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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttttcattttgctccctgaatgattggatctccgttttggcgttagtatgtcagattcttagtgttgttagtgacaattgttttttttcatcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACATGCTACCTTTGTTCCCCACACCGCTGGAAGATACTCTGTGAAGAGATTCA

Basic information

species Arabidopsis thaliana
transcript AT3G11940.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S101_208V6.1 (Physcomitrella patens), 3'ss of exon 1
gtttttcattttgctccctgaatgattggatctccgttttggcgt-tagtatgtcagattcttagtgttgt-tagtgacaattgttttttttcatcttgt--agGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACATGCTACCTTTGTTCCCCACACCGCTGGAAGATACTCTGTGAAGAGATTCA
    ||    | | |  ||    || |   |     ||| || |  |  || |  |  || ||         || | |     |          |  |||  || |||  ||||||    | |  ||||||||||  ||    |  |  || |||||||||||||| ||||| ||||||||| | ||||| |||||| | || |
----ttggagtggatgtctttgagaatctctagtattttaggtgaatgataagataagtttttgacacgacctaataatccgggggggggggggttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCATGCTACCTTTGTGCCCCATACCGCTGGACGGTACTCCGTGAAGCGTTTTA
















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|125189528|gb|EL204482.1|EL204482
EST:     TAACGAAGTCAAGCTCTTCAGCCGCTGGACCTATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCA
genomic: TAACGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCA
EST: gi|164065049|gb|ES123279.1|ES123279
EST:     TCACTAACGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTC
genomic: TCACTAACGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTC
EST: gi|124751767|gb|EH841897.1|EH841897
EST:     CGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
genomic: CGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
EST: gi|124712289|gb|EH803691.1|EH803691
EST:     CTCTTCAACCGCTGGACCTATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
genomic: CTCTTCAACCGCTGGACCTATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
EST: gi|164185792|gb|ES084602.1|ES084602
EST:     CTTCAACCGCTGGACCTATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
genomic: CTTCAACCGCTGGACCTATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
EST: gi|125046467|gb|EL118736.1|EL118736
EST:     GACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
genomic: GACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
EST: gi|164097318|gb|EL999042.1|EL999042
EST:     TCACTAACGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAG
genomic: TCACTAACGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAG
EST: gi|163966043|gb|EL976017.1|EL976017
EST:     ATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
genomic: ATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
EST: gi|116465715|gb|EG508307.1|EG508307
EST:     TCACTAACGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
genomic: TCACTAACGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
EST: gi|116480566|gb|EG523158.1|EG523158
EST:     TCACTAACGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
genomic: TCACTAACGAAGTCAAGCTCTTCAACCGCTGGACCTATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
EST: gi|125077624|gb|EL140342.1|EL140342
EST:     CTTCAACCGCTGGACCTATGACGACGTTACG                         GTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT
genomic: CTTCAACCGCTGGACCTATGACGACGTTACGgtaaattatt ... catcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtatgtcagattcttagtgttgttagtgacaattgttttttttcatcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACATGCTACCTTTGTTCCCCACACCGCTGGAAGATACTCTGTGAAGAGATTCA
                                  ttgttttttttcatct  CT-rich tract
                                aattgttttttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttcattttgctccctgaatgattggatctccgttttggcgttagtatgtcagattcttagtgttgttagtgacaattgttttttttcatcttgtagGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACATGCTACCTTTGTTCCCCACACCGCTGGAAGATACTCTGTGAAGAGATTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - ttgctcc
- - - - - - - - - - - - - - - - - -gttttgg