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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttttgactttttttaagtgttgcattttgtttgtatgtttttgaggatactcaatgttttagtttccatgagttgcag

Basic information

species Arabidopsis thaliana
transcript AT3G14100.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 5
GTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttttgactttt---tttaagtgttgcat---tt--tgtttgtatgtt--tttgaggatactcaatgtt-ttagtttccatgagttgcag------
 ||||| |||||||||||||| |||||||| ||||| | ||||||||| || ||||| ||| || ||||  || || |   || || ||||  ||   ||  | ||| |  |    ||||   | ||| ||     | |||||  |  |     |       
ATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAGgttagttcagatttctgagttaaaatgttaaataaattgatatttatgggccagtttgtttaaacttaaaaaaatcagtttagacaaacattaaaaaagc

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 5
GTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttttgacttttt--ttaagtgttgcattttgtttgtatgtttttgaggatactc-aatgttttagtttccatgagttgcag--------------
 ||||| |||||||||||||| |||||||| ||||| | ||||||||| || ||||| ||| || ||||   | || |   |||| | |     | | ||||     |||||   | |||   |     |  |||  |  |  |  |               
ATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAGgttagttcacatttctgagttaaatatattgatatttttgggccattttgtttaaactttgaaaaagtgttttttaaaaaatttattttttaagaaaaag

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 5
GTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttt---tgactttttttaagtgttgcattttgtttgtatgtttttgag-gatact-caatgttttagtttccatga--gttgcag--------------------------
|||||| |||||||||||||| |||||||| ||||| | |||||| ||||| || |||||| ||  ||||   |   ||  ||  |    |   |||   |  |||| |    |  ||| ||     ||||| |  | ||| |  ||||  |                          
GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtag

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S84_50V6.1 (Physcomitrella patens), 5'ss of exon 6
GTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttttgactttttttaag--------tgttgcattttgtttgtatgtttttgagga--tactcaatgtttta-gtttccatgagttgcag--------------------------
 |||||||||||||||||||| |||||||| ||||| |  || ||||| || |||||  || ||   || |   | ||||  ||        ||  || | | || ||  || |  | ||||  | |   ||||||    |   | | || |                              
ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAGgtgttttatttttattttctagactatatttggcgcttctggtatggctgctgattaggaattgcatgatgtttagtatggactttagctattatttattttctatgttgcttgtaccag

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|125036037|gb|EL108306.1|EL108306
EST:     TATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAA                         GTCATTTCAACATTTTTGTTGGAGATCTCAGTC
genomic: TATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttttg ... tgagttgcagGTCATTTCAACATTTTTGTTGGAGATCTCAGTC
EST: gi|164080017|gb|ES142040.1|ES142040
EST:     ACTGGTCAGAGGGAAGATACATCAA                         GTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAA
genomic: ACTGGTCAGAGGGAAGATACATCAAgtaagttttg ... tgagttgcagGTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAA
EST: gi|124763185|gb|EH853315.1|EH853315
EST:     GAAGATACATCAA                         GTCATTTCAACATTTTTTGTTTGGAGATCTCAGTCCAGAGGTCACTGATGC
genomic: GAAGATACATCAAgtaagttttg ... tgagttgcagGTCATTTCAACA-TTTTTG-TTGGAGATCTCAGTCCAGAGGTCACTGATGC
EST: gi|164156024|gb|ES090214.1|ES090214
EST:     CACTGGTCAGAGGGAAGATACATCAA                         GTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAA
genomic: CACTGGTCAGAGGGAAGATACATCAAgtaagttttg ... tgagttgcagGTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAA
EST: gi|125256540|gb|EL270625.1|EL270625
EST:     TATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAA                         GTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACT
genomic: TATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttttg ... tgagttgcagGTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACT
EST: gi|124929517|gb|EL007055.1|EL007055
EST:     GTATGCCACTGGTCAGAGGGAAGATACATCAA                         GTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAA
genomic: GTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttttg ... tgagttgcagGTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAA
EST: gi|124707430|gb|EH798832.1|EH798832
EST:     TCAGAGGGAAGATACATCAA                         GTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCAC
genomic: TCAGAGGGAAGATACATCAAgtaagttttg ... tgagttgcagGTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCAC
EST: gi|125281343|gb|EL295428.1|EL295428
EST:     GTCAGAGGGAAGATACATCAA                         GTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCA
genomic: GTCAGAGGGAAGATACATCAAgtaagttttg ... tgagttgcagGTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCA
EST: gi|125207379|gb|EL222333.1|EL222333
EST:     TATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAA                         GTCATTTCAACATTTTTGTTGGAGA
genomic: TATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttttg ... tgagttgcagGTCATTTCAACATTTTTGTTGGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAAgtaagttttgactttttttaagtgttgcattttgtttgtatgtttttgaggatactcaatgttttagtttccatgagttgcag

- - - - - - - - - - - - - - - - - - - - - - - - GGAAGA