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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcattactgagattttatttttctgagctttttattcgactgttaataagtgacagaggggtagtatgatttcgtagcccatgccattgatacaagtgatttttttttgttggactaatatgtaattgaacgttcactatgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAAAATACTGGCAAATTTATGAAAGAACTTTGGACACTTCTTCTAAGCGCAC

Basic information

species Arabidopsis thaliana
transcript AT2G29210.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G29210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g05220.t01 (Vitis vinifera), 3'ss of exon 3
gtaagctcattactgagattttatttttctgagctttttattcgactgttaataagtgacagaggggtagtatgatttcgtagcccatgccattgatacaagtgatttttttttgttggactaatatg-taattga-acgttcactatgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAAAATACTGGCAAATTTATGAAAGAACTTTGGACACTTCTTCTAAGCGCAC
                                                       ||  |       |   |||| | |  |   | |   || | ||        |||| | | |  | ||||| || | || |  | | || || ||| || |||  |||||||| |||||  |||| ||| | || || || || |||||||||||||| || || ||||||||||| |||||| | |||||||| || || |
-------------------------------------------------------gtttctataaaatttgatgactccagaaggccttttatcgttagcttcttcttttgtgtctaagcctaatgtgatcatcgttatgctccctttgt-tgcagGATGTGAATGGAAAGGAAGTTCAAATATCACTGACCGGGTTTATGGAGAAAAATACAGGTAAGTTTATGAAAGAGCTTTGGGCGCTTCTTCTCAGTGCGC

upper sequence: AT2G29210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S181_116V6.1 (Physcomitrella patens), 3'ss of exon 3
--gtaagctcattactgag-------attttatttttctgagctt-----tttattcgactgttaataagtgacagaggggta-gtat-gatttcgtagcccatgccat------tgatacaagtgatttttttt-tgttggactaatat-gtaattgaacgttcactatgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAAAATACTGGCAAATTTATGAAAGAACTTTGGACACTTCTTCTAAGCGCAC
  |   |||||      ||       || |||   ||| ||| |       |||    | |||| | ||    |  |    |  || | ||| |    |  ||||   |      |  |||| ||||| || ||  |||||| ||||| | |||  |    |||      | ||  ||   ||  |||| ||  |  |||||||   ||| || || ||||||||||||||||| || || ||||||||||| |||||||   |  |  |||| ||||
gtgagtgctcaccgtgaagctgttgaatattacacttcagagatggtcaacttaacttaatgttcacaaagagcgcattcattcgtgttgatgtgaacgttcatgttgtattctgtagtaca-gtgatcttcttaatgttggtctaatcttgtagctttgtgttg-----ggatccagAATGTAGATGGAAAACATGTTCAGATTCAGCTTACAGGCTTCATGGAGAAAAATACGGGAAAGTTTATGAAAGAGCTTTGGAGTTTGTTAATAAGTGCAC

upper sequence: AT2G29210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S55_128V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagctcattactgagattttatt-tttctgagctttttattcgactgttaataagtgacagaggggtagtatgatttcgtagcccatgccattgatacaagtgatttttttttgttggactaatatgtaattgaacg---------------ttcactatgtatg---tagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAAAATACTGGCAAATTTATGAAAGAACTTTGGACACTTCTTCTAAGCGCAC
||  |  ||  |     || || |    |  |  || |  |      |  |   |  | | ||      |  |    ||   | ||       |   |||   |    |||| |  | | |     |   ||||    |               |||| |     ||    ||   ||  |||| ||  |  |||||||   ||| || || ||||||||||||||||| || ||||| |||||||| |||||||   |  |  | ||||| |
gtgggtgcacaatgtgaatcttctgaccttcgtactgtgaagagagttaatgccactttatagtttaacaagacagatttacacccgtgaatgtccgtactgttttcattttgtactcgtaagcgcacaaaatttggtggtaataccccttgttttcatttgtcgtggtccagAATGTAGATGGAAAACATGTTCAGATTCAGCTTACAGGCTTCATGGAGAAAAATACGGGAAAATTCATGAAAGAGCTTTGGAGCTTGTTGATGAGCGCTC

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|86064964|gb|DR360721.1|DR360721
EST:     TTGAAGATGAAGTGCTGATTAACTTTATCTATGGTCTGCTTGACGGGAAG                         GTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAA
genomic: TTGAAGATGAAGTGCTGATTAACTTTATCTATGGTCTGCTTGACGGGAAGgtaagctcat ... atgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAA
EST: gi|86064967|gb|DR360724.1|DR360724
EST:     TTGAAGATGAAGTGCTGATTAACTTTATCTATGGTCTGCTTGACGGGAAG                         GTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAA
genomic: TTGAAGATGAAGTGCTGATTAACTTTATCTATGGTCTGCTTGACGGGAAGgtaagctcat ... atgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAA
EST: gi|86064966|gb|DR360723.1|DR360723
EST:     TTGAAGATGAAGTGCTGATTAACTTTATCTATGGTCTGCTTGACGGGAAG                         GTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAA
genomic: TTGAAGATGAAGTGCTGATTAACTTTATCTATGGTCTGCTTGACGGGAAGgtaagctcat ... atgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAA
EST: gi|86064965|gb|DR360722.1|DR360722
EST:     TTGAAGATGAAGTGCTGATTANCTTTATCTATGNTCTGCTTGACGGGAAG                         GTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAG
genomic: TTGAAGATGAAGTGCTGATTAACTTTATCTATGGTCTGCTTGACGGGAAGgtaagctcat ... atgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAG
EST: gi|86064963|gb|DR360720.1|DR360720
EST:     TTGAAGATGAAGTGCTGATTAACTTTATCTATGGTCTGCTTGACGGGAAG                         GTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAA
genomic: TTGAAGATGAAGTGCTGATTAACTTTATCTATGGTCTGCTTGACGGGAAGgtaagctcat ... atgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgatttttttttgttggactaatatgtaattgaacgttcactatgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAAAATACTGGCAAATTTATGAAAGAACTTTGGACACTTCTTCTAAGCGCAC
                   gactaat  putative branch site (score: 2)
                      taatatgtaattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctcattactgagattttatttttctgagctttttattcgactgttaataagtgacagaggggtagtatgatttcgtagcccatgccattgatacaagtgatttttttttgttggactaatatgtaattgaacgttcactatgtatgtagGTAGTGAATGGTAAGGAGATTCAGATAACGCTAACTGGATTCATGGAGAAAAATACTGGCAAATTTATGAAAGAACTTTGGACACTTCTTCTAAGCGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC