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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagctttttccatttcagttactgcatgatgtgatatccatttttaactagtgttgttctaatttctaacccatcttctgttccgttgataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG

Basic information

species Arabidopsis thaliana
transcript AT1G06890.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 3
-gtatagctttttccattt--cagttactgca--tgatgtgatatccatttttaactagt--gttgttctaatttctaacccatcttctgttccgttgataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG
 | | | | ||||        || ||| | ||  |||||||   |   ||    |||| |   |    |||| || |  |  |   ||  ||  ||      |||||||| || || ||||||||||| ||||||||| | |||||||| || ||||||||||| ||||||||
agcacaacattttattgcaagcatttatttcaattgatgtgccctttcttccacactaatcaatccacctaacttatgccgaaatgtcctttatgtc-----tagATGACAAAGCTGGCTATCATCCCATGCACTGTTATTTTGGAGACTCTTTTCTTCAGGAAGAAGTTCAG

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 3
----gtatagctttttccatttcagttactgcatgatgtgatatccatttttaactagtg-ttgttctaatttctaacccatcttctgttccgttgataa-tagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG
     |  |  | | |  ||| |||||     ||   ||| |  || |  |||  || |  ||  || |    |||||  ||  |    | | || |||  ||||||||||| || || |||||||| ||||||||  |||| ||||| || ||||||||||| ||||||||
ggtcttgaatatgtatttattgcagtt-taatatttggtgttccccttccttagataataattaatcca---cctaactgatgctgaaatgcctttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 2
------gtatagctttttccatttcagttactgcatgatgtgatatccatttttaactagtgttgttctaatt-tctaacccat-cttctgttccgttgataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG
      ||||   | |||  ||| |||||   | || || || | | | | ||       |  |  || |     |||||  || ||    | || || |   ||||||||||| || || |||||||| ||||||||  | || ||||| || ||||||||||| ||||||||
ggtcttgtatgagtattt--attgcagtt---gaataat-tggtgttcctcttccttagataataatcaatccacctaactgatgctgaaatgcctttaaatttagATGACTAAGCTGGCAATCATCCCGTGCACTGTCATTTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 4
---gtatagctttttccatttc-agttactgcatgatgtgatatccatttttaactagtgttgttctaatttctaacccatcttctgttccgttg-ataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG
   || |   ||||  |  ||| | ||| ||  | | |   | |  | |||||| |  |    |   || |||| |     ||    |    ||| ||   ||||||| ||||| || ||||||||||| ||||||||  |||| ||||| ||||| ||||| |  |||||
tctgtttgaattttgactcttctatttagtgtttca-gaattttataattttaatt--ttgcctctaaacttctgatattactctcttggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 4
---gtatagctttttcca-----tttcagttactgcatgatgtgatatccatttttaacta-----gtgttgttc-------taatttct-aacccatcttctgtt--ccgttgataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG
     ||   || |||       |  |   || | |||| |    | |   |  ||  | |     |||||  ||       |  ||||| |||  || || | ||    ||  ||   ||||||| || || || ||||| ||||| ||||| |||||||||||||| ||||||||||| || |||||
gtaaaattaattcttctgaatattccctactattacatgttcaacttttggtcctttgccatttcagtgtttctcaagagagtggtttctgaacttatgttatattgtttgtgtattccagATGACAAAGCTGGCAATCATTCCCTGTACTGTACTCTTGGAGACCCTTTTCTTCAGGAAGAAATTCAG

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|124971619|gb|EL045366.1|EL045366
EST:     TAGGACTATTGAACCTCAGCCTGGGCTTTAATTCTGTCGGTTTTTACCAG                         ATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACC
genomic: TAGGACTATTGAACCTCAGCCTGGGCTTTAATTCTGTCGGTTTTTACCAGgtatagcttt ... ttgataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaactagtgttgttctaatttctaacccatcttctgttccgttgataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG
                                 tcttctgttccgtt  CT-rich tract
                   taatttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagctttttccatttcagttactgcatgatgtgatatccatttttaactagtgttgttctaatttctaacccatcttctgttccgttgataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA