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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagaattaaaattgcttatagctttatagaattatggttttttaactagtatatgtagtaatatttcaattttttccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTGGATCAATACGGGCAGACCATTTTGGATT

Basic information

species Arabidopsis thaliana
transcript AT1G11910.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G11910.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G39240.2 (Glycine max), 3'ss of exon 8
------gtaagcaagaattaaaattgcttat-----agctttatagaattatggttttttaactagtatatgtagtaatatttcaattttttccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTGGATCAATACGGGCAGACCATTTTGGATT
        |    |   || | ||||| |||     || | || | || |     |   ||  | || | | |  |   || |    ||||   || |||||||| |||| || |||||||||||||| ||||||||| |||||||| | |||||  | |||||||||||||| |   | || || || || || |||||||
taattctcattgcattgtttatattgcatatgaaaaaggtcta-acaaatgcttctgactagtttgtttctatgatcgcatattgggttttgttct-tgtagACTGTAATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGCCAAGAATGCAAGACTGTTGTTGCAGAGTATGGACAAACAATATTGGATT

upper sequence: AT1G11910.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G11670.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------------------------------------------gtaagcaagaattaaaattgcttatagctttatagaattatggttttttaactagtatatgtagtaatatttcaattttttccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTGGATCAATACGGGCAGACCATTTTGGATT
                                                                                                |||  ||     ||     || | |  | || | |   |||   || | || |     | |  | | | | ||   || |   | |||||||| |||| ||||||||||| || || || ||||||||||||||||| ||| |  | |||| | | |||||  ||||||| || || || || ||||| |
gtatgaataaatgcttgtaaatgtagcttgtaaatgtaggcagctatttagattttcatttccaattagaatttcattgtctgtaaagcatgcttttaactaatgggaaaggggtctaaaaattgtacaaacaaatg--cttctgacca-----tatgatcaaaatacatgattatgtttttgtagACTGTAATTACCATGATAAATCAAGCAATCGGAGCAGCTGGAGTTGTAAGCAAAGAATGCAGGTCCGTTGTCAATCAATATGGACAAACAATCTTGGAAT

upper sequence: AT1G11910.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G01500.1 (Glycine max), 3'ss of exon 8
------------------------------------------------------------------------------------gtaagcaaga-attaaaattgcttat--agctttatagaattatggttttt---taactagtatatgtagtaatatttcaattttttccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTGGATCAATACGGGCAGACCATTTTGGATT
                                                                                     | |    |   || | ||||| | |  |     ||  ||  |  | || |   || || || | | |  | | || |    ||||   || |||||||| | || || |||||||||||||| ||||||||| |||||||| | |||||  | ||||||||  |||| |   | || || || || || |||||||
gtatgaataaatgagtgtagatatagattgattaatgtttatgtagtattcaacaattatgggggtctttagacattgataattctcattgcgttgtttatattgcatgtgaaaaaagatctaacaaatgcttctaactagcttgtttctatgatcacatatgtggttttgttct-tgtagACTGTCATAACTATGATAAACCATGCAATTGGAGCATCTGGAGTTATGAGCCAAGAATGCAAGACCATTGTTGCAGAGTATGGACAAACAATATTGGATT

upper sequence: AT1G11910.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 8
--------gtaagcaagaattaaaat----tgcttatagctttatagaattatggttttttaactagtatatgtagtaatatttcaattttttccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTGGATCAATACGGGCAGACCATTTTGGATT
                ||  | |||     | ||| ||||  ||||| | |     | |  || || |   |||   | |  |||| | | |  | |    || || |  |  | |||||||| ||||| ||||||||  | ||||||||||||||| | ||||||||||| || |  || || ||| | || ||  ||||||
caaataaaacggctgtgatatgaaagcccatacttttagcgctatagcaatgcatctctaaaaata-tggttgtttaattgattcagtctgt--ctttctcagGCTGTTGTTGCTATGATAAATCATGCCATTGGAGCCACCGGAGTTGTTAGCCAGGAATGCAAGACTGTAGTTGCACAGTATGGGGAAACAATCATGGATT

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|47832120|gb|CK121804.1|CK121804
EST:     GCTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACG                         ACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
genomic: GCTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
EST: gi|163966471|gb|ES185363.1|ES185363
EST:     CTGGTACATCTTTGCTTGCCGGTCCAACG                         ACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
genomic: CTGGTACATCTTTGCTTGCCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
EST: gi|125263241|gb|EL277326.1|EL277326
EST:     CTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTGACCGGTCCAACG                         ACTATAATCACCATGATAAA
genomic: CTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTG-CCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCATGATAAA
EST: gi|116484531|gb|EG527123.1|EG527123
EST:     GCTGTTCTGCGATAGCAGATTCTGGTACATCCTTGCTTGCCGGTCCAACG                         ACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGT
genomic: GCTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
EST: gi|152033756|gb|BP560644.3|BP560644
EST:     GCTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACG                         ACTATNATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
genomic: GCTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
EST: gi|116417009|gb|EG459601.1|EG459601
EST:     GCTGTTCTGCGATAGCAGATTCCGGTACATCTTTGCTTGCCGGTCCAACG                         ACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
genomic: GCTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
EST: gi|164224743|gb|ES107130.1|ES107130
EST:     GATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACG                         ACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
genomic: GATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
EST: gi|164226379|gb|ES040669.1|ES040669
EST:     GCCGGTCCAACG                         ACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
genomic: GCCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
EST: gi|124766639|gb|EH856769.1|EH856769
EST:     GCTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACG                         ACTATAATCACCAT
genomic: GCTGTTCTGCGATAGCAGATTCTGGTACATCTTTGCTTGCCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCAT
EST: gi|164055544|gb|ES185027.1|ES185027
EST:     TCTTTGCTTGCCGGTCCAACG                         ACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC
genomic: TCTTTGCTTGCCGGTCCAACGgtaagcaaga ... ccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatggttttttaactagtatatgtagtaatatttcaattttttccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTGGATCAATACGGGCAGACCATTTTGGATT
         ttttaac  putative branch site (score: 2)
                                 tttcaattttttccct  putative PPT
       ttttttaactagtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaagaattaaaattgcttatagctttatagaattatggttttttaactagtatatgtagtaatatttcaattttttccctgtgtagACTATAATCACCATGATAAACCATGCTATTGGAGCAGCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTGGATCAATACGGGCAGACCATTTTGGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA