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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagctatacatgaattacataacctatactcgtggcttaatatccattcttttgtttcag

Basic information

species Arabidopsis thaliana
transcript AT4G39080.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: LOC_Os10g10500.1 (Oryza sativa), 5'ss of exon 16
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtag---tagaagctatacatgaat---------------tacataacctatactcgtggcttaatatccattcttttgtttcag
||||||| ||  | ||||| || |||||||| ||||| || ||||||||||| || || || || || || || |||||||| ||||| |||||||| |||||    |     || | | || | |  |||                ||||     | | |   || | | ||    |  | ||  | |||
AATTCAGTGAAGTCTTTGTTCACCAGCTGATCCACACAATTGAGTTTGTGCTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtacctctgaacttacatgatacataacaatgccacctcttaatgtcacatggaagaaattgacggttgagtaattctattgttcgtgcag

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GRMZM2G058910_T01 (Zea mays), 5'ss of exon 16
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagctata-catgaattacataaccta---tactcgtggcttaata--tccattcttttgtttcag-------------------------------------------------------------------------------------------
| ||| | ||  | ||||| || || ||||||||||| ||||| ||||| || || || || || ||||||||||| ||||| ||||| |||||||| |||||    || |  ||||  || | | | ||||| | |||    ||  |   |    |||  ||| || ||| | | ||                                                                                            
AGTTCGGTGAAGTTTTTGTTCACCAACTGATTCACACGATAGAATTTGTTCTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctattttaagcagtatctttatttacacagcctcacctatgcacagtcccatacttcctttgtttggctgcaccctaatccacataggtgcattggagtgcagccaaacaagtcattttattacctcactggctactaacgtgctactgatattctcctttcag

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GRMZM2G104418_T02 (Zea mays), 5'ss of exon 7
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagctatacatg---aattacataacct-atactcgtggcttaatatccattcttttgtttcag------------------------------------------------------------------------------------------------------
| ||||||||  | ||||| || |||||||||||||| || || ||||| ||||| || || || ||||| ||||| ||||| || || |||||||| |||||    || |  ||||  ||  |    | ||||| | ||| |    |    | |   || | | ||   |  |                                                                                                         
AGTTCAGCGAAGTTTTTGTTCACCAGCTGATTCACACGATCGAATTTGTTCTTGGTGCAGTCTCAAACACAGCTTCGTACCTTCGCCTTTGGGCTCTGAGgtagtgttacttcaagcattatgtctttatttacacagcctcacctacacaacatcccatacttcctaagggcttgtgtggctgcaccctaatccacatggatagattggagtgcagccaaacaagttttttttataacttcaatggctactaacgagctactgatattctcccttcag

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA06G03040.1 (Glycine max), 5'ss of exon 16
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatg-agtagtagaagctatacatgaattacataacctatactcgtggcttaatatccattcttttgtttcag--------------------------
| ||||||||| | |||||||| || || || || || ||||| |||||||||||||||||||| ||||| ||||| || || ||| ||||||| |||||||| | ||| | |   | |  |    | |     ||  | | ||  | | |||  |   |   ||| |  |                             
ACTTCAGCGAGGTTTTTGTGCACCAACTTATACATACAATAGAATTTGTGCTTGGAGCTGTTTCTAACACGGCTTCGTATCTACGTTTATGGGCCCTCAGgtaggtagttgaaagcgtttgatgctattctttgaatttttgctttttggttatgaataaaaatttagcatggatatgggcttcctatttccccccttca

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA11G12120.1 (Glycine max), 5'ss of exon 16
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagctatacatga-attacataacctatactcgtggcttaatatccattcttttg---tttcag----------------------------------------------------------------------------------------------------------
| ||||||||  | ||||| ||||| || || || |||||||| ||||| |||||||| || || || || ||||||||||| ||||||||||| || |||||||  || ||    | | || |   |||  |  |   || || | | |  | ||   |     |||     |||                                                                                                           
AGTTCAGCGAAGTCTTTGTACATCAACTCATACATACCATAGAATTTGTACTTGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtcta-taagtcccaaacgttctattctaatagtaatgcttgagtcccactagaaacaaggttggaacctcacatcatgcagtttattacttttgtatatctattcgtctatagatatgtttgatgcatgtattgaattgctttgcacatttactgatgttttccttttctgtacccag

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA12G04330.1 (Glycine max), 5'ss of exon 16
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagctatacatga-attacataacctatactcgtggcttaatatccattcttttgtttcag-------------------------------------------------------------------------------------------------------------
| ||||||||  ||||||| ||||| || || || |||||||| ||||| || ||||| || || || || ||||||||||| ||||||||||| || |||||||  || ||    | | || |   |||  |  |   || || | | |  | ||   |     |||   |                                                                                                               
AGTTCAGCGAAGTATTTGTACATCAACTTATACATACCATAGAATTTGTACTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtcta-taagtcccagacgttctattctaatagtaattcttgagtcccactagaaacaaggttgaaaccttacatcatgcagtttattacttttgtttatctattcgtctatagatatgtttgatgcatgtattgaactgctttacgcatttactgatgttttccttttctgtacccag

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA04G03010.1 (Glycine max), 5'ss of exon 17
-AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagcta-tacatgaattac-ataacctatactcgtggcttaatatccattcttttg---tttcag---------------------
 | ||||||||| | |||||||| || || || || || ||||| |||||||||||||||||||| ||||| || || |  || ||| | ||||| ||||| |   ||   | || || | |   ||||||    |      || |     |  |||   ||||  | ||   || | |                     
GACTTCAGCGAGGTTTTTGTGCACCAACTTATACATACAATAGAATTTGTGCTTGGAGCTGTTTCTAACACGGCATCGTCTCTACGTTTGTGGGCCCTCAgttgaaagcgtttgatgcgactctctgaatttttgtttttggtaatgaaaacaaaattaacattgatatgggcttcctgtttccccccttcaaataggtg

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 16
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatg-agtagta----gaagctat---acatgaattacataacctatactcgtggc-ttaatatccattcttttgtttcag------------------
| || || ||  | ||||| || || || ||||| |||||||||||||| |||||||| || || || || ||||| ||| | ||| ||||||| |||||||| | || |  |    |||| |||   | |||   | |  | |  | |   |      ||| || |||  |       ||                   
AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtaggcaggaacaacctgaagttatttcatatggcatgctgagctaaaatgtgcactgctaaaatgcatggtagaaagccaaagttatgtctatagaata

upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: PP1S6_159V6.1 (Physcomitrella patens), 5'ss of exon 15
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagctatacatgaattacat-aacctatactcgtggcttaatatccattcttttgtttcag-----------------------------------------------------
| ||  | ||  || | || || ||  ||||||||||||| ||||||||| | || || || |||||||| |||||||| ||||| || |||||  | |||||   |   |    |  ||| |||  || | | ||   | | |  |   ||  |  |  || ||    ||| |                                                     
AGTTTGGTGAAGTACTCGTCCACCAAATGATTCACACCATTGAGTTTGTGTTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgccatgtttgtgata-atggctttcgtcaatgcagagtaattatttggtgccggtttttaaagttctgatgatatggtttttcacattttgaagttttgcacttggtctttgtgtatgcag

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|125045792|gb|EL118061.1|EL118061
EST:     TGGGTTCTCAG                         TCTTGCCCACTCGGAGCTGTCATCAGTCTTCTATGAGAAGGTCCTCCTTCT
genomic: TGGGCTCTCAGgtatgagtag ... tttgtttcagTCTTGCCCACTCGGAGCTGTCATCAGTCTTCTATGAGAAGGTCCTCCTTCT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagctatacatgaattacataacctatactcgtggcttaatatccattcttttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT