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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgatagaagagaaattggcagagaaactattggaaataaattgagttttttgtgtgctagagaatgggaattgatcgactttatttctaacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT

Basic information

species Arabidopsis thaliana
transcript AT3G10920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G059991_T01 (Zea mays), 3'ss of exon 1
gattgatagaagagaaattggcagagaaactattggaaataaattg--agttttttgtgtgctagagaatgggaattgatcgactttatttctaacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
 ||| | |    | |  || |   ||      ||| |   | ||||  |  |   ||| | ||      | | | ||     || | |||   |   | |||||||||| |||||||| || ||||||||||||||    ||    || 
-attcacatgtaatatttttgggaagttttccttgtattgagattgccaactaactgt-tcctctgctctagaagtttgctaacataattatcatttttcagGTCATGTGAACCATTCAATCTTCTGGAAGAACCTCAAGCCCATTAGC
















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|125195156|gb|EL210110.1|EL210110
EST:     CTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAG                         GTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
genomic: CTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAGgtgtgtttgt ... taacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
EST: gi|301501665|gb|HO207205.1|HO207205
EST:     TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAG                         GTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
genomic: TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAGgtgtgtttgt ... taacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
EST: gi|301501762|gb|HO207302.1|HO207302
EST:     TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAG                         GTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
genomic: TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAGgtgtgtttgt ... taacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
EST: gi|125213955|gb|EL228679.1|EL228679
EST:     CTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAG                         GTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
genomic: CTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAGgtgtgtttgt ... taacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
EST: gi|116426619|gb|EG469211.1|EG469211
EST:     TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAG                         GTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
genomic: TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAGgtgtgtttgt ... taacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
EST: gi|47828007|gb|CK117691.1|CK117691
EST:     TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAG                         GTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
genomic: TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAGgtgtgtttgt ... taacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
EST: gi|164089583|gb|EL994184.1|EL994184
EST:     TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAG                         GTCATGTCAAC
genomic: TGCTTCCACTGTTGTTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAGgtgtgtttgt ... taacgtgcagGTCATGTCAAC
EST: gi|152034351|gb|BP825996.2|BP825996
EST:     GCTTCCACTGTTGGTTAAGTTGCAGAGCGCCATCAAATTCAACGGGGGAG                         GTCATGTCAAACATTCGATTTTCTGGAAGAACCTTGCTCCTTCCA
genomic: GCTTCCACTGTTG-TTAAGTTGCAGAGCGCCATCAAATTCAACGGCGGAGgtgtgtttgt ... taacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttttttgtgtgctagagaatgggaattgatcgactttatttctaacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT
                                          ttctaac  putative branch site (score: 1)
                                    ctttatttct  CT-rich tract
                                     tttatttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgatagaagagaaattggcagagaaactattggaaataaattgagttttttgtgtgctagagaatgggaattgatcgactttatttctaacgtgcagGTCATGTCAACCATTCGATTTTCTGGAAGAACCTTGCTCCTTCCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC