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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtatctactggcaaaacaatttagtacttctttttactatctatgtagaaaactgtagcttttctcaactagtgacctcactgttactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTA

Basic information

species Arabidopsis thaliana
transcript AT3G02780.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 4
gtgggtatctactggcaaaacaatttagtacttctttttactatcta--tgtagaaaactgtagcttttctcaactagtgacctc--actgttactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTA
    |||| |||||   |     | || |  |||   | ||||| ||  | ||        | |||  | |  | |  |    ||  ||| |   | | |||| || || || || || || || |||||| | ||||||||||||||||| || |||||||||||||| ||| ||||||| |||||||| || || || ||
----gtatatactgtgtaccttctataattgttcaaatgactatataaatctactttgtcattgctgctttttatttattttttcccactttgtattaccagGAGTAAGAAACGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTA

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 4
gtgggtatctactggcaaaacaatttagtacttctttttactatct--atgtagaaaactgtagcttttctcaactag---tgacctcactgttactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTA
    |||| |||||   |     | || |  |||     ||||| |  || ||        | |||  | |    |     |  || |||| |   | | |||| || || ||||| || || || |||||| | ||||||||||||||||| ||||||||||||||||| ||| ||||||| || ||||| || || || ||
----gtatatactgtgtaccttttatatttgttcaaacaactatatcaatctactttgtcattgctgctttttgtttactttccccccactttgtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTA

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 4
gtgggtatctactggcaaaacaatttagtacttctttt----tactatctatgtagaaaactgtagcttttctcaactagtgacctcactgttactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTA
              | |   || |||  | ||||||||    | | ||     |     ||| |  ||||||| |  |  |    ||| |   ||| | |||| ||| ||||||||||||||||||||||  | ||||| || || |||   |||||||||| ||| || ||| ||||||||||  |||| || ||||| ||
--------------gtattccattttctttcttcttttggaatgccattatgctttgtcactatgacttttcttagttgtttgt-tcatt--cactaaccagGAGTGCGGAATGCTGCACAAAGAAAGCTGTTGGATGAACTCGGCATTCCTGCTGAAGATGCACCTGTTGATCAGTTCACTCCACTGGGCCGCATGCTTTA

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|47828035|gb|CK117719.1|CK117719
EST:     CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAG                         GTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAG
genomic: CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAGgtgggtatct ... tactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAG
EST: gi|164077763|gb|ES153245.1|ES153245
EST:     CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAG                         GTGTGAGGAATGCTGCACAAAGAAAGCTTC
genomic: CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAGgtgggtatct ... tactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTC
EST: gi|116477195|gb|EG519787.1|EG519787
EST:     CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAG                         GTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTAATGTAG
genomic: CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAGgtgggtatct ... tactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAG
EST: gi|116387556|gb|EG430148.1|EG430148
EST:     CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAG                         GTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAG
genomic: CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAGgtgggtatct ... tactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAG
EST: gi|116477196|gb|EG519788.1|EG519788
EST:     CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAG                         GTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTAATGTAG
genomic: CAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCACTAGgtgggtatct ... tactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatgtagaaaactgtagcttttctcaactagtgacctcactgttactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTA
                                   acctcac  putative branch site (score: 3)
      tagaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtatctactggcaaaacaatttagtacttctttttactatctatgtagaaaactgtagcttttctcaactagtgacctcactgttactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG