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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatcattgatgcactagtcttggttccaaggatgtaatgaaatctaactctttttgttttggtttatctttag

Basic information

species Arabidopsis thaliana
transcript AT4G34670.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g10340.1 (Oryza sativa), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtag--attgaagtcacattaatttcatcattgatgcactagtcttg--gttccaaggatgtaatgaaatctaactctttttgttttggtttatctttag
||||||||| |||    | || | |||  | |||||||||||  |||| ||||||||||| |||||||| || || |||||||| || ||||||||||||||     ||| | |||      ||||||    |        ||  ||    || |   |  | |    |  |  |||||   |||   |           
TGAGAAGGCGACATCCAGTATTTTCCCCCTTCAGAATGTGTTTGTCCGCAAAGTGAAGATTCTAAAGGCCCCGAAATTTGACCTGGGGAAGCTCATGGAGgtgactgttgcattcagtaccgtttcatttcaggcttgtatgttgtgtcaatcaacaaacttgacatgacttgtctctt---gttccag-----------

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os02g18550.1 (Oryza sativa), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatcattgatgc----actagtcttggtt--ccaaggatgtaatgaaatctaactctt-tttgttttggtttatctttag
 |||||| ||||     | || | |||  | || |||||||||||||| || ||||||||| | ||||| || |||||||| ||||| ||| | |||||||| ||   |  | |   | ||  |    | |||||    | |  || |||||   |      | |||| | |   |   || || | |||||  | |  ||  
CGAGAAGTCAACTTCAAGTATATTCCCTCTCCAAAATGTGTTCATCCGCAAGGTGAAGATCTTGAAGGCACCGAAGTTTGATCTTGGGAAGTTGATGGAGgt-gaggaaccttattctcatgcctagctagatgcctttagtgctcctggttattcttctgagaaatgtattagcatggttattggctttggaatcttatt--

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os12g21798.1 (Oryza sativa), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtag--attgaagtcacattaatttcatcattgatgcactagtcttggttccaaggatgtaatgaaatctaactctttttgttttggtttatctttag
 |||||||| |||    |||||| |||| | |||||||||||  | || ||||| |||||||| ||||| || || |||||||| || ||||| ||||||||     ||  | ||  ||  ||||  |||||  ||  || || |  |     |    | | || ||| |  ||   | |||  || |  |       
CGAGAAGGCCACATCAAGCATCTTCCCGCTTCAGAATGTGTTTGTGCGCAAAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgttacaatctaatccattt--tcatt--tgaccttgtat--gacatgaatcagcattgtaatgtggct---tgtgtcatgttccag------

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G030915_T08 (Zea mays), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatcattgatgcactagtcttggttccaaggatgtaatgaaatctaactctttttgttttggtttatctttag
||||||| | ||     |||||| |||  | || || || |||||||| || |||||||| || ||||| |||||||| || ||||| ||||||||||||||| ||||      |||  ||   |  || |||   | || ||   | ||    |  |  |    |  ||||  ||   | |  |           
TGAGAAGTCTACCTCCAGCATCTTCCCACTTCAAAACGTCTTCATCCGCAAGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAGgta-attg----ttcatgcatgcaa--atagattttccagactatctccctgttacttgttagcctaaaacttgttgcttctcag-----------

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatcattgatgcactagtcttggttccaaggatgtaatgaaatctaactctttttgttttggtttatctttag
||||||| | ||     |||||| |||  | || || || |||||||| || |||||||| || ||||| |||||||| || ||||| || ||||||||||||  |    |  ||||  ||   |  || |||   | || ||   | ||    |  |  |    |  ||||  ||   | |  |           
TGAGAAGTCTACCTCCAGCATCTTCCCACTTCAAAACGTCTTCATCCGCAAGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAACTCATGGAGgtaatt----gctacatgcatgcaa--atagattttccagactatctccctgttactttttatcctaaaacttgttgcttctcag-----------

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G00890.1 (Glycine max), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcac-attaatttcatcattgatgcactagtcttggtt--ccaaggatgtaatgaaatctaactctttttgttttggtttatc--tttag
|||||||||||||    ||||||| ||  | |||||||||||||| |||||||| |||||||| || ||||| |||||||| |||||||| || |||||||||  |     | |     |||||  | ||   |    |  |  ||  |    || | |  | |||  |||   | ||| |   |   |  |     | | 
TGAGAAGGCAACATCTAGCATCTATCCTCTACAGAATGTGTTCATTCGTAAAGTTAAGATCCTTAAAGCTCCAAAGTTTGATCTTGGAAAACTGATGGAGgtatgtcctttttattgcaaattttcttatacctatgtttattatgtctaatgaatgttacagtgagttcttgatttttgtagctgaatagaaagggtca-

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA06G11940.1 (Glycine max), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattga--agtcacattaatttcatcattgatgcactagtcttggttccaa-ggatgtaa-tgaaatctaactctttttgttttggtttatctttag
|||||||||||||    | ||||| ||  | |||||||||||||| |||||||| |||||||| || ||||| |||||||| ||||| || || ||||||||| ||||   | |    | ||     || ||    | || || ||  |   ||   ||| || ||  |    |   || | ||  ||   |   ||  |
TGAGAAGGCAACATCTAGTATCTATCCTCTACAGAATGTGTTCATTCGTAAAGTTAAGATCCTGAAAGCTCCAAAGTTTGATCTTGGGAAACTGATGGAGgtatattgtccattttattcaaaaatctccttacccctctggtttttatgttaataaatgaaactgttaatccatcattgtagtgctgaactgatttggg

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA10G39050.1 (Glycine max), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatcattgatgcactagtcttggttccaa---ggatgt--aatgaaatctaactctttttgttttggtttatct-ttag
 ||||||||||||    | || |||||  |||||||||||||  | |||||||| |||||||| || ||||| |||||||| ||||| || || |||||||||  ||      | || || ||  |  |  | |    ||| | | || | |   | || |  ||  ||  ||  || |||  |   |   ||   |  |||
CGAGAAGGCAACATCTAGTATTTACCCTCTGCAGAATGTGTTTGTTCGTAAAGTCAAGATCCTGAAAGCTCCTAAGTTTGATCTTGGGAAACTGATGGAGgtaattttttaata-ataaacttggttgtcta-gtctgagtttggttttccattagaatattaaactaatacttgctttttgagaaataagttgcatgctag

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA01G44700.1 (Glycine max), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatcattgat-gcactagtcttggttccaaggatgt---aatgaaatctaactctttttgttttggtttatct--ttag
|||||||||||||    |||| || ||  | ||||||||||| || |||||||| ||||| || || ||||| |||||||| || ||||| || |||||||||  |     | |    || ||  || ||||  ||| |    |  ||   | | ||||   |||||  ||    | ||| | | ||  |  |     | | 
TGAGAAGGCAACATCTAGCATATATCCTCTACAGAATGTGTTTATTCGTAAAGTTAAGATTCTTAAAGCTCCAAAGTTTGATCTAGGAAAACTGATGGAGgtatgtgctttttatcgcaaatt--tccttgaccgcagtttcttatgtctaatgaatgttacaatgagttcattatttttctatcttaatgaaaaaggtcaa

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G28780.2 (Glycine max), 5'ss of exon 4
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagatt----gaagtcacattaatttcatcattgatgcactagt-cttggttccaaggatgtaatgaaatctaactctttttgttttggtttatctttag
||||||||| |||    | || |||||  |||||||||||||  | |||||||| |||||||| || || || |||||||| ||||| || || |||||||||  ||      | | |  ||  ||| ||  ||    || |  | | |  |   ||  || |  ||  | ||||   |  |||     || |   ||| |
TGAGAAGGCGACATCTAGTATTTACCCTCTGCAGAATGTGTTTGTTCGTAAAGTCAAGATCCTGAAAGCCCCTAAGTTTGATCTTGGGAAACTGATGGAGgtaattttttgataataaagttcttttgatttttttctcaatcatgcctcatgaaaaatattttctgttacctaaacttggttgccc-agtctgagtttgg

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 6
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatc-attgatgcactagtcttggttccaaggatgtaa------tgaaatctaactctttttgttttggtttatctttag
 |||||||||||     ||||||| || || |||||||||| ||| || ||||| |||||| | || ||||| |||||||| ||||||||||| |||||||||  ||    |   | |  ||||||   |  ||   ||| | |    | ||   |  | |      | |||   ||  | | |    ||  |||||    | 
CGAGAAGGCAACTTCAAGCATCTATCCTTTACAGAATGTGTACATTCGGAAAGTTAAGATCTTGAAAGCTCCTAAGTTTGATCTTGGAAAGCTGATGGAGgtatttttttttttaactcttttcatttgtctattttctaatttaacatacataaacattaaaccattaaaaaaaaaaacctgtcacctt--tttatgccaa-

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S174_49V6.1 (Physcomitrella patens), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattga-agtcacattaatttcatcattga-tgc----actagtcttggttccaaggatgtaatgaaatctaactctttttgttttggtttatctttag
|||||||||||| || || |||||||| |||||||||   || ||| | || |||||||| || |||||||||||||| || ||    || || ||||||||   | || ||||||   ||||||||  | |  ||     | | |||  ||     ||| ||||||    |   | |       |||||  |    | |||
TGAGAAGGCAACTCAAGGTATCTACCCCTTGCAGAATACTTTTATCAGGAAGGTGAAGATTCTCAAGGCTCCCAAGTTCGATCTGATGAAACTTATGGAGgtgagtcgacagtcacg--aatttcatgctcgggtgttgtaattcgtcgcggggattaggttgtaattgttttacaatgaaacgcttttgtctcgcgtgtag

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatcattgatgcact---------agtcttggttccaag--gatgtaatgaaatctaactctttttgttttggt-ttatctttag------------------------------------------------------------------------------------------
|||||| ||||| ||||| || |||||  | || ||    |||||| | ||||||||||| || |||||||||||||| ||||||   ||| | |||||||||  |  ||||     |    |     | || | |           || | || | |  ||  ||||||| | | |        | | |     || |  |||||                                                                                            
TGAGAAAGCAACGCAGGGTATTTACCCACTTCAAAACACTTTCATCAGGAAAGTGAAGATTCTGAAGGCTCCCAAGTTCGACCTTATGAAGTTGATGGAGgtacgtctaagtgtggatgtcgtgcatgtggacgaatcttgttgttgagccgtgctgcacagtggatgtaagggagttatctaggtgtggacgcagtgtcgtctttgacgggtgtaatcgtttgatggatatgattgttaagatactggtgcgatcctgatctggttctgacaatactggcaccgttgcgtttgacag

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S80_113V6.1 (Physcomitrella patens), 5'ss of exon 4
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacat---taatttcat--cattgatgcactagtcttggttccaaggatg-----taatgaaatctaactctttttgttttggttta-tctttag--------------------------------------------------------
 ||||||||||| ||||| ||||||||| |||||||   ||||||| | || ||||||||  | |||||||| ||||| |||||    ||| | ||||| |||  ||  | ||   |    |||||  |   |  |||| | |  |   || |       |      |  |    | |   | ||||  |||| |||   | |||||                                                        
CGAGAAGGCAACGCAGGGGATCTACCCGCTGCAGAACACGTTCATCAGGAAGGTGAAGATATTGAAGGCTCCGAAGTTCGACCTCATGAAGTTGATGGAAgtacgttttactcgtttgttcaattttgtagtacagatgaattgttacgggattttgtatttcttctttgttgtttttgttttttttgttttttgttcgctttttaggcttacgaatttagcagtttttgtgtttgttttacaagatgttttgccgtatgtag

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S17_306V6.1 (Physcomitrella patens), 5'ss of exon 5
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatcattgatgcactagtcttggttccaaggatgtaatgaaatctaactctttttgttttggtttatctttag----
|||||||||||| || || ||||||||  | |||||   ||||||  | |||||||||||||| |||||||||||||||||| |    ||||||||||||||   |  |  |   | |         ||||   |    |  ||   | |    |   |      ||| |  ||| | ||    |    |  | |     
TGAGAAGGCAACCCAAGGAATCTACCCACTCCAGAACACGTTCATTAGGAAAGTGAAGATCCTCAAGGCTCCCAAGTTTGACTTAATGAAGCTCATGGAGgtgagtctattttttactggggattatattggcacttccgcattttatacccttaaaaagactgttcttatgcttgtcgtaagtgccactgatcatcccg

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|163973066|gb|ES103302.1|ES103302
EST:     AGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAG                         GTGCATGGAGATTACACAGCAGAGGATGTTGG
genomic: AGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaa ... ttatctttagGTGCATGGAGATTACACAGCAGAGGATGTTGG
EST: gi|47829184|gb|CK118868.1|CK118868
EST:     AAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAG                         GTGCATGGAGATTACACAGCAGAGGATGTTGGTGTGAAGGTAGACAGGCCA
genomic: AAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaa ... ttatctttagGTGCATGGAGATTACACAGCAGAGGATGTTGGTGTGAAGGTAGACAGGCCA
EST: gi|163969766|gb|ES054792.1|ES054792
EST:     CCCAAGTTTGACCTTGGAAAGCTCATGGAG                         GTGCATGGAGATTACACAGCAGAGGATGTTGGTGTG
genomic: CCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaa ... ttatctttagGTGCATGGAGATTACACAGCAGAGGATGTTGGTGTG
EST: gi|164033190|gb|ES109242.1|ES109242
EST:     AAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAG                         GTGCATGGAGATTACACAGCAGAGG
genomic: AAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaa ... ttatctttagGTGCATGGAGATTACACAGCAGAGG
EST: gi|86059960|gb|DR355717.1|DR355717
EST:     AAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAG                         GTGCATGGAGATTACACAGCAGAGGATGTTGGTGTGAAGGTAGACAGGCCA
genomic: AAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaa ... ttatctttagGTGCATGGAGATTACACAGCAGAGGATGTTGGTGTGAAGGTAGACAGGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAAGGCAACACAGGGCATCTACCCGTTGCAGAATGTGTTCATCCGTAAAGTGAAGATCCTAAAGGCTCCCAAGTTTGACCTTGGAAAGCTCATGGAGgtagattgaagtcacattaatttcatcattgatgcactagtcttggttccaaggatgtaatgaaatctaactctttttgttttggtttatctttag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA