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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatcttacttcttttcttgcaagtctaattaaatctcattttgttctccattatgaaaccttttctttttcgaaattgcagGCTGCTGCACTGGCTCTTCGAAAAGTTCCTCAGTGCAATAGTTCATGGACAGATGAATACATCCGCCA

Basic information

species Arabidopsis thaliana
transcript AT3G13930.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 13
---------------------------------------------------------gtgcatcttacttcttttcttgcaagtctaattaaatctcattttgttctccattatgaaaccttttctttttcgaaattgcagGCTGCTGCACTGGCTCTTCGAAAAGTTCCTCAGTGCAATAGTTCATGGACAGATGAATACATCCGCCA
                                                         ||| ||  |   | |    |  ||       |||| | || |  ||  |||||      ||    |  |  || ||  | ||||||||| || |||||||||||||| || |||||||| ||||| || ||||    ||| |  ||||||||
gtaattgccgttttcttgtttcttatgtctaccaaccattgagttgtcgcagattgggtgtatgatgtatatcagttcacagact--gttaattttc-tcctgacctccagatctgaattgatcttaatttgatgt-gcagGCTGCAGCTCTGGCTCTTCGAAAGGTCCCTCAGTGTAATAGCTCGTGGATGAGTGATTTTATCCGCCA

upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------------------------------------------------------------------------------------------------gtgcatcttacttcttttcttgcaagtctaattaaatctcattttgttctccattatgaaaccttttctttttcgaaattgcagGCTGCTGCACTGGCTCTTCGAAAAGTTCCTCAGTGCAATAGTTCATGGACAGATGAATACATCCGCCA
                                                                                                                      || |||  |      |||||||  | |  ||||| |  |  || || | |     || |||| |         |   ||  |||||||||||  |||||||||| ||||||||||||||||||||||| |||||  |||| |||||||||||
gtatgttgtctttaagattgagatagtttacttctgagatgtgaagattggcattttgattatttttgttctggaggaactttagaacacatcacaccatctaacactcactgcaaatgttcatgatcaaagatttcttgtcatttcaattatactt--ttatgct-tgtggcat-aaacttcaatgggaccttgatgacagGCTGCTGCTTTGGCTCTTCGCAAAGTTCCTCAGTGCAATAGTTCCTGGACCAATGATTACATCCGCCA

upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 14
------------gtgcatcttacttcttttctt---gcaagtctaattaaatctcattttgttctccattatgaaaccttttcttt-ttcgaaattgcagGCTGCTGCACTGGCTCTTCGAAAAGTTCCTCAGTGCAATAGTTCATGGACAGATGAATACATCCGCCA
             || ||  |||| | || |||   | |   ||| ||       |   ||   |   |||  |||  |  |  |  ||    |||||||||||||||  |||||||||||||||||||||| |||||||||||||||||  |||| || || || ||
cagccttgagaaatggatgctactaccttactttaggaatagctacttgggaggaacggtgacatgatttagaaaatttcataataatttcttattgcagGCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACCAATGACTATATTCGTCA

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|125088443|gb|EL147198.1|EL147198
EST:     AAGAGGCTTCCGGTGGGAAAAGGATATCTGTAAATGATCTTGTTATTAAG                         GCTGCTGCACTGGCTCTTCGAAAAGTT
genomic: AAGAGGCTTCCGGTGGGAAAAGGATATCTGTAAATGATCTTGTTATTAAGgtgcatctta ... gaaattgcagGCTGCTGCACTGGCTCTTCGAAAAGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaaatctcattttgttctccattatgaaaccttttctttttcgaaattgcagGCTGCTGCACTGGCTCTTCGAAAAGTTCCTCAGTGCAATAGTTCATGGACAGATGAATACATCCGCCA
 gtctaat  putative branch site (score: 3)
                                ccttttctttttcg  putative PPT
                                  ttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatcttacttcttttcttgcaagtctaattaaatctcattttgttctccattatgaaaccttttctttttcgaaattgcagGCTGCTGCACTGGCTCTTCGAAAAGTTCCTCAGTGCAATAGTTCATGGACAGATGAATACATCCGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG