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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaaaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA

Basic information

species Arabidopsis thaliana
transcript AT3G25800.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 7
acaaaaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
     || |      | |   |    | | |  |      |||         | ||   || |    |   | |   |  |  | ||   | | ||  |||| || ||  |||| || || ||||| || ||||||||| |  |||| ||||||||||| ||||| ||  | |||||||| ||||||||||| ||||| |
ttgttaacgtacaacaatactgctaatctttattggtacttgtcaacagctaaatgctgatctaattgtactgactgttccagttttgacttttttgcagGACGCCACTCTTGAACAACTGCTTCCCATTTTTCTTTCTTTGCTGAAGGATGAGTTCCCTGATGTTCGACTCAACATTATAAGCAAACTTGATCAAGTTA

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
------acaa--aaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
      | ||  ||   | | || ||     ||  || |||||   |  |||||  ||||  |||  ||||     || | |  |  || || | ||    |||  |||| |||||||||||||| || ||||| || || ||||| || ||||| ||||| || || || |||||| | |||||||||||||| ||||| |||||||
taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttgg--tgtaaatgt---gcatctcagttctaccttatcttc---attgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 7
acaaaaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgtt---gttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
| ||||   |||  |    |  |   |||  ||  |    |||  | |  | | | | | || || | || | ||  |||  |     || | |  |||  |||| |||||||||||||| || ||||| || || ||||| || ||||| ||||| || || || || ||| | |||||||||||||| ||||| |||||||
ataaaagatagtaca--caaaatctattttctaggctaattgtgatagcagtagttttt-tggtgtaaatgtgaatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 7
-acaaaaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
   ||   |     |||| |  |||      || |  |   | ||||  ||  |   | |       |   |     || | ||  |||| | ||||  ||||||||||||||||||| || ||||| || ||||| || || ||||| ||||| || || ||||||||| | || || || ||||| ||||| |||||||
tttaatgctacaactaat-gctgtggcagcattgtttaacctttttttctttcaaaatttccaagaaactatgcctgtttatgtgtttttctttattgcagGATGCAACAATTGAGCAGCTTCTTCCTATTTTTCTCTCCCTTTTGAAGGATGAATTTCCTGATGTACGCCTAAATATCATAAGCAAGCTTGATCAAGTGA

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 6
acaaaaatgagttta--attgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgca---gattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
    || |||  | |  ||| |  |   ||     | ||   | || || |  |||  ||| | ||| |   |||||         ||  |  || ||  |  |||||||||||||||| || || |||||||| ||||||||||| ||||| ||||| || || ||||||||  | || || || ||||| ||||| ||| | |
---caattgatctcacaattcaaatttattgggagtgcat--ttttctgttaagatcatgtttcttgaattggatttctgaactttgtcttggttgctgatgcagGATGCAACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAA

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|125014859|gb|EL087128.1|EL087128
EST:     ATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG                         GATGCAACAATTGAGCATCTCCTTCCAATCTT
genomic: ATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAGgtaagagagt ... tctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTT
EST: gi|164131740|gb|EL975680.1|EL975680
EST:     GATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG                         GATGCAACAATTG
genomic: GATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAGgtaagagagt ... tctattttagGATGCAACAATTG
EST: gi|86040356|gb|DR336111.1|DR336111
EST:     GATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG                         GATGCAACAATTGAGGCATCTCCTTCCAATCTTTCTTTCTCTATTTGAAAG
genomic: GATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAGgtaagagagt ... tctattttagGATGCAACAATTGAG-CATCTCCTTCCAATCTTTCTTTCTCTATT-GAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
                        ttttaac  putative branch site (score: 2)
                                     ttgttttttctatttt  putative PPT
                                     ttgttttttctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaaaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA

-caaaaat
- - - - - - - - - - - - - - - - - - - - -gttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacttca