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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactgttgtcgaatctcttagcatgaaaatgaaatagatctacgtttttggaagcaaattcaaagatcggatattttttttttgttggtgatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTGTGGAAGAGAGGAATCTTGTATCTGTAGGGTACAAGAATGTGATTGGTGC

Basic information

species Arabidopsis thaliana
transcript AT1G22300.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G22300.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g05720.t01 (Vitis vinifera), 3'ss of exon 1
-------ttactgttgtcgaatctcttagcatgaaaatgaaatagatctacgtt-tttggaagcaaattcaaagatcggatattttttttttgttggtgatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTGTGGAAGAGAGGAATCTTGTATCTGTAGGGTACAAGAATGTGATTGGTGC
        || | |  | ||||   ||  |||     |  |||   | ||| |  |||      | |||  | ||| || | | || ||| |        || | |||| ||||| || || ||||||||||||||| |  | |||||||| || || ||||| ||||||||||| |||||||| || || || ||||| ||||| ||
gcaggagataatttgtttgaatt--ttgacattttctt--aatgagtttacttcatttcttgttatatttgatgattggttttgttatttctccct----tgtttcagAGATGGTTGAAGCAATGAAGAAAGTTGCTAAATTGGATGTGGAACTGACAGTGGAGGAGAGGAATCTGGTATCTGTTGGATATAAAAATGTTATTGGGGC

upper sequence: AT1G22300.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S67_176V6.1 (Physcomitrella patens), 3'ss of exon 1
-------ttactgttgtcgaatctcttagcatgaaaatgaaatagatctacgtttttggaagcaaattcaaagatcggatattttttttttgttggtgatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTGTGGAAGAGAGGAATCTTGTATCTGTAGGGTACAAGAATGTGATTGGTGC
       |||||||    || | | ||||   ||||  |||||  | ||  |      |   | |  |    ||| |    |   ||   | |||   ||  |||||| ||||||||| ||||||||||||| ||  |||||||||||||||| || || || ||| | |||||  | ||||| || ||||||||||||||||||||
acatgaattactgtgaaggagtattttag---gaaagcgaaatgtaccttagcgacatgtttcga--tgggtgatggaccgtgcgttgggtcttgtgaat--tgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAGTAGAGGAGCGAAATCTCTTGTCTGTGGGTTACAAGAATGTGATTGGTGC

upper sequence: AT1G22300.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 1
-----ttactgttgtcgaatctcttagcatgaaaatgaaatagatctacgtttttggaagcaaattcaaagatcggatattttttttttgttggtgatga-tgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTGTGGAAGAGAGGAATCTTGTATCTGTAGGGTACAAGAATGTGATTGGTGC
     |     |||| | | |    |   || || || |   |||||   ||| | | ||    |  | |  ||      |  | | |||  | ||   | |||||||||||||||| ||||||||||||| ||  ||||||| ||||| || || ||||| ||| | |||||  | || || || ||||||||||| || || ||
aaaagtagtatttgtaggaacga--actgtgcaactgcacgtgatct---tttcttggagtcgttgtatatgtccacagctcatgtattgc-gttgccaactgcagAAATGGTGGAGTCGATGAAGAAAGTCGCGAAGCTTGACGTGGAACTTACAGTGGAGGAGCGAAATCTCTTGTCCGTGGGTTACAAGAATGTAATCGGAGC

upper sequence: AT1G22300.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
ttactgttgtcgaatctcttagcatgaaaatgaaatagatctacgtttttggaagcaa-attcaaagat--cggatattttttttttgttggtgatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTGTGGAAGAGAGGAATCTTGTATCTGTAGGGTACAAGAATGTGATTGGTGC
    ||  || |     |  || | |  | ||   | |  |   ||    ||  |     ||    |||   |||   | |  |    || ||||   |||||| ||||||||| ||||||||||||| ||  ||||||| |||||||| || ||||| ||| | |||||  | ||||| || |||||||| |||||||| ||
-gtttgcagttgggaggcagag-acgtgagtgcggttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtggtgcgttttgtga-attgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC

upper sequence: AT1G22300.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S46_127V6.1 (Physcomitrella patens), 3'ss of exon 1
---ttactgttgtcgaatctcttagcatgaaaatgaaatagatctacgtttttggaagcaaattcaaagatcggatattttttt-tttgttggtgatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTGTGGAAGAGAGGAATCTTGTATCTGTAGGGTACAAGAATGTGATTGGTGC
     |   | |  ||| |  | ||  | |    | |    || || ||   |  |     |||    | | |  | |||| |  || ||   |     |||||| ||||||||  |||||||||| |||||  |||||||||||||||| || || || ||| | |||||  | || || || || |||||||| || || ||
aaccaatcatag--gaaacattcagggtcatgtcgtagggtatttaagtcagtatatctgcatttg--gcttgtttgttttgtgattcgtaatttgaactgcagAGATGGTGGAATCGATGAAGAAGGTTGCCAAGCTTGATGTGGAGCTGACAGTAGAGGAGCGAAATCTCTTGTCCGTGGGTTATAAGAATGTCATCGGAGC

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|47828946|gb|CK118630.1|CK118630
EST:     AAAGCAGGTTTACTTGGCTAAGCTCTCCGAGCAAACCGAAAGATACGATG                         AAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTG
genomic: AAAGCAGGTTTACTTGGCTAAGCTCTCCGAGCAAACCGAAAGATACGATGgtattttccg ... gatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTG
EST: gi|47830317|gb|CK120001.1|CK120001
EST:     AAAGCAGGTTTACTTGGCTAAGCTCTCCGAGCAAACCGAAAGATACGATG                         AAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTG
genomic: AAAGCAGGTTTACTTGGCTAAGCTCTCCGAGCAAACCGAAAGATACGATGgtattttccg ... gatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTG
EST: gi|47831981|gb|CK121665.1|CK121665
EST:     AAAGCAGGTTTACTTGGCTAAGCTCTCCGAGCAAACCGAAAGATACGATG                         AAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTG
genomic: AAAGCAGGTTTACTTGGCTAAGCTCTCCGAGCAAACCGAAAGATACGATGgtattttccg ... gatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTG
EST: gi|47828961|gb|CK118645.1|CK118645
EST:     AAAGCAGGTTTACTTGGCTAAGCTCTCCGAGCAAACCGAAAGATACGATG                         AAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTG
genomic: AAAGCAGGTTTACTTGGCTAAGCTCTCCGAGCAAACCGAAAGATACGATGgtattttccg ... gatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttggaagcaaattcaaagatcggatattttttttttgttggtgatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTGTGGAAGAGAGGAATCTTGTATCTGTAGGGTACAAGAATGTGATTGGTGC
                          atattttttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactgttgtcgaatctcttagcatgaaaatgaaatagatctacgtttttggaagcaaattcaaagatcggatattttttttttgttggtgatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTGTGGAAGAGAGGAATCTTGTATCTGTAGGGTACAAGAATGTGATTGGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA