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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGCTTGCTAAAGTTTGTAATGACATCTTGTCTGTCATTGATAAGCATCTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtcatctttattatactctgaccattcatgtgatatttgtgtgactaagaatgagatcatttccgtttgactaaagttaaatgtttaagttatt...

Basic information

species Arabidopsis thaliana
transcript AT1G22300.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G22300.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv18s0001g05720.t01 (Vitis vinifera), 5'ss of exon 2
ATGAGCTTGCTAAAGTTTGTAATGACATCTTGTCTGTCATTGATAAGCATCTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtcatctttattatactctgaccattcatgtgatatttgtgtgactaagaatgagatcatttccgtttgactaaagttaaatgtttaagttatt-
|||||||  | ||  | || |||||||| ||||| ||||||||||| |||||||| ||||| ||     | | ||| |||||||| || | ||| || |||||||    || |   |  |  | |     |   | | | ||||   | | |  || |      | |   |    |      |||   | |      ||  
ATGAGCTGTCAAAGATCTGCAATGACATATTGTCCGTCATTGATAATCATCTCATCCCATCATCCTCAACAGGGGAATCAACTGTTTTCTACTATAAGATgtgaggaatatttgactcttcttttccttttgtttattagattttgattattggga-tacttcaaatgatgagcaaacttgattatgagatgggacaataa
















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|124738167|gb|EH829569.1|EH829569
EST:     CATCGTCTAACGCTGTGGAGTCAACCGTCTTTTTCTACAAAAT                         GAAAGGAGATTACTATCGCTATCTTGCGGAG
genomic: CATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTATCTTGCGGAG
EST: gi|47828946|gb|CK118630.1|CK118630
EST:     CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAAT                         GAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
genomic: CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
EST: gi|124850151|gb|EH934588.1|EH934588
EST:     CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAAT                         GAAAGGAGATTACTATCGCTATC
genomic: CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTATC
EST: gi|164228562|gb|ES198977.1|ES198977
EST:     CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTT-CTACAAAAT                         GAAAGGAGATTACTATCGCTA
genomic: CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTA
EST: gi|47830317|gb|CK120001.1|CK120001
EST:     CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAAT                         GAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
genomic: CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
EST: gi|124917656|gb|EH991530.1|EH991530
EST:     CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAAT                         GAAAGGAGATT
genomic: CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATT
EST: gi|47831981|gb|CK121665.1|CK121665
EST:     CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAAT                         GAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
genomic: CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
EST: gi|47828961|gb|CK118645.1|CK118645
EST:     CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAAT                         GAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
genomic: CTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
EST: gi|164136677|gb|EL978538.1|EL978538
EST:     CCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAAT                         GAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
genomic: CCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCTGAACG
EST: gi|125222347|gb|EL236432.1|EL236432
EST:     TCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTAACAAAAT                         GAAAGGAGATTACTATCGCTAT
genomic: TCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTA-CAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTAT
EST: gi|124815923|gb|EH900789.1|EH900789
EST:     TCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAAT                         GAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCT
genomic: TCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtca ... ttctatgtagGAAAGGAGATTACTATCGCTATCTTGCGGAGTTCAGTTCTGGTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAGCTTGCTAAAGTTTGTAATGACATCTTGTCTGTCATTGATAAGCATCTCATTCCATCGTCTAACGCTGTGGAGTCAACTGTCTTTTTCTACAAAATgtgagtgtcatctttattatactctgaccattcatgtgatatttgtgtgactaagaatgagatcatttccgtttgactaaagttaaatgtttaagttatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG