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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatctggcttagttttggtgcaatgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcag

Basic information

species Arabidopsis thaliana
transcript AT1G75330.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g47590.1 (Oryza sativa), 5'ss of exon 4
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatc-tggcttagttttggtgcaatgctcg-gtactcttactaaat-tacactgcttcacgcttacatattatgttcaattgcag-----------------------------------------------------
||| ||||  |||||||||||||||||  |||| || |||||||| ||||| |||||||| ||||| |||  | |    ||||  ||||||||||||  ||| |  |||  |    |  ||   | |||  | ||   ||   |   |  || | |  |   | | |   |||    | |     |   | |  ||||                                                      
AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTCTGGGCCAGCATGGGCCAAAAGGAGGAAGCTGAATATAGAAAAAAAGTGTTCCAAGGATTCACGgttagaatacctccttttatgctcttgttccgatgttctgtctgcacaaactcattttacacataatatctcagtagtcctctccactattatctgcatatgggatctggctaatactttattctcaatactttgtttctttgttcctgcag

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G157210_T01 (Zea mays), 5'ss of exon 7
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatctggcttagttttggtgca-atgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcag---
||| ||||  |||||||| ||||||||| |||| || |||||||||||||| |||||||| ||||  ||   | |     |    ||||| ||||||  ||||    |   ||| |       ||| ||    |   |  |   ||||   |||  |     |   | | | ||       |||     |     |    
AGCAGTTAAGGGAGCAGACGTTGTGTACACAGATGTTTGGGCCAGTATGGGACAAAAGGAAGAAGTTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgtttttcacactttctagattctacgtgtactccaagtacatatacatagcataaacccgtgaggcgattgagttacaactagagaaattat

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G349547_T01 (Zea mays), 5'ss of exon 4
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatctggcttagttttggtgca-atgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcag---
||| ||||  |||||||| ||||||||| |||| || |||||||||||||| |||||||| |||   ||   | |     |    | ||| ||||||  ||||    |   ||| |       ||| ||  | |   |  |   ||||   |||  ||    |   | | | ||       |||     |     |    
AGCAGTTAAGGGAGCAGACGTTGTGTACACAGATGTTTGGGCCAGTATGGGACAAAAGGAAGAAATTGATTATAGAAATCAGAAGTCCCAGGGATTCACGgtatgtttgtttttcacactttctagattctgcgtgtactccaagtacatatacataacataagcccgtgaggcgattgagttacaactagagaaattat

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G046748_T02 (Zea mays), 5'ss of exon 5
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatctggctt-agttttggtgcaatgctcggtactcttactaaat-tacactgctt---cacgcttacatattatgttcaa-ttgcag
||| ||||  |||||||||||||||||  |||| || |||||||| ||||| |||||||| ||||| ||   | |     |    ||||| ||||||  |||     |   || |  ||  ||  | |||  |||   |||| |  ||    |||| || |||  || ||   | ||       | |  ||| ||  |  ||
AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTTTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgttttcacactttctagaatttccgtgtcttgctggacacca--actacatatactttgattaagcccgtgaggcgactgagttaaaactagag

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G050371_T01 (Zea mays), 5'ss of exon 4
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatctggcttag--ttttggtgcaatgctcggtactcttactaaat-tacactgcttcacgcttacatattatgttcaattgcag---
||| ||||  ||||||||  |||||||| |||| || |||||||||||||| |||||||| ||||| ||   | |     |    ||||| ||||||  ||||    |   ||| |       |||  |||  | |       | | ||||  | || || ||||  || | | ||  |     |   || | || ||    
AGCAGTTAAGGGAGCAGACATTGTGTACACAGATGTTTGGGCCAGTATGGGACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgtttttcacactttctagaatttctgcgtgtcttactggactccaagtacatatacatagcataa-gcccatgaggtg-attgagttacaacta

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G062142_T01 (Zea mays), 5'ss of exon 6
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatctggcttagttttggtgca-atgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcag---
||| ||||  |||||||| |||||||||  ||| || |||||||||||||| |||||||| ||||  ||   | |     |    ||||| ||||||  ||||    |   ||| |       ||| ||  | |   |  |   ||||   |||  |     |     | | ||       |||     |     |    
AGCAGTTAAGGGAGCAGACGTTGTGTACATAGATGTTTGGGCCAGTATGGGACAAAAGGAAGAAGTTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgtttttcacactttctagattctgcgtgtactccaagtacatatacatagcataagcctgtgaggcgattgagttacaactagagaaattat

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G03360.1 (Glycine max), 5'ss of exon 4
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgta---aacataagtttaatctggcttagttttggtgcaatgctcggtactcttacta-aattacactgcttcacgcttacatattatgttcaattgcag--
||||||||  ||||| ||||||||||| ||||| || |||||||| ||||| |||||||| ||||| |||   || ||  |||  ||  ||||||| ||||||    ||||||  ||  |||| | |  ||||  | ||    ||    |   |  || |  |    || ||   ||  | ||  || ||| ||||  |   
AGCTGTTAAAGGAGCTGATGTTGTGTATTCAGATGTCTGGGCCAGCATGGGGCAAAAGGAAGAAGCTGAATACCGTCGCCAAGTTTTTAAAGGATTTCAGgtactttacataatatt--tctgtcattattttcttacagccatctaatcaaatggtacagatggggtggttagtgcagagatcataggttgaatttaaaaa

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G03280.1 (Glycine max), 5'ss of exon 4
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgta---aacataagtttaatctggcttagttttggtgcaatgctcggtactcttactaaat-tacactgcttcacgcttacatattatgttcaattgcag--
 |||||||  ||||| ||||||||||| ||||| || |||||||| ||||| |||||||| ||||| |||   || ||  |||| ||  ||||||| ||||||    ||||||  ||  |||| | |  ||||  | ||     |    |   |  || |  |    || ||   ||  | ||  | |||| | ||  |   
GGCTGTTAAAGGAGCTGATGTTGTGTATTCAGATGTCTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGAATACCGGCGCCAAGCTTTTAAAGGATTTCAGgtactttacataatatt--tctgacattattttcttacagccacctaatcaaatggtacacatggggtggttagtgcagaaatcatgtgttgagtttaacga

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 4
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatctggcttagttttggtgcaatgctcggtactcttactaaattacactgcttc--acgcttacatattatg---ttcaattgcag----
||||||||  |||||||||||||| |||||||| || ||||| || ||||| |||||||| || |||  |  ||||||| |||  || |||||||| ||||||    |   |||||    ||||    ||  |  |||  | | | ||   | | |       ||||    |  ||  || || |     || ||   |||    
AGCTGTTAGAGGAGCAGATGTTGTATACTCAGATGTTTGGGCTAGCATGGGGCAAAAGGAAGAGGCCTCATATCGCCGGCAAGTGTTTCAAGGATTTCAGgtacctgttgttttaaa--agcttgcaatttat-taat--ttgattcttacattgatgcttgttgctcaggaaactatcacatcacaaactttaacatcagtatc

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|164093412|gb|EL981290.1|EL981290
EST:     GGAAAGCATTCCAAGGATTCCAG                         GTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
genomic: GGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
EST: gi|86080147|gb|DR375904.1|DR375904
EST:     GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAG                         GTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
genomic: GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
EST: gi|86074354|gb|DR370111.1|DR370111
EST:     GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAG                         GTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
genomic: GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
EST: gi|125314592|gb|EL328677.1|EL328677
EST:     GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAG                         GTGGATAGAAGCTCTGATGAAGTTGGCGGGTCAAA
genomic: GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGAT-GAAGCTCTGATGAAGTTGGCGGGTCAAA
EST: gi|125212292|gb|EL227246.1|EL227246
EST:     GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAG                         GTGGATGAAGCTCTGATGAAGTTGGCGGGT
genomic: GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatctggcttagttttggtgcaatgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC