCTTATTCTGCTGCATCACTGAAAGCTG

Basic information

species Glycine max
transcript GLYMA11G20520.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 11
aactctaggcattcatacatatggaacttgatcccagatttaataggataggtgattcttcaatgttatctaacatgttatggttgaaaattatgtgcagAATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAGTGGGCTGATTTCAATGTTGATGCTTATTCTGCTGCATCACTGAAAGCTG
           ||  |   |   | | | |  |   |  ||  |  || ||     | ||| |||      ||  |  | |  |  |   |  | || ||||||| |||||||| |||||| | || || || || ||||| || || |||||||||||||||||||||||||| ||||| |||||  |||| |||||||
------gtaagttagtgtgtccagtattggtactttgtgttcttttgacag-----ttttctatg--gctgaaatttgtgttatctattgtcttctgtagAATGTTCCTCCTGCGGTTTTGATCCGGTTCCTTAGAGAGCATCGATCTGAGTGGGCTGATTTCAATGTTGATGCATATTCCGCTGCTACACTTAAAGCTG

upper sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 11
--aactctaggcattcatacatatggaacttgatcccagatttaataggataggtgattcttcaatgttatctaac-atgttatggttgaaaattatgtg--cagAATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAGTGGGCTGATTTCAATGTTGATGCTTATTCTGCTGCATCACTGAAAGCTG
     |  | | |    |   |   ||| |   |||   | |||    |||| ||  || |   ||  | | |    |||||   |||     || |     |||||||| ||||| |||||| ||||||| || |||||||||||||| ||||||||||||||||| | ||||||||| ||||||||||||||| |||||||| 
ctttattgaagtagcagtgt-tccagaattc--tccttaacttat--agatatgtctttatgggattatgtgtgtttatgtttctgtttctttttttcctgccagAATGTTCCTCCGGCAGTTCTGGTTCGCTTCCTGAGGGAGCACCGGTCAGAGTGGGCTGATTTTAGTGTTGATGCCTATTCTGCTGCATCATTGAAAGCTA
















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|8670112|gb|BE191219.1|BE191219
EST:     CTGTGCAAAAGCTTCTATGTTGCTTCAA                         AATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAG
genomic: CTGTGCAAAAGCTTCTATGTTGCTTCAAgtgagtcttg ... ttatgtgcagAATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAG
EST: gi|27426486|gb|CA938006.1|CA938006
EST:     TTACATTCCTTGGAGGAATTCTCTGTGCAAAAGCTTCTATGTTGCTTCAA                         AATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAG
genomic: TTACATTCCTTGGAGGAATTCTCTGTGCAAAAGCTTCTATGTTGCTTCAAgtgagtcttg ... ttatgtgcagAATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAG
EST: gi|254348193|gb|GR851872.1|GR851872
EST:     CTTCTATGTTGCTTCAA                         AATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAG
genomic: CTTCTATGTTGCTTCAAgtgagtcttg ... ttatgtgcagAATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAG
EST: gi|14516259|gb|BI094931.1|BI094931
EST:     TTACATTCCTTGGAGGAATTCTCTGTGCAAAAGCTTCTATGTTGCTTCAA                         AATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAG
genomic: TTACATTCCTTGGAGGAATTCTCTGTGCAAAAGCTTCTATGTTGCTTCAAgtgagtcttg ... ttatgtgcagAATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggataggtgattcttcaatgttatctaacatgttatggttgaaaattatgtgcagAATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAGTGGGCTGATTTCAATGTTGATGCTTATTCTGCTGCATCACTGAAAGCTG
                      atctaac  putative branch site (score: 2)
                                      ttgaaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactctaggcattcatacatatggaacttgatcccagatttaataggataggtgattcttcaatgttatctaacatgttatggttgaaaattatgtgcagAATGTCCCTCCTGCAGTTTTGGTTCGTTTTCTGAGGGAGCACCGCTCAGAGTGGGCTGATTTCAATGTTGATGCTTATTCTGCTGCATCACTGAAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttatg