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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttaaattttcaatcttttagcagcatgtcctagaatctattctttagcttggatatgaatgagctttttctgtttgttaccattttagGTGCATCCATATGTAGCTACTGGGAACAAGAACTCGAAGTTTGGTATTAGGAACGAGAAGCTTCAATGGTTTCTGGATGAAGTGAAGGCACATCCCAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G11880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ12224 (Selaginella moellendorffii), 3'ss of exon 2
gtatggttaaattttcaatcttttagcagcatgtcctagaatctattctttagcttggatatgaatgagctttttctgtttgttaccattttagGTGCATCCATATGTAGCTACTGGGAACAAGAACTCGAAGTTTGGTATTAGGAACGAGAAGCTTCAATGGTTTCTGGATGAAGTGAAGGCACATCCCAAAG
                                      |    |  | |||   ||  || | |  | |||    ||   |||| |  ||| |||| ||||| ||||| || || || ||||| ||||| |||||||| ||| | ||||||||||| || |||||| |||||||  | ||    |||||||| |
--------------------------------------gtgagtggtgtttcaatttcatct-agcgtgctcgcgctcaatgtttc--tttcagGTTCATCCTTATGTCGCGACAGGCAACAAAAACTCCAAGTTTGGCATTCGCAACGAGAAGCTCCAGTGGTTTTTGGATGAGATAAAACAGCATCCCAATG
















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|125227906|gb|EL241991.1|EL241991
EST:     TAAGCAGGTCAATGTGTTGTTGCGTATCAATCCTGATGTTGATCCTCAG                         GTGCATCCATATGTAGCTACTGGGAACAAGAACTCGAAGTTTG
genomic: TAAGCAGGTCAATGTGTTGTTGCGTATCAATCCTGATGTTGATCCTCAGgtatggttaa ... accattttagGTGCATCCATATGTAGCTACTGGGAACAAGAACTCGAAGTTTG
EST: gi|125062831|gb|EL131031.1|EL131031
EST:     GTCAATGTGTTGTTGCGTATCAATCCTGATGTTGATCCTCAG                         GTGCATCCATATGTAGCTACTGGGAACAAGAACTCGAAGTTTGGTATTAGG
genomic: GTCAATGTGTTGTTGCGTATCAATCCTGATGTTGATCCTCAGgtatggttaa ... accattttagGTGCATCCATATGTAGCTACTGGGAACAAGAACTCGAAGTTTGGTATTAGG
EST: gi|47831454|gb|CK121138.1|CK121138
EST:     GTAAGCAGGTCAATGTGTTGTTGCGTATCAATCCTGATGTTGATCCTCAG                         GTGCATCCATATGTAGCTACTGGGAACAAAAACTCGAAGTTTGGTATTAGG
genomic: GTAAGCAGGTCAATGTGTTGTTGCGTATCAATCCTGATGTTGATCCTCAGgtatggttaa ... accattttagGTGCATCCATATGTAGCTACTGGGAACAAGAACTCGAAGTTTGGTATTAGG
EST: gi|163982340|gb|ES074072.1|ES074072
EST:     GTAAGCAGGTCAATGTATTGTTGCGTATCAATCCTGATGTTGATCCTCAG                         GTGCATCCATATGTAGCTACTGGGAAC
genomic: GTAAGCAGGTCAATGTGTTGTTGCGTATCAATCCTGATGTTGATCCTCAGgtatggttaa ... accattttagGTGCATCCATATGTAGCTACTGGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctattctttagcttggatatgaatgagctttttctgtttgttaccattttagGTGCATCCATATGTAGCTACTGGGAACAAGAACTCGAAGTTTGGTATTAGGAACGAGAAGCTTCAATGGTTTCTGGATGAAGTGAAGGCACATCCCAAAG
                                              ccatttt  CT-rich tract
     attcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggttaaattttcaatcttttagcagcatgtcctagaatctattctttagcttggatatgaatgagctttttctgtttgttaccattttagGTGCATCCATATGTAGCTACTGGGAACAAGAACTCGAAGTTTGGTATTAGGAACGAGAAGCTTCAATGGTTTCTGGATGAAGTGAAGGCACATCCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC