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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaaaacccgcttttcaaatgtcaaaatttccttcttctttttctggtttattgtgatgtataatatgaaactaaacttgaatatgcttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAG

Basic information

species Arabidopsis thaliana
transcript AT5G01220.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G01220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g04920.1 (Oryza sativa), 3'ss of exon 6
gtatgtaaaacccgcttttcaaatgtcaaaatttccttcttctttttctggtttattgtgatgtataatatgaaactaaacttgaatatgcttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAG
    ||||         | | | |      ||||     ||| |   | |    ||| | ||||   ||   ||  |  | | ||    ||    | ||||||||||||| ||||| |||||||| |||||||| || |||| ||| ||  | |||||| ||  | | ||   ||  |   |||
----gtaagcattatactcccatttc----atttatactttcataaacagtcagatttttatgtg--atgaaaacattgattcgatccggca---aacagGGTTCCTTCATAGAGCTGCTGATCTAACATTAGTGCCATCTGTTGCTATCAGCAAAGATTTTGAAACTGCCCATGTTATATCAG

upper sequence: AT5G01220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G14200.1 (Glycine max), 3'ss of exon 6
gtatgtaaaacccgcttttcaaatgtcaaaatttccttcttctttttctggtttattgtgatgtataatat-gaaactaaacttgaatatgc--ttttat-cagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAG
                       | |  | ||   ||  |||||  | || |  | |  ||   ||| | | |  |   ||| |||||||||  ||||||  ||  || || || ||||| |||||||||||||| || || || |||||||||| ||||||||||  || |||| | | ||| ||||
----------------------gtatgtatatgctctctttcttcctttgttcaacttggaatcatatttttgtgaaataacatgaatatgctattttatgtagAATTTCTGCATAGAGCAGCTGATCTTACATTGGTGCCATCAGCTGCCATTGCAAAAGATCTTGAAGAAGCTCGAGTAACAGCAG
















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|116409173|gb|EG451765.1|EG451765
EST:     CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAA                         GGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTG
genomic: CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAAgtatgtaaaa ... cttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTG
EST: gi|116431123|gb|EG473715.1|EG473715
EST:     CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAA                         GGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTG
genomic: CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAAgtatgtaaaa ... cttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTG
EST: gi|86057508|gb|DR353265.1|DR353265
EST:     CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAA                         GGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTG
genomic: CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAAgtatgtaaaa ... cttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTG
EST: gi|116409166|gb|EG451758.1|EG451758
EST:     CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAA                         GGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTG
genomic: CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAAgtatgtaaaa ... cttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTG
EST: gi|116409154|gb|EG451746.1|EG451746
EST:     CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAA                         GGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCAT
genomic: CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAAgtatgtaaaa ... cttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCAT
EST: gi|116409155|gb|EG451747.1|EG451747
EST:     CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAA                         GGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCC
genomic: CCCAAGATACACTTTTAGTTGGTTGGTAAAACCAATGTGGTCTATAATAAgtatgtaaaa ... cttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctggtttattgtgatgtataatatgaaactaaacttgaatatgcttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAG
                            aactaaa  putative branch site (score: 2)
                                             cttttatc  putative PPT
                  tataatatgaaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaaaacccgcttttcaaatgtcaaaatttccttcttctttttctggtttattgtgatgtataatatgaaactaaacttgaatatgcttttatcagGGTTCCTTCACAGAGCGGCTGATCTTACATTAGTTCCTTCTGCTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG