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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctgttgcttgatcagctccttttaactaacttattctacttggttgtaaaacaaatatcataatctctgactgtgtctaatattttgaagGGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAG

Basic information

species Arabidopsis thaliana
transcript AT3G14100.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
--gtaagttctgttgcttgatcagctccttttaactaacttattctacttggttgtaaaacaaa--tatcataatctctgactgtgtctaatattttgaagGGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAG
   |  || ||||  |         |  |      |    ||| | | |  ||||  ||   |   |  |  |   | | | | | |||      |  | | ||||| || ||||||||||| || || |||||||| || || || ||||| |||||||| ||||| |||||||||
atatttgtactgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattttattttttctggcggctcca-gAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 6
----gtaagttctgttgcttgatcagctcct--tttaactaacttat--tctacttg-gttgtaaaacaaatatcataatctctgactgtgtctaatattttgaagGGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAG
    ||    ||  | | | || |   |  |  || ||  ||  |||  | |||||   ||||   | |||||    |   | ||  |||| ||  | ||    || |||||||| ||||||||||| || || |||||||| || ||||| ||||| |||||||| |||||||||||||||
gaatgtggactcactagttagaccttattatgattaaatgaagctatcttttactttcattgtcgga-aaatagatgacattatgtttgtg-ctggtttt----agAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG
















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|125049053|gb|EL121322.1|EL121322
EST:     TCTTTTCCAGTTGTTC                         GGATGCGAGAGTTATGTGGGACC-AAAAACTGGGCGCTCGAGAGGCTTTGG
genomic: TCTTTTCCAGTTGTTCgtaagttctg ... tattttgaagGGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGG
EST: gi|124862380|gb|EH946817.1|EH946817
EST:     GTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTC                         GGATGCGAGAGTTA
genomic: GTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTCgtaagttctg ... tattttgaagGGATGCGAGAGTTA
EST: gi|164124295|gb|EL997437.1|EL997437
EST:     GTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTC                         GGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCG
genomic: GTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTCgtaagttctg ... tattttgaagGGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCG
EST: gi|125278964|gb|EL293049.1|EL293049
EST:     GTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTC                         GGATGCGAGAGTTATGTGGG
genomic: GTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTCgtaagttctg ... tattttgaagGGATGCGAGAGTTATGTGGG
EST: gi|164012874|gb|ES123181.1|ES123181
EST:     TTTCTGTCTTTTCCAGTTGTTC                         GGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGG
genomic: TTTCTGTCTTTTCCAGTTGTTCgtaagttctg ... tattttgaagGGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacttggttgtaaaacaaatatcataatctctgactgtgtctaatattttgaagGGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAG
                                       gtctaat  putative branch site (score: 3)
        ttgtaaaacaaatatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctgttgcttgatcagctccttttaactaacttattctacttggttgtaaaacaaatatcataatctctgactgtgtctaatattttgaagGGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG