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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G68060.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 6
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaatacatttccgaaaaaaga-agtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcag---------
||||| ||| |||||| | || ||||||||||| ||||||||||||||||| ||||| ||||| || || ||||||||||||||  ||||||| ||||| ||||  |  |  | |   |      || | | |  | | ||   |   |  |  |    |    |  |  |||         |         
GCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTGGTGGTGCAGCTGCTAATGCTGTCAGAGATTACCAGCGGAAAGTTCAAGAAATGAATgtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcacacttag

upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 5'ss of exon 6
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaatacatttccgaaaaaagaagtatagaatctttactcaac-tgatgaaggaatatttcttgc-----tctacttttgcag-------
||| |||||||||||  | || || ||||| || ||||||||||| ||||| ||||||||||| ||||| || || ||||| ||  | || |||||||| ||||      |   | ||   |  | | ||     || |||| || || | ||  |    || ||  |||     |  |||| ||| |       
GCTCACTCAGACTGTCAGAGAGCTCGAAGAAGCTGTTCTTGCTGGAGGTGCAGCTGCAAATGCTGTGAGAGACTATCAGCGCAAAGTCCAGGAGATGAATgtaat---gcatgatgccctgagcacacgttcctgatgtttattctacctaatagaatggtaattgatgccaatttacacttatgctgatgtcag

upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaa---gttaatac--atttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcag----------------
||| || ||||||||  | || || |||||  | ||||||||||||||||| || |||||||| || || || |||||||||||  |||| |||||||| ||||    | ||| |  || |||    |||    |   |  | ||     | ||  |  || |  ||  ||    | | |||| ||                 
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttag

upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 6
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaa---gttaatacatttccgaaaaaagaagta---------tagaatctttactcaactgatgaaggaatatttcttgctctacttttgcag---------------------
||| || || |||||  | ||||| |||||||| || ||||| |||||||| ||||||||||| ||||||||||| ||||||||  ||||||| ||||| ||||   ||||| |   ||| | |     ||            |  | |||| | |  | |||     |   |  || |  | || |||||||                      
GCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCTGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAATgtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatt-tatttttgcatggtttatttgacattctttag

upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G05100.1 (Glycine max), 5'ss of exon 6
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaatacattt-ccgaaaaaagaagtatagaatctttactcaactgatgaag-gaatatttcttgctcta-cttttgcag-------------------------
|||||| || || ||  | ||||| |||||||| || ||||| |||||||| ||||||||||| ||||| ||||| || ||||| |||||||| ||||| ||||  |   ||| || || |    |    | ||   | |||||||||    |  |  ||  ||  ||      | ||||||  |                         
GCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCTGCAAATGCTGTGAGAGATTATCAACGGAAATTTCAAGAAATGAATgtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatag

upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G26540.1 (Glycine max), 5'ss of exon 6
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaa-ggaatatttcttgct----------ctacttttgcag---------------------
||| || || |||||  | || || |||||||| || ||||| |||||||| || |||||||| ||||||||||| ||||||||  ||||||| ||||| ||||  |   | |  ||   |  | |    |    |  ||| ||  | |  |||  | | |   ||| | |           || |||||||                      
GCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCCGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAATgtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttag

upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 6
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatat-ttcttgctctacttttgcag-------------------------------------------------------
 || || || |||||| |||| || |||||||| ||||| ||||||||||| ||||||||||| || || |||||||| |||||  ||||||||||||| ||||  |   |  |||   ||| || || ||| |||  ||     |     |  |||  ||| || ||||      || |||                                                        
ACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTGGTGGTGCAGCTGCAAATGCTGTCAGAGATTACCAACGGAAAGTTCAAGAGATGAATgtaatgtgccattttt---aaacaataaatattgaacattg--caagtcatttcaggcttatatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcag

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|47831253|gb|CK120937.1|CK120937
EST:     CTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAAC                         GAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
genomic: CTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaat ... acttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
EST: gi|124737755|gb|EH829157.1|EH829157
EST:     CAAGAGATGAAC                         GAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
genomic: CAAGAGATGAACgtaagttaat ... acttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
EST: gi|163986081|gb|ES077849.1|ES077849
EST:     AGCGGAAGTTTCAAGAGATGAAC                         GAAGAACG-AAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA
genomic: AGCGGAAGTTTCAAGAGATGAACgtaagttaat ... acttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG