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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatcaactgcgagctattctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtctctctgg...

Basic information

species Arabidopsis thaliana
transcript AT4G16760.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 9
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgt--atttgtcatca--actgcgagctat---tctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtc---tctctgg-----------------------------------------------------
||||||||| ||| ||    |||| ||||| || ||  |||||||| | ||||||||||| ||||| || |||||||||||||||||  ||| ||| |||||   | ||  ||      |  |  || |   |   | | |||    ||  |   |  | |    | |||  | |||| ||| |  |   ||| || |||   ||  |                                                       
TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcag

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM5G864319_T01 (Zea mays), 5'ss of exon 9
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatcaactgcgagctattctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtctctctgg------------------------------------------------------------------------------------------
 |||||||| ||| ||    |||||||||| || ||  |||||||||| ||||||||||| ||||| || |||||||||||| |||| ||||  || ||||| | | |  |   |||   ||  |   || | |    | |   |  |  |   | | | || |   |   |  || |   || | ||     |   |                                                                                            
CGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgttt--ctgatggcactagccaataatcgtagtt--ttggctactactagttgagtatgtgcgacatgacagattgtgttccacattagttaaagaaaaagacatagaagatgtttttgcttttcctctactccattttggacaatgatatagtaataggcatcctttgggggaacctgcag

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G052389_T01 (Zea mays), 5'ss of exon 9
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgt--atttgtcat---------------caactgcgagctattctcac-ttactagaata-aatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtctctctgg---------------------------
||||||||| ||||||    |||||||||| || ||| ||||||| || |||||||| || ||||| |||||||||||||| || ||  |||  || |||||  |||   |||               | |   ||| |  || |||   |  ||| |   ||| | |  |    ||   | || ||   || |   |   | | || ||| | | |                             
TGGACATGGTTACTTGAACAGCAGTGGGCTTCCTGAGTTGTTTGCGGTCTATGTTCCCGCTTGCACTTACGAAGGAGACAACGTCGTTTTGCTTTTGCAGgtttattacccatattccttagtcctgacgatgtcgatcatttatcatgcttttagcacgtaatgtatttgactgaagccaattttttttatttcattgtgtgtgttttgtttttgtttttgtcaatggtgtggtgatacctgcag

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA11G03800.1 (Glycine max), 5'ss of exon 9
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatcaactgcgagctattctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtct--ctctgg----
||| ||||| ||| | ||  ||||||| ||||| ||| | |||||||| ||||||||||||||||| || |||||||||||||||||||| |  ||||||||  |||| |  |  |   |    |   || | | |    |||     | |  |  |||  | |  |||  | ||   ||   | ||  |  |    | |      
TGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGTATGAAGGAGACAATGTTGTGCTTCTGTTACAGgt--ttgttaaaagataaaaatcttatacaatcattttgttaa--tcattattt--aattaagtctttactaagtccttccacagctgttaacaggatttaatgtg

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA14G14990.1 (Glycine max), 5'ss of exon 8
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatcaactgcgagctattctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtct--ctctgg----
||| ||||| ||| | ||  ||||||| ||||| ||| | |||||||| ||||||||||||||||| || |||||||||||| ||||||| |  ||||||||  |||| |  |  |   |    |   || | | |    |||  |  | |  |  |||  | |  |||  | ||   ||     ||  |  |    | |      
TGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGTATGAAGGAGACAATATTGTGCTTCTTTTACAGgt--ttgttaaaagataaaaatcttatacaatcattttgttaa--ccattattt--aattaagtctttactaagtccttccacggctgttaacaggatttaatgtg

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA01G41600.1 (Glycine max), 5'ss of exon 9
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatcaactgcgagctattctcacttactagaataa--atctgtcagctca------aatagatttcttagcatgtggct-cgttatcttatgtctctctgg
 || ||||| ||| | ||  ||||||| ||||| ||| | |||||||| ||||||||||||||||| || |||||||||||| ||||||| |  ||||||||  |||| |  |  |   |    |   || | | |    |||  ||   | |  |||      | ||  |   |   ||  ||    |   || | ||||        
CGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGTATGAAGGAGACAATATTGTGCTTCTTTTACAGgt--ttgttaaaagttaaaaatgttatacaatcattttgttaatcattatttaattcagtctttactaagtccttccacagatgttaacaggatttaatgtg-------

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA17G15320.1 (Glycine max), 5'ss of exon 10
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatcaactgcgagctattctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtctctctgg----
||| ||||| ||| | ||  ||||||| || || ||| | ||||| || ||  ||||| ||||||||||||||||||||||   ||||||||  |||||||| |||   ||    |         |   ||  | || | |   | | |  | | | | |  ||| | |  |  |  ||| |   |  ||   | | ||     
TGGCCATGGTTACCTTTGCAGCAGTGGTCTGCCTGAGTTATTTGCAGTCTACATTCCTTCCTGCACATACGAAGGAGACAACACTGTGCTGCTTTTACAGgttttttaaat--gttatatatagcttgtacc-attatattgtgt-tatttgttgataaatttttttaatgaaatttctcatctgcaaattggtttgtgcatca

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 5'ss of exon 7
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatca-actgcgagctattctca-cttactagaataaatc-tgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtctctctgg
||| ||||| ||| | ||  | |||||||| |||||| | ||||| || ||||| |||||||| ||||| |||||||||||| |||||||||  |||||||| | ||  ||   | |  ||  |||| | | |||  |    |   || | ||    |||||    || | |   | ||     |   ||  |   |  ||  
TGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACATATGAAGGAGACAATATTGTGCTGCTTTTACAGgtctgtgaaattgtaatatga-ttattttaatcttgatgctttctgtcatttccatgcaaattatgttgtaacattttgagatatagactgttaattgcct--

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S209_135V6.1 (Physcomitrella patens), 5'ss of exon 9
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatcaactgcgagctattctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtctctctgg
 |||||||| |   ||||    |||||  | || || || | |||||  || || |||||||||||||||||||||||||||    | || |   | || ||| |||   |   |       | |    |  | |  |  || ||  ||  | ||   |    ||   |  |  || |  |  |||  |     || |  
AGGACATGGCTTTCTGTGTGCAAGTGGCTTACCTGAACTCTATGCTGCCTACGTGCCTGCCTGCACATACGAAGGAGACAATACGATACTTCTCCTTCAAgtacttgctttatgcctatccatttgaaaatctgcaggtttacattagtttgttcctttgtggttgaaaagacatgtccaggaatcgaagactacttttc

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ35164 (Selaginella moellendorffii), 5'ss of exon 9
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatca-actgcgagctattctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtctctctgg
||| ||||||||| | || | |||||| || || ||  ||| ||||| |||||||||||| ||||| ||||| ||||||||||| || || |   | ||||||    || ||| || | |   |  | |  | ||    | |   |  | |||                                                
TGGGCATGGATACCTCTGCTCCAGTGGTCTTCCAGAATTGTATGCTGCATATGTTCCTGCATGCACCTACGAGGGAGACAATGTCGTTCTTCTTCTTCAGgtaa--atcttcatacagtgtcttcatgttgcgtatctaagttt-tgagacag------------------------------------------------

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ24114 (Selaginella moellendorffii), 5'ss of exon 9
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatcaactgcgagctattctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtctctctgg
||| ||||||||| | || | |||||| || || ||  ||| ||||| |||||||||||| ||||| ||||| ||||||||||| || || |   | ||||||  | |  | | | | |   |  | |  | ||    | |   |  | |||                                                
TGGGCATGGATACCTCTGCTCCAGTGGTCTTCCAGAATTGTATGCTGCATATGTTCCTGCGTGCACCTACGAGGGAGACAATGTCGTTCTTCTTCTTCAGgtaaatcttctta-cagtgtcttcatgttgcgtatctaagttt-tgagacag------------------------------------------------

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|116448274|gb|EG490866.1|EG490866
EST:     ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAG                         GTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT
genomic: ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtca ... tattgtttagGTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT
EST: gi|116441440|gb|EG484032.1|EG484032
EST:     ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAG                         GTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT
genomic: ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtca ... tattgtttagGTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT
EST: gi|116448277|gb|EG490869.1|EG490869
EST:     ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAG                         GTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT
genomic: ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtca ... tattgtttagGTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT
EST: gi|301501186|gb|HO206726.1|HO206726
EST:     ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAG                         GTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT
genomic: ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtca ... tattgtttagGTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT
EST: gi|116479261|gb|EG521853.1|EG521853
EST:     ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAG                         GTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT
genomic: ATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtca ... tattgtttagGTTGCTCGATTCCTCATGAAGACAGTCGCCCAGCTGGGATCTGGAAAGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgtatttgtcatcaactgcgagctattctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtctctctgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC