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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttcttgagcag

Basic information

species Arabidopsis thaliana
transcript AT5G61780.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 3
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaa--agttttcttcatattaacagtttaaaccttttttttttct-tgagcag----------------
|||||| | || ||  | ||||| || ||||| |||||||||||||||||||||||||| || ||||| |||||||| ||   | | || | |  |||   | ||  || ||  | |  | || || |    || | ||  ||  ||   |   |   |   | ||  |  |||  |                 
GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatgtgaattttagatcttctttgaatt-tacttaaatgcatagatatcgattgtgtttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatgttacag

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: AC207890.3_FGT002 (Zea mays), 5'ss of exon 2
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttcttgagcag
|||||| | || ||  | || ||||| ||||||||||||||||| |||||||||||||||||||| || || ||||||||   ||| ||||   ||||   | |    | |    |     |||| |    || |||  | |  ||| |  |||  | |  | |    | | |||
GCTCGCCGTGGTGGAGTTGACGAGCCCTTTGCATGGGAAAGCAGAGAGTTTCTAAGGAAGCTTTGTATAGGGAAGgtgctacatttgaacttcatatcttctctaaactctcgtatcattcattgtatt-cttcctttttttggacaatgcaaaattataatctgctgtta-cag

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttcttgagcag
|||||  | || ||  | |||||||| ||||||||||||||||| |||||||| |||||||| ||||| || ||||||||   ||| ||||   ||||   |  | | | | |  |     |||| |   || | ||  | || ||| |  |||  | |  | |    | | |||
GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatttgaacttcatatcttctccgagctctcatatcattcattgta---ttcttttttttttgacactgcaaaattataatctcctgttaacag

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G00910.1 (Glycine max), 5'ss of exon 3
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtg-------------ctttgtttaaactcttta-------tcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttct-tgagcag-----------------
|| || ||||| ||| |||||||||| ||||| |||||||| || ||||||||| |||||||||||||||| |||||               ||| |||   | |||||       | |||  ||||   ||| | ||  ||   ||||  ||| |   ||||     ||| |   ||||      || ||| | |                 
GCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCGTGGGAAAGTAGAGAGTTTCTACGGAAGCTTTGCATTGGGAAGgtaggcaaactgtattttttttttggtcactttagttgcgcttactcgtgtgaagtaa-tcattaaaagtaaaatatttatcagtattttttttttcatttttttcaaagcctctgacctggtatatgattggaacag

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA05G33320.1 (Glycine max), 5'ss of exon 3
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttcttgagcag-----------------
|| || ||||| ||| |||||||||| |||||||||||||| || ||||||||| ||||||| |||||||| |||||        | |  | ||| |   |   || |||  || | |     ||  |   |   |   | ||       |||| | || |   |   ||| | |                 
GCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCATGGGAAAGTAGAGAGTTTCTACGGAAGCTCTGCATTGGGAAGgtaggcaaaatgatatttttttt-ttcccgttttagtagctcttactctggtagtctgcttgtgttttttttagataaatcattctaagtctctgacctggtatatgattggaacag

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G38010.1 (Glycine max), 5'ss of exon 3
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttg----tttaaac-----tcttta--tcacttatgtgttataagttatggaattgaaaagttttcttcatatta--acagtttaaaccttttttttttcttgagcag-------------------------------
|| || ||||| ||| | || ||||||||||||||||||||||| |||||||| |||||||| ||||| || ||||||| |||    || |||      || ||   | | | |  || ||  | |  |   | |  |  |||   ||  | ||    | | | || | |    ||| |||                                      
GCGCGTAGAGGTGGTGTGGACGAGCCTTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgcgttgaaaattgaaatagagttcattggttgattcagttgctactactactactacttgagtgttggttttgtcttgtttctggtgaagcgtgcaatttgtctctgatgtgatgggtatgttggaaatttttttggaacag

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G17050.4 (Glycine max), 5'ss of exon 3
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttg---tttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaac--agtttaaaccttttttttttcttgagcag--------------------------------------------------------------
|| || ||||| ||| | || ||||| ||||||||||||||||| |||||||| |||||||| ||||| || ||||||| |||    || || |     ||| | || || |  |  |  |   | |   |    | |||     | |   ||| |     |||| | ||  ||  |                                                                 
GCGCGTAGAGGTGGTGTGGACGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgcgttgaaaattgaaatagagttcattgat-tgattcagttgctactactactaccactactttgatctgatcgagtgtggtggttttgtcttgttttggtgaaagcgtgcaatgtgtctctgatgtgatggttttgttgggattttattttttttttggaacag

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 5'ss of exon 3
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgct--ttgtttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttcttgagcag
|| || || || ||  | |||||||| ||||||||||| ||||| |||| | |||||||||| ||||||||||||||||   | ||| | |   ||      || |  | ||||    ||    ||  ||        |   ||        | |  |  | |  ||  || |  ||
GCCCGTAGGGGTGGAGTTGATGAGCCGTTTGCATGGGACAGCAGAGAGTATTTAAGGAAGCTCTGCATTGGAAAGgtgcccatagttaacatgtttcggttttttttggctatataacattctcttttaagacagatgttgcatc-------ttactcaatataattctttaaatag

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ35031 (Selaginella moellendorffii), 5'ss of exon 2
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttcttgagcag
|| || || |     |  ||||||||||| |||||||| ||| |||||||||| |||||    ||||| || |||||  | |||| |  |||   |   | ||    || |   | | |    ||    ||  |   ||| |                                 
GCCCGAAGGGACACCAGCGATGAGCCTTTCGCATGGGACAGCCGGGAGTTTCTCAGGAACAAATGCATCGGGAAGgt-ttgtgttcatgctcgccactccctaccacttctc--tcacgctcgtg----gtcgtggccatctag-------------------------------

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ17443 (Selaginella moellendorffii), 5'ss of exon 2
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttcttgagcag
|| || || |     |  ||||||||||| |||||||| ||| |||||||||| |||||    ||||| || |||||  | |||| |  |||   |   | |     || |   | | |    ||    ||  |   ||| |                                 
GCCCGAAGGGACACCAGCGATGAGCCTTTCGCATGGGACAGCCGGGAGTTTCTCAGGAACAAATGCATCGGGAAGgt-ttgtgttcatgctcgccactccctgccacttctc--tcacgctcgtg----gtcgtggccatctag-------------------------------

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|86069265|gb|DR365022.1|DR365022
EST:     CTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG                         GAGGTTGCTTTCAAAGTGGATTACCAAGTGG
genomic: CTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtt ... tcttgagcagGAGGTTGCTTTCAAAGTGGATTACAAAGTGG
EST: gi|86069266|gb|DR365023.1|DR365023
EST:     CTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG                         GAGGTTGCTTTCAAAGTGGATTACAAAGNGGAAGCAATTGCCGGAAGAGAA
genomic: CTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtt ... tcttgagcagGAGGTTGCTTTCAAAGTGGATTACAAAGTGGAAGCAATTGCCGGAAGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttcttgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA