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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatattttgtacctttatttactcttaaccatgaaataagatgcagtctttaggagaaataaaatttgggcttttcaatgtttttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATGCACCTTCGACAATATTTCTTGATGAGATCGACGCGATCATAAGCCAACG

Basic information

species Arabidopsis thaliana
transcript AT2G34560.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 7
gtgaaatattttgtacctttatttactcttaaccatgaaataagatgcagtctttagg-----agaaataaaatttgggcttttcaatgttt-------ttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATGCACCTTCGACAATATTTCTTGATGAGATCGACGCGATCATAAGCCAACG
       || |  | |  | ||  |   | || | |   || |   | ||| ||||       |    |||  || |   |||||  |||         | |||| ||||| |||||| |  | | ||||||||| || || ||||| ||||||||||| |||||||||||||||||||| || || || || || ||||||||
----tcaatctaattcaatcatggaacttaaaacttttgatcaatagaagtatttaaatatttaattttaatgttggtatttttctgtgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG

upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 7
---gtgaaatatttt-gtacctttatttactcttaaccatgaaataagatgcagtctttaggagaaataaaatttggg-cttttcaatgttt---ttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATGCACCTTCGACAATATTTCTTGATGAGATCGACGCGATCATAAGCCAACG
    ||   |  ||  |||      | || |     |  |  | |   ||       ||||||      ||  |   | |||||  || | |   | |||| ||||| |||||| |  | | ||||||||| || || ||||||||||||||||| || |||||||| |||||||| || || || ||||| ||||| ||
tccttgttgttcttaagtatagaactatatttcactctttttattcccatttctctattaggactggagaatctaatgtctttttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG

upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G26100.1 (Glycine max), 3'ss of exon 7
--------gtgaaatattttgtacct-ttatttactcttaaccatgaaataagatgcagtctttaggagaaataaaatt-tgggcttttcaatgtttttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATGCACCTTCGACAATATTTCTTGATGAGATCGACGCGATCATAAGCCAACG
         | | ||||||   |  | | | ||| | |   |  |||| ||   ||   | ||  | | |  || | ||      |||    ||   | |||||||||| ||||||||  | | |||  | || || || || |||||||||||||| || ||||||||||||||||| || || || ||||| || |||||
aatagttaattacatatttacaatatatcagttagtttaggc--tgaattagtgtgttattttgtgaatacgtacatttacaaaatttattttggactgcagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAACTTGCAAGGCATCATGCACCCTCAACAATATTTCTTGATGAAATTGATGCAATCATTAGTCAACG

upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G26100.2 (Glycine max), 3'ss of exon 2
-------------------------------gtgaaatattttgtacct-ttatttactcttaaccatgaaataagatgcagtctttaggagaaataaaatt-tgggcttttcaatgtttttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATGCACCTTCGACAATATTTCTTGATGAGATCGACGCGATCATAAGCCAACG
                                | | ||||||   |  | | | ||| | |   |  |||| ||   ||   | ||  | | |  || | ||      |||    ||   | |||||||||| ||||||||  | | |||  | || || || || |||||||||||||| || ||||||||||||||||| || || || ||||| || |||||
gttagttagttacccattagttcaatagttaattacatatttacaatatatcagttagtttaggc--tgaattagtgtgttattttgtgaatacgtacatttacaaaatttattttggactgcagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAACTTGCAAGGCATCATGCACCCTCAACAATATTTCTTGATGAAATTGATGCAATCATTAGTCAACG

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|125161367|gb|EL188519.1|EL188519
EST:     TACTACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG                         GTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGA
genomic: TACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAGgtgaaatatt ... tgtttttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGA
EST: gi|164212823|gb|ES145804.1|ES145804
EST:     TACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG                         GTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATC
genomic: TACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAGgtgaaatatt ... tgtttttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATC
EST: gi|47831791|gb|CK121475.1|CK121475
EST:     TACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG                         GTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATG
genomic: TACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAGgtgaaatatt ... tgtttttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataagatgcagtctttaggagaaataaaatttgggcttttcaatgtttttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATGCACCTTCGACAATATTTCTTGATGAGATCGACGCGATCATAAGCCAACG
                                             tgtttttc  CT-rich tract
                     agaaataaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaatattttgtacctttatttactcttaaccatgaaataagatgcagtctttaggagaaataaaatttgggcttttcaatgtttttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATGCACCTTCGACAATATTTCTTGATGAGATCGACGCGATCATAAGCCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC