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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgattcgattctacttctgtttttagttgttttatgcagcaaataagtctgtattaacatccgcttcttctttgaaaaaagGATTACTATTTAGCCTCTGCAAGGGAGCTGATTAGGATCAATGGAACAACCAAAGCTCCAGTGATGAATTATGCTGCAGAAACCTCACTTGGGGTGGTGA

Basic information

species Arabidopsis thaliana
transcript AT3G21250.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G20360.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------------------------------------gtacatgattcgattctact-tctgtttttagttgttttatgcagcaaataagtctgta---ttaacatccgcttcttctttgaaa-----aaagGATTACTATTTAGCCTCTGCAAGGGAGCTGATTAGGATCAATGGAACAACCAAAGCTCCAGTGATGAATTATGCTGCAGAAACCTCACTTGGGGTGGTGA
                                                                                          ||  || |    ||| | | || |||  || ||   | ||| | | |  || |   ||   ||   ||    || |  ||| |||     | |||  || |||  |||||| || |||||  |||| |||||||||||||| || ||||||||||| ||||||| |||||| || || |||||||||||||| |
gtttaatttctttactttctaatttttatttgttagaatttatttccttataaaaatatttatacagaaaaccttaataaacagtaaatataattgttaactttccattctcggttcctaattagatcatggatctagcaacttcctagcctttgtattttattttgttttaaaattttaatagGGATATTATCAAGCCTCGGCGAGGGAATTGATAAGGATCAATGGAACCACAAAAGCTCCAGTCATGAATTTTGCTGCTGAGACATCACTTGGGGTGGTTA

upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G20770.1 (Glycine max), 3'ss of exon 6
--gtacatgattcgattctacttctgtttttagtt-gttttatgcagcaaataagtctgtattaacatccgcttcttctttgaaaaaagGATTACTATTTAGCCTCTGCAAGGGAGCTGATTAGGATCAATGGAACAACCAAAGCTCCAGTGATGAATTATGCTGCAGAAACCTCACTTGGGGTGGTGA
   |||    ||  ||  |  |   |||           |||     ||  ||    | | ||||  |    || | ||   ||||  |   || |||  |||||| ||||||||  | || |||||||||||||| || |||||||| || ||||||| ||| || || || |||||||| ||||| |
gtttaccaactttcatatttttctagttcccgtcccagcttagatcacagctagaattttcttaatctttttttttcctcctaaaagGGA--TATTATCAAGCCTCAGCAAGGGAATTAATGAGGATCAATGGAACCACAAAAGCTCCTGTCATGAATTTTGCAGCCGAGACATCACTTGGTGTGGTTA

upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g02440.t01 (Vitis vinifera), 3'ss of exon 5
gtacatgattcgattctacttc-tgtttttag---------ttgttttatgc-----agcaaataagtctgtattaacatccgcttcttctttgaa--aaaagGATTACTATTTAGCCTCTGCAAGGGAGCTGATTAGGATCAATGGAACAACCAAAGCTCCAGTGATGAATTATGCTGCAGAAACCTCACTTGGGGTGGTGA
||| || ||  | ||||||||    || || |         || || | |||       || | || |||| || | |||||  || |  ||   |  ||||||  || ||||||||||||||||| ||||| || ||||||||||||||||| ||||| || || |||| |||||| || || || |||||||| ||||| |
gtagataatggggttctactttacattctttgatctctcacttattctttgctactagacataaaaatctg-ataaccatcctgttttcattctgactaaaagGGGTATTATTTAGCCTCTGCAAGAGAGCTAATAAGGATCAATGGAACAACAAAAGCCCCCGTTATGAGTTATGCAGCTGAGACATCACTTGGAGTGGTCA

upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 17
-------------------gtacatgattcgattctacttctgtttttagttgttttatgcagcaaataagtctgtattaacatccgcttcttctttgaa--aaaagGATTACTATTTAGCCTCTGCAAGGGAGCTGATTAGGATCAATGGAACAACCAAAGCTCCAGTGATGAATTATGCTGCAGAAACCTCACTTGGGGTGGTGA
                    ||| || || |||    ||  | || || | |  |  |  || ||||  | |||| ||||  |||   || | ||||  |  ||||||  || ||||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||||||||||| || || || |||||||| ||||| |
gtagatactattttttagcatacgtgctttgatctctctattcttctttgctaatagacaca-caaa--aatctg-attattatctcgttttccttttgactaaaagGGGTATTATTTAGCCTCTGCAAGAGAGCTAATAAGGATCAATGGAACGACAAAAGCTCCTGTTATGAATTATGCAGCTGAGACATCACTTGGAGTGGTCA

upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 6
--------------------gtacatgattcgattctacttctgtttttagttgttttatgcagcaaataagtctgtattaacatccgcttcttctttgaaaaaagGATTACTATTTAGCCTCTGCAAGGGAGCTGATTAGGATCAATGGAACAACCAAAGCTCCAGTGATGAATTATGCTGCAGAAACCTCACTTGGGGTGGTGA
                     |||||   | | |    |||||  ||    ||   | || ||    | ||||| | |||| |||    ||| | ||    ||||||  || ||||||||||||||||||||||| || ||||||||||| ||||| |||||||| || ||||||||||| || ||  | || ||||| ||||| |
gtagataatgatttcttactttacattccttggtctctcttcttcttc---ttcactaatacaaagcaaaagtccg-atta-cattgttttccttttgactaaaagGGGTATTATTTAGCCTCTGCAAGGGAGCTAATAAGGATCAATGGTACAACAAAAGCTCCTGTAATGAATTATGCAGCCGAGTCATCCCTTGGAGTGGTCA

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|124738098|gb|EH829500.1|EH829500
EST:     AAGTAATTATCATAGCCCTTCTTGCTTTGGCAGCCACGAAAGTTGTTCAG                         GATTACTATTTAGCCTCTGCAAGGG
genomic: AAGTAATTATCATAGCCCTTCTTGCTTTGGCAGCCACGAAAGTTGTTCAGgtacatgatt ... ttgaaaaaagGATTACTATTTAGCCTCTGCAAGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttatgcagcaaataagtctgtattaacatccgcttcttctttgaaaaaagGATTACTATTTAGCCTCTGCAAGGGAGCTGATTAGGATCAATGGAACAACCAAAGCTCCAGTGATGAATTATGCTGCAGAAACCTCACTTGGGGTGGTGA
                         tattaac  putative branch site (score: 1)
                               catccgcttcttcttt  CT-rich tract
                                            tttgaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgattcgattctacttctgtttttagttgttttatgcagcaaataagtctgtattaacatccgcttcttctttgaaaaaagGATTACTATTTAGCCTCTGCAAGGGAGCTGATTAGGATCAATGGAACAACCAAAGCTCCAGTGATGAATTATGCTGCAGAAACCTCACTTGGGGTGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG