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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcgtttctagttttatatccattccgatttcatcctactggtaacactagtactatatgcatag

Basic information

species Arabidopsis thaliana
transcript AT5G50950.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 8
CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcgtttctagttttatatccattccgatttcatcctactggtaacactag-tactatatgcatag------------------------------
||||| |||||||||||||| ||||| || || || |||||||||||||||||    |    | |   ||   |   | |  | || ||   |    || | |||   | | || | | |                                
CTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGGgtaatctttaaattt--cttcggagttaatgtgtttacagtgtcgcagtgatactctctgccatttactttatctttgtcctggtactttctgtacgccctc

upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 8
CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatc-tcgtttctagttttatat---ccattccgatt---tcatcctactggtaacactagtactatatgcatag----------------------
||||| |||||||||||||| ||||| || || || ||||| ||||||||||| ||  ||  ||   |||| | ||      ||   |||    |||   || | |||   |   | |   |   |                        
CTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGGgtaaattgtcaattaatgtttgagataatttgtttacattgatacatttgaccgataaatttcaaatttggtttttgtttctaaattttattgagttacc

upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 5'ss of exon 6
---CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatct------------cgtttctagttttatatcca--ttccgatttcatccta-----ctggtaacactagtactatatgcatag----------
   ||||| ||||||||||  ||||| || || ||||| |||||||||||||||||| |              | ||| | ||| |  || ||  ||   ||  |||| |       |  |||  ||  |  | |||   |            
TATCTTGCTCAAGGTGGAATGGCTGTAGGCACAGGATTGAACACTAAGAAAGGgtatgttctccaagattggacatttgttgttctccattcagatttatatgccatcgtggatttttcttaatccttattttgtatatttgttcttcatatg

upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 9
CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcgtttctagttttatatccattccgatttcatcctactggtaacactagtactatatgcatag------------------------------
|||||||||||||| |||||||| ||||| ||||| ||||| |||||||||||| |   | ||   | |||| | | | |  | |||  |  | |   | |  || || |  | || ||                                
CTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGGgtatgtgctgctttatggttta-agcaaatatgcttttcttttcccaatcatgctggtcccttttgaatgttttgttttggcactatttttaatttttgga

upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EFJ18116 (Selaginella moellendorffii), 5'ss of exon 7
CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcgtttctagttttatatccattccgatttcatcctactggtaacactagtactatatgcatag
|||||||||||||||||||| || || || ||  | |||||||||||||||||  |   | |||||  |  ||         ||  |   ||| ||  |  ||                  
CTTGCACAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGGgtacgt---gcttctacgtccatgctgccaatgacgttg-cctgcttctctcag-----------------

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|116422670|gb|EG465262.1|EG465262
EST:     CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
genomic: CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcg ... atatgcatagGTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
EST: gi|116467405|gb|EG509997.1|EG509997
EST:     CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
genomic: CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcg ... atatgcatagGTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
EST: gi|116443356|gb|EG485948.1|EG485948
EST:     CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
genomic: CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcg ... atatgcatagGTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
EST: gi|125268428|gb|EL282513.1|EL282513
EST:     CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATCGCTGCTGCAGTAG
genomic: CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcg ... atatgcatagGTTTGATGTAAAGATCGCTGCTGCAGTAG
EST: gi|116456305|gb|EG498897.1|EG498897
EST:     CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
genomic: CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcg ... atatgcatagGTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
EST: gi|125026225|gb|EL098494.1|EL098494
EST:     CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAA
genomic: CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcg ... atatgcatagGTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAA
EST: gi|116428316|gb|EG470908.1|EG470908
EST:     CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
genomic: CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcg ... atatgcatagGTTTGATGTAAAGATCGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGGgtatatctcgtttctagttttatatccattccgatttcatcctactggtaacactagtactatatgcatag

- - - -  GGTGGA
- - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - AAGAAA