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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGGGCATGGCAGAGGTACAACTTAAGTCTTGGTCTTGGTCTCAACAAAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcgagatttatcttagtgtaatccaattttcattgaccaaactcttatcaaacaatacaaatcgaacgcag

Basic information

species Arabidopsis thaliana
transcript AT2G13360.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G13360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G14740.1 (Glycine max), 5'ss of exon 4
GAGAAGGGCATGGCAGAGGTACAACTTAAGTCTTGGTCTTGGTCTCAACAAAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcgagatttatcttagtgtaatccaattttcattgaccaaactc-ttatcaaacaatacaaatcgaacgcag----------------------
 |||||||||||| |||| ||||| || ||  | |||||||| || |||||||| ||||| |||||||||||||||||||| || || ||  ||||||||||| || | ||  |  |        | | |  ||  ||||  | | |  |  |  ||    ||  || || | |   |                       
TAGAAGGGCATGGAAGAGATACAATTTGAGCTTAGGTCTTGGACTGAACAAAGTTGCTGGGAAGGTTTTCAGAATTGGACATCTTGGCAACTTGAATGAGgta-atgttgatttccaatcacccatcagcatataatcatgaaactagtttatcctctcggaactcagattgcatttatttgtagtgaagttaagaaattt

upper sequence: AT2G13360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G41460.1 (Glycine max), 5'ss of exon 5
GAGAAGGGCATGGCAGAGGTACAACTTAAGTCTTGGTCTTGGTCTCAACAAAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtac-----atatcgagatttatcttagtgtaatc-------caattttcattgaccaaactcttatcaaa--caatacaaatcgaacgcag--------
 || ||||||||| |||| ||||| || ||  | |||||||| || |||||||| ||||| |||||||||||||||||||| || ||  |  |||||||||||      || || | | |    | ||  |||||        ||| |    |  |  |||||   |   |   | |   | |  || | ||        
TAGGAGGGCATGGAAGAGATACAATTTGAGCTTAGGTCTTGGACTGAACAAAGTTGCTGGGAAGGTTTTCAGAATTGGACATCTTGGCCACTTGAATGAGgtaatgttgatttccaaactcccatcagcataatcatgaaactaatctatcctctcagaactcaggttgcatttatttgtagtgaaatgaagtaatttaa

upper sequence: AT2G13360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv06s0009g03740.t01 (Vitis vinifera), 5'ss of exon 4
GAGAAGGGCATGGCAGAGGTACAACTTAAGTCTTGGTCTTGGTCTCAACAAAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcgagatttatcttagtgtaatccaattttcattgaccaaactcttatca--aacaatacaaatcgaacgcag-----------------------
 |  ||||||||| |||| |||||||||||  | ||||| || || |||||||| |||||||||||||||||||| || || || ||  |  | ||||| |||    ||       |||||  | ||     || ||   |  |   | |||||  |  |  | || | ||     | |                        
CAAGAGGGCATGGAAGAGATACAACTTAAGCTTAGGTCTAGGCCTGAACAAAGTTGCTGGAAAGGTTTTCAGAATAGGCCATCTCGGCCACCTTAATGATgtatggttcatttcccatcttcctata---tgatattagatagcttgaatcttaaaagtattactagagattagttggaaaaccataagattgcaggccaaac

upper sequence: AT2G13360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S19_25V6.1 (Physcomitrella patens), 5'ss of exon 4
GAGAAGGGCATGGCAGAGGTACAACTTAAGTCTTGGTCTTGGTCTCAACAAAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcgagatttatcttagtgtaatccaattttcattgaccaaactc--ttatcaaacaatacaaatcgaacgcag----------------------
 |  |  || |   ||| ||||||||| ||||||||  |||||||||||||||| || || || |||||| | |||||||| || ||||| || || ||||||  | |  | |   | | |||| |  |   | |   | || | |  | |      |||  |||     | |  | | |                      
AAAGATAGCTTACAAGAAGTACAACTTGAGTCTTGGAATTGGTCTCAACAAAGTTGCAGGGAAAGTTTTCCGCATTGGACATCTCGGAAACGTTAACGAGgtatgttttcacaaa-accctagtatc-ttgtactggtagtgtctatgcacagcctccaatgaatgagtcttgctctccgttcccctggcatgtttttatgt

upper sequence: AT2G13360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ08434 (Selaginella moellendorffii), 5'ss of exon 4
GAGAAGGGCATGGCAGAGGTACAACTTAAGTCTTGGTCTTGGTCTCAACAAAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcgagatttatcttagtgtaatccaattttcattgaccaaactcttatcaaacaatacaaatcgaacgcag
||  | ||||||| | | ||| ||||| ||  | ||  | || |||||||||||||| || ||||||||||| ||||| ||||| ||    || || |||||    |      | | | ||| || ||   || |||||     |||     | ||        ||            
GAAGATGGCATGGAAAAAGTATAACTTGAGCTTGGGAGTGGGACTCAACAAAGTGGCAGGCAAGGTTTTCAGGATTGGGCACCTGGGTTTCGTAAACGAGgtgagaagttctttctttttta-tggaa---aactttcacgactcaagaagctttcttttgccccag-----------

upper sequence: AT2G13360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ15151 (Selaginella moellendorffii), 5'ss of exon 4
GAGAAGGGCATGGCAGAGGTACAACTTAAGTCTTGGTCTTGGTCTCAACAAAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcgagatttatcttagtgtaatccaattttcattgaccaaactcttatcaaacaatacaaatcgaacgcag
||  | ||||||| | | ||| ||||| ||  | ||  | || |||||||||||||| || ||||||||||| ||||| ||||| ||    || || |||||    |      | | | |||  | ||    | || ||     |||     | ||        ||            
GAAGATGGCATGGAAAAAGTATAACTTGAGCTTGGGAGTGGGACTCAACAAAGTGGCAGGCAAGGTTTTCAGGATTGGGCACCTGGGTTTCGTAAACGAGgtgagaagttctttcttttttatcgaaa----acttgcacgactcaagaagctttcttttgtcccag-----------

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|116484714|gb|EG527306.1|EG527306
EST:     AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
genomic: AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
EST: gi|125066766|gb|EL133518.1|EL133518
EST:     AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGTCTTGCGGG
genomic: AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGG
EST: gi|124751701|gb|EH841831.1|EH841831
EST:     TGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAG
genomic: TGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAG
EST: gi|125069777|gb|EL135433.1|EL135433
EST:     AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGA
genomic: AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGA
EST: gi|164229638|gb|ES060497.1|ES060497
EST:     AGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGNTGTT
genomic: AGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
EST: gi|124758904|gb|EH849034.1|EH849034
EST:     AGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCAGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
genomic: AGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
EST: gi|124741773|gb|EH832935.1|EH832935
EST:     AAATGTGAATGAG                         TTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
genomic: AAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
EST: gi|125210847|gb|EL225801.1|EL225801
EST:     AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGT
genomic: AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGT
EST: gi|124757367|gb|EH847497.1|EH847497
EST:     AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGTC
genomic: AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTC
EST: gi|124771954|gb|EH862084.1|EH862084
EST:     AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGT
genomic: AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGT
EST: gi|124808903|gb|EH894783.1|EH894783
EST:     AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAG
genomic: AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAG
EST: gi|124990927|gb|EL063196.1|EL063196
EST:     GTTTTCAGAATTGGACACCTAGGAAATGTGAANGAG                         TTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
genomic: GTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
EST: gi|124780999|gb|EH870942.1|EH870942
EST:     TTGGACACCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGAATGT
genomic: TTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGA-TGT
EST: gi|116473689|gb|EG516281.1|EG516281
EST:     AAGTGGCTGGAAAGGTTTTCAGAATTGGACCCCTAGGAAATGTGAATGAG                         TTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT
genomic: AAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcg ... tcgaacgcagTTGCAACTTCTCGGGTGTCTTGCGGGAGTGGAGATGATACTGAAGGATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGGGCATGGCAGAGGTACAACTTAAGTCTTGGTCTTGGTCTCAACAAAGTGGCTGGAAAGGTTTTCAGAATTGGACACCTAGGAAATGTGAATGAGgtacatatcgagatttatcttagtgtaatccaattttcattgaccaaactcttatcaaacaatacaaatcgaacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA