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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttagtctgaaatcagaatcctattcataattccataacaatcagaattgaaatgatcattcgttctttcatctttggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCATTGGAGACCCTCCAGAAGAGAGATTTGATTTGGCATTCTGTGGAAGTCTT

Basic information

species Arabidopsis thaliana
transcript AT3G48420.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G36600.1 (Glycine max), 3'ss of exon 7
---gtgagttttag-tctgaaatcagaatcctattcataattccataacaat----cagaattgaaatgatcattcgttctttcatctttggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCATTGGAGACCCTCCAGAAGAGAGATTTGATTTGGCATTCTGTGGAAGTCTT
    |||     |  | |    ||  | |   |||| ||| | || |    |       |  |||  |     | |  |      |   |  || || || || || || ||||||||||||   || |||||||| || || ||||||||||| || ||||| || ||||||||||| ||||||||||||||||| |||
agaatgaaagccatctttactttctcagtaacattcttaaatgcaaattggttttgtgaacatgaggttgctttccactgacattttcatccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCATTGGTGATCCTCCTGAGGAGAGATTTGACTTGGCATTCTGTGGAAGCCTT

upper sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G18320.1 (Glycine max), 3'ss of exon 8
---------gtgagttttagtctga-aatcagaatcctattcataattccataacaatcagaattgaaatgatcattcgttctttcatctttggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCATTGGAGACCCTCCAGAAGAGAGATTTGATTTGGCATTCTGTGGAAGTCTT
          |||  |||| | |   | | | | || ||     || |   ||        |  |||  |     |  | |      |   |  || || || || || || ||||||||||||   || |||||||| || || ||||||||||| || ||||| || ||||||||||||||||| ||||| ||||| |||
ttgctagcaatgatctttactttctcagtaacattcttaaatgcaaattggtattg--tgaacatgaggtagctttctgctgacattttcatccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCATTGGTGATCCTCCTGAGGAGAGATTTGATTTGGCTTTCTGCGGAAGCCTT

upper sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 3'ss of exon 7
---------------------gtgagttttagt--ctgaaatcagaatcctattcataa--ttccataacaatcagaattgaaatgat-cattcgttctttcatctttggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCATTGGAGACCCTCCAGAAGAGAGATTTGATTTGGCATTCTGTGGAAGTCTT
                     |   | | || |  ||  | |   |     | || |||  ||  ||| |  | ||   |||  |  | ||     ||||  |  | |    ||| ||||| || ||||||||||| |||  ||| || ||||| ||||| |||||||||||||| || || || ||  |||||||||||||||| || ||||| |||
gtaagttgtttctttctttatgaatgctctatttactacacttgaatgatgaatcctaaatttttatagctgtgagttgtgaggtctttcaacaaatcttcaaaatctatggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCATTGGAGATCCCCCTGAGGAACGATTTGATTTGGCATTTTGCGGAAGCCTT

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|86078346|gb|DR374103.1|DR374103
EST:     CTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGG                         ATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCAT
genomic: CTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGGgtgagtttta ... ggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCAT
EST: gi|19798937|gb|AU230227.1|AU230227
EST:     CTAGCAGCTCCAAAAGCTCCGGGAATGACTTGTATAGTTACAAAGAGTGG                         ATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCAT
genomic: CTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGGgtgagtttta ... ggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCAT
EST: gi|124777261|gb|EH867204.1|EH867204
EST:     ACTTGTATAGTTACAAAGAGTGG                         ATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCAT
genomic: ACTTGTATAGTTACAAAGAGTGGgtgagtttta ... ggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCAT
EST: gi|86086839|gb|DR382598.1|DR382598
EST:     CTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGG                         ATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCAT
genomic: CTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGGgtgagtttta ... ggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCAT
EST: gi|125301859|gb|EL315944.1|EL315944
EST:     GTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGG                         ATACACGGCTGA
genomic: -TAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGGgtgagtttta ... ggaattgtagATACACGGCTGA
EST: gi|125141495|gb|EL178996.1|EL178996
EST:     ATAGTTACAAAGAGTGG                         ATACACGGCTGTATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCA
genomic: ATAGTTACAAAGAGTGGgtgagtttta ... ggaattgtagATACACGGCTG-ATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccataacaatcagaattgaaatgatcattcgttctttcatctttggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCATTGGAGACCCTCCAGAAGAGAGATTTGATTTGGCATTCTGTGGAAGTCTT
 ccataac  putative branch site (score: 3)
                                ttctttcatctttg  putative PPT
              aattgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttagtctgaaatcagaatcctattcataattccataacaatcagaattgaaatgatcattcgttctttcatctttggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCATTGGAGACCCTCCAGAAGAGAGATTTGATTTGGCATTCTGTGGAAGTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG