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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT

Basic information

species Arabidopsis thaliana
transcript AT5G06600.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
    ||   | ||| || |      |||    |  |   |  | |||||||   |   ||  |   |  |   ||| ||      ||||||||  |||||| || ||||| ||||| || ||||| || || ||||||||||| ||||||||||| ||||| || |  ||||||||| |||||||||
---gttggacatttatttttgttatatgtaagataat--aaatagtgtttc--atcaatgtacaactactctctcgattc-----agGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT

upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 6
gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctctt-ttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
                     |   ||  | ||  |  || ||  | ||   ||| |  ||  | || ||  ||| |  ||     ||| |||||||||||| ||||||||  ||||| | ||||| |||||||| || || || || |||||||| ||||| |||| ||||||||   | |||||||
---------------------gtgaatattataacaaacattt--tattatatgtctacgatttgttattaactttgcgttgacccagGAAACTGTTGTGGAAGGAACAATTGAACAATTATTTGAAGGCCACCACATAAACTATATCGAGTGCATTAATGTTGATTATAAATCTAACAGAAAAGAAT

upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 6
gtaatttttcttttgttgtca-ggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
            |   | | |     |||| |||  | |       |  ||  | ||| | | || || ||||| |          |||||||||||||||| ||||||||  ||||| | || || |||||||| || ||||||||||||||||| || || || | ||||||||   | |||||||
-----------gtgaatatgacaataatgaattatcattacaccaat--ttactttttattaacttttctttctacac--------agGGAACTGTTGTGGAAGGAACAATTGAACAATTATTCGAAGGCCACCACATTAATTACATTGAGTGCATTAACGTGGACTATAAATCTAACAGAAAAGAAT

upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 2
gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
    |||  | |    | |   |     |   |   || | |   ||  || | ||  || ||   | ||        ||     |||||||   |||||| ||| |||||||| || | || ||||| |||||||||||||| || ||||| || ||||| || | |||||||||  ||||||| |
---gtttgccatccaatttt--gttgaaaaaaaagcctgactgactgactcatattaatgtgcagctattc-------ttctcacagGGAACCACTGTGGAAGGAGCAATACAAAAATTGTTCGAGGGTCACCATATGAATTATATCGAGTGTATTAATGTTGAGTCTAAATCTACCAGGAAAGAGT

upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 6
gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
           | ||  ||    |   | |  |    |||||   | ||   |||| |  || | ||| || |   ||  |    |||||||||| |||||||| |||||||| ||  | ||||| || ||||||||||| |||||||||||||| ||||| || |  ||||||||| | || ||||
--------gtatatgaggtttaaca--gctgcagctttcagt-atttttcactgttctgaagttttttattttatattactggacagGGAACTGTAGTGGAGGGGACAATACAGCAGTTGTTTGAAGGGCACCATATGAACTACATTGAGTGCATCAATGTGGACTACAAATCTACAAGAAAGGAAT

upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
---------gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctc----ttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
         |   | |  |  |||||||  |       |    || |  | | | ||   ||  |    ||       |||    |||    ||  |||||| || |  |||||||| || |||||| | |||||||| ||||| ||||||||||| || || ||||| ||||| |||||||| || || ||||| || |
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT

upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 6
------gtaatttttcttttgttgtcaggccatgatttactac--tcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
       ||| | |   || | | |     |  | ||| | |   |   | |||   |  |||||    |      |   |  ||  || |  ||||||||| ||| ||||| ||||| || ||||| || || || || || ||||| ||||| |||||||| ||||| |||| |||||| ||||||||||| |
gtatggataaatctctgttagctatgtcttctcggttttcaagagtagctgggtacattatgtttactggtgggaatccttctgtgcttttacagGGAACTGCTGTCGAGGGCACAATCCAGCAACTGTTCGAAGGGCATCACATGAACTACATAGAGTGCATCAATGTTGATTATAAATCAACACGGAAAGAGT

upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ19227 (Selaginella moellendorffii), 3'ss of exon 6
gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
                          ||| |   |  |  ||||   ||    | | ||    | | || |  ||  || ||   ||||||| | ||| || ||||| || ||||| ||||||||||| || |||||||| ||||| || ||||| || || ||||  |||||||| |||||||| |
-------------------------gtgagtactttgtacgttgaacttcaaagctattc--ttatcttctactcacttctc---agGGAACCGCTGTTGAAGGAACGATTCAACAGCTTTTTGAGGGTCATCATATGAACTACATCGAATGCATCAACGTCGATTACAAATCTACGCGGAAAGAGT

upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 4
gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttc--gtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
                             |||||| ||       | ||  |    ||  |  | || |  |  |  | |   ||  || | |||| ||| || || || ||||| || ||||| || ||||||||||||||||| ||||| ||||| ||||| || |  || || || || || ||||
----------------------------gtttactgct------attttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATGAATTATATTGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAAT

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|164135218|gb|ES030859.1|ES030859
EST:     TGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAG                         GGAACTGTTGTGGAGGGAACAA
genomic: TGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttc ... ttttctgtagGGAACTGTTGTGGAGGGAACAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
               tttcttgtttttgagc  CT-rich tract
                                 ttttttctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA