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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtcacgtttcccccatttctgttgtgatttttgcaataaatttattcacaaagttgttttcttaataaatatgtgtaattttctatctatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATATCTCAACTTAACTCGTATTTATACTAAACCTAAAGGGATGAATCCTGAT

Basic information

species Glycine max
transcript GLYMA04G39690.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 7
actgtcacgtttcccccatttctgttgtgatttttgcaataaatttattcacaaagttgttttcttaataaatatgtgtaattttctatctatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATATCTCAACTTAACTCGTATTTATACTAAACCTAAAGGGATGAATCCTGAT
   || |   ||     ||| | |    ||||  ||| ||||| || || ||       ||||   | |||     | ||| |||  || |||  | |||||| |||||||||||||| |||||||| |||||||| || || ||||||||  |  |  ||||||| || || || ||||| || |  |||||||| |||
---gtaaatgttgttaaattaccggcaggatt--tgcgataaacttgtttac-------ttttgccattaag---atataaattt--atttatcttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATACTTGGATCTAACTCGAATCTACACAAAACCAAAGGCAATGAATCCGGAT

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 3'ss of exon 7
----actgtcacgtttcccccat--ttctgttgtgatttttgcaataaatttattcacaaagttgttttcttaataaatatgtgtaattttctatctatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATATCTCAACTTAACTCGTATTTATACTAAACCTAAAGGGATGAATCCTGAT
        |    ||| ||  ||  |  | || |  |  ||    | |  || ||||     ||  |  |||  |   | || ||    |   ||   |||| |||||| || ||||||||||||||||||||||| || || || || ||||| |||||  | |||||||| || || || || || || || |||||||| |||
tggtgtcattgtttttgccaaataatcttattctagtcattcatttgaggtttttca-----tttctccctttttggttgtg-gtttgatatgattattgctgcagTGCTCACCTGGAGTGGAACCTTGATGGTCTGCTAGAAAAGATATGGGAGTATCTTGATTTAACTCGCATATACACAAAGCCCAAGGGAATGAATCCCGAT
















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|163920656|gb|EH039949.1|EH039949
EST:     CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAG                         TGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
genomic: CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAGgtaatacttc ... tatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
EST: gi|58024862|gb|CX711603.1|CX711603
EST:     CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAG                         TGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
genomic: CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAGgtaatacttc ... tatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
EST: gi|58023958|gb|CX710699.1|CX710699
EST:     GGATAAGCTACTTCATTACTGCCCAATCAG                         TGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
genomic: GGATAAGCTACCTCATTACTGCCCAATCAGgtaatacttc ... tatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
EST: gi|15816018|gb|BI788293.1|BI788293
EST:     CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAG                         TGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
genomic: CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAGgtaatacttc ... tatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
EST: gi|207731163|gb|GD706594.1|GD706594
EST:     CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAG                         TGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
genomic: CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAGgtaatacttc ... tatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
EST: gi|57575753|gb|CX548728.1|CX548728
EST:     CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAG                         TGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA
genomic: CTTGAGGAACTGGAGATCTTGGATAAGCTACCTCATTACTGCCCAATCAGgtaatacttc ... tatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcacaaagttgttttcttaataaatatgtgtaattttctatctatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATATCTCAACTTAACTCGTATTTATACTAAACCTAAAGGGATGAATCCTGAT
                 tcttaat  putative branch site (score: 3)
                                    ttttctatct  putative PPT
              ttttcttaataaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgtcacgtttcccccatttctgttgtgatttttgcaataaatttattcacaaagttgttttcttaataaatatgtgtaattttctatctatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATATCTCAACTTAACTCGTATTTATACTAAACCTAAAGGGATGAATCCTGAT

-ctgtcac
- - - - - ttccccc
- - - - - - - - - - tctgttg
- - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - attcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtgt