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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag

Basic information

species Arabidopsis thaliana
transcript AT5G22440.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os02g21660.1 (Oryza sativa), 5'ss of exon 5
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttgaacttctcgatctttctccatacatttatcagt-atctaaaacctgagttgttcctttgactgcag-----------------------
|||||| || ||   | | |||||||||||||||||||| |||||||| |||||||| || |||||||| ||||| || |||||||| || ||||| || ||  || |  |     || | |     | |||    |   ||  || |  || |     |  | |  |||| |||   ||| |  |                        
TGCTGTTGGCAACTGTGCTATGGAGGAGAAGCAGATCTTCCAAAATGTGCAGATGAGCGTGAACTTCCTTGTTTCCCTTTTGAAGAAGAATTGGCAGAACgtatgtgatcatgtgttccttatagcatagata---caaaatttatctgccacttggacatcagcctagttattctgatgatttgacatgttatttgtatcatcgtgcag

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g64090.1 (Oryza sativa), 5'ss of exon 5
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagta--acaacaccctctt--------gaacttctcg----atctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag
|||||| || ||   | | |||||||||||||| || || |||||||| || ||||| || |||||||| || ||||| |||||||| || ||||| || || ||||   ||| |   ||||        | | | |  |    || | ||| |   | ||  |   |||   ||     | ||  | | || |||    
TGCTGTAGGCAACTGTGCTATGGAGGAGAAGCAAATTTTCCAAAATGTGCAAATGAGCGTGAACTTCCTTGTCTCTCTTTTGAAGAAGAATTGGCAGAACgtaagtactccaatattttctttataacacggagtacatgcaacatttatctactccctttgtttcatattataagttgcatttacttcctttacttttt

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G023748_T02 (Zea mays), 5'ss of exon 5
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgt-tagtaacaacaccctcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcc-tttgactgcag
|||||| || ||      |||||| |||||||||||||| || ||||| || |||||||| ||||||||||| || |||||||| || || ||||| ||||| |  |    ||| |    | || ||   | |  |  || | |   | |  |    ||         ||  |    | ||  |||||
TGCTGTTGGCAACTGCGGCATGGATGAGAAGCAGATCTTCCAGAATGTGCAAATGAGTGTCAACTTCCTCGTGTCGCTCTTGAAAAAGAATTGGCAGAATgtatgttcctcacatctgtataaaattaatgcttatgttctaaaatatgactatccactgggctaactgtcatcttgtgtgtttgcag

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA11G35450.4 (Glycine max), 5'ss of exon 5
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttga-acttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag----------------
 ||||| || ||| ||   |||||||| ||||| ||||| |||||||||||  |||||||||||||||| || ||| | ||||| || |||||||||||||| ||||  |   | | ||  | | ||||  | ||   | | |    |      | | | |    || | | ||| |   | |  |                 
AGCTGTGGGCAATGTTAGTATGGAGGAAAAGCAAATCTTCCAAAATGTTCAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATgtgagtagtagtccacactcaatatttcttaaactcattgcctctggtgccttctttttta---ttgtgcttttcttgaaattatatgttcttgttgctgttt

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA11G35450.2 (Glycine max), 5'ss of exon 5
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttga-acttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag--------------------
    || || ||| ||   |||||||| ||||| ||||| |||||||||||  |||||||||||||||| || ||| | ||||| || |||||||||||||| ||||  |   | | ||  | | ||||  | ||   | | |    |      | | | |    || | | ||| |   | |  |                     
----GTGGGCAATGTTAGTATGGAGGAAAAGCAAATCTTCCAAAATGTTCAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtccacactcaatatttcttaaactcattgcctctggtgccttctttttta---ttgtgcttttcttgaaattatatgttcttgttgctgttttatg

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 3
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttgaacttct------cgatctttctccatacatt---------tatcagtatctaaaacctgagttgttcctttgactgcag
 ||||| || ||| ||   |||||||| ||||| ||||| |||||||||||  |||||||||| ||||| || ||| | ||||| || |||||||||||||| ||||  |   | || |  |  || |        ||   |     | | ||         | | | | ||| |||  |   | |||| | |  |||   
AGCTGTGGGGAATGTTAGTATGGAGGAAAAGCAAATCTTCCAAAATGTTCAACTGAGTGTTAATTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATgtgagtagtagtccactatcaatattttgttaagtcattgcttctggtgccttcttttttgatgtgattttcttaaagttatat-gttcttgtttctgttt

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 4
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaa-caacaccc----tcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag---------------------------------------------------------------
 ||||| || ||| ||  ||||||||| ||||| ||||| |||||||| ||  |||||||||||||||| || ||| |  |||| || || ||||| || ||  |||  | || |      | |  ||  | | | ||| | |  ||   | | | |   |     |  ||| || |  |||| | | |                                                                 
AGCTGTGGGGAATGTTAGCATGGAGGAAAAGCAAATCTTCCAAAATGTACAACTGAGTGTTAACTTCCTTGTCTCTTTGCTGAAAAAGAATTGGCAGAACgtgggtagtccactcttatgatttcaaatgttttgctctatttttatg-gtcttttatcgtgctgcatgtgaattttctcttttaatacttgcaatatttgatctaattgaaccttccaatcaaagactgaacaaactctattcttaatttcag

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA12G31040.1 (Glycine max), 5'ss of exon 5
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctc----ttgaacttc-tcgatctttctccatacatttatcagtatctaaaacct--gagttgttcctttgactgcag--------
 || || || ||| ||  ||||||||| ||||| ||||| |||||||| ||  |||||||||||||||| || ||| | ||||| || || ||||| || || ||||    ||| ||     |||||     | | |   |||      ||||  | |||| |      |   |||| |   ||  | |            
AGCCGTGGGGAATGTTAGCATGGAGGAAAAGCAAATCTTCCAAAATGTACAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAATTGGCAGAACgtgagtagtc-cactcttaaaattgaataaaattgttgcatctaagcctattttactgtatttttgtttttgaagttatgatttcaaattttttgctctat

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 8
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacacc---ctct-tgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag----------
|||||| |||||       ||||||||||||||||||||||||||||| ||  |||| ||||| ||||| || ||  | |||||||| |||||||||||||| |||     |||    |||| | |  || | || ||    | |||  ||       |  | | |     | | |   |  | ||  ||          
TGCTGTGGGTAACTGCAGTATGGAGGAGAAGCAGATCTTTCAAAATGTGCAACTGAGCGTTAATTTCCTTGTCTCCTTGTTGAAGAAGAACTGGCAAAATgtgagttgattcacttagctctgttagtttatggaactaaaccaataggttatgataaagtttatattaaggctctcaatcagtctttaggtacctcact

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv08s0007g03340.t01 (Vitis vinifera), 5'ss of exon 5
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagt--aacaacaccctcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcc-tttgactgcag-------------
|||||| || ||      ||||||||||||||||||||| || ||||| ||  | ||||| |||||||| || ||  | ||||||||||| ||||||||||| |||  | ||||  |   || ||| |  | |     ||  |  |||| |  ||   |||     |||    |    ||  ||||||              
TGCTGTGGGCAACTGCAGCATGGAGGAGAAGCAGATCTTCCAGAATGTGCAACTTAGTGTCAACTTCCTTGTCTCATTATTGAAGAAAAATTGGCAAAATgtaagttcagcaacctcacatttaacatgacaaagcagct--aaccattaagtaggtcctatgctttgaaaattagggttcaactgcatgactatgtaccct

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 5'ss of exon 3
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttgaactt---ctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctt--tgactgcag-----------------------------------------------
 ||  |||||||   |   |||||||| ||||| ||||| || ||    || ||| |||||||||||||||| || || |||||||| |||||||| ||||| ||||        |  ||  | ||     |  | | |||  |    ||  |  |   ||   |  |   || ||   |  ||     |                                                
CGCCATCGGTAACTGTGATATGGAGGAAAAGCAAATCTTCCAGAACACACAAATGGGTGTTAACTTCCTCGTGTCCCTGTTGAAGAAGAACTGGCAGAATgtaagtacatttgttcctttctatttgaatgcagtatatctgaaggtgttcttgtgatgcttgtattttcattattaagtgatggtcatacaatgtctaagttcagtattttatctaacgtttgaatttttgtaacag

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 5'ss of exon 3
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaa------caccctcttgaacttctcgatct-ttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag-------------------------------------------------
|||  | || |||  |  ||||||||||||||||||||| |||||   ||||||| |||| |||||||| || || ||  ||||||| |||||||| ||||| || |||||       |   || | |  ||  ||| || |||    ||    ||| ||| | ||  |  |  ||  || ||    ||   |                                                 
TGCCATTGGAAATTGTGACATGGAGGAGAAGCAGATCTTCCAAAACACTCAGATGGGTGTCAACTTCCTTGTATCCCTGCTGAAGAAGAACTGGCAGAATgtaagcaacaaactcaatagtttcatcatatttccgacctgttccttttattcgtattagtttgtattaattcggtatttactcgagcttgcgtcgctgatcacatctctaagtattctgttcatactttttcttgtggcag

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ34353 (Selaginella moellendorffii), 5'ss of exon 3
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag
 || || || ||  |    ||||||||||||||| |||| || || |||||| | || |||||||||||||| || ||  | ||||| ||||||||||| || ||||  |  | |        ||||||  |||||   | |    ||| |      | |  || |                    
AGCGGTGGGCAACATCGAGATGGAGGAGAAGCAGGTCTTCCAGAACGTTCAGCTCAGCGTTAACTTCCTCGTCTCGCTGCTCAAGAAGAACTGGCAAAACgtaagtagtagtagc-------gcttctc--tcttttctcgtg-gcttaacttcgattgattccag--------------------

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 3
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag
 || || || ||  |    ||||||||||||||| |||| || || |||||| | || |||||||||||||| || ||  | ||||| |||||||| || || ||||  |  | |   |    ||| ||    |     | ||  ||     || || |                           
AGCAGTGGGCAACATCGAGATGGAGGAGAAGCAGGTCTTCCAGAACGTTCAGCTCAGCGTTAACTTCCTCGTCTCGCTGCTCAAGAAGAACTGGCAGAACgtaagtagtaggagcgcttctctcttttc----tcgtggcttaacttcgattgtttccag--------------------------

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|116413764|gb|EG456356.1|EG456356
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|116413742|gb|EG456334.1|EG456334
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCCCAATGGGTCCCCCAA
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAA
EST: gi|116413756|gb|EG456348.1|EG456348
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|116413757|gb|EG456349.1|EG456349
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTT
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|86077020|gb|DR372777.1|DR372777
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|164210785|gb|ES166040.1|ES166040
EST:     AGTGTTAACTTCCTCGTTTCTCTCTTGAAG-AAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGG
genomic: AGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGG
EST: gi|164055778|gb|ES200563.1|ES200563
EST:     GATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCNCAATGGGTCCACCAAACCGAGTTTTC
genomic: GATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAG-AAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|116413743|gb|EG456335.1|EG456335
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|86080991|gb|DR376748.1|DR376748
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA