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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttataaagtttgttcctttgtctccgcctgaaaaattgttaacgttatacgcgaaggagactaagcaagttctgatattttttaacttatgcattttggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGTTGAAGGCTCTGTCTCAGATTATTGATCCTGATTTTGGGACAGATATTGT

Basic information

species Arabidopsis thaliana
transcript AT3G24430.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 2
--gttataaa-gtttgttcctttgtctccgcctgaaaaattgttaacgttatacgcgaaggagactaagcaagttctgatattttttaacttatgcattttggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGTTGAAGGCTCTGTCTCAGATTATTGATCCTGATTTTGGGACAGATATTGT------
      ||||  |    |   |||| |   |     | | | |||| |  ||||  | ||  || |   || |   | || ||| |  | ||    || |       ||| | |   |  | |  ||   |      ||  |||  | ||  | ||||||||||| ||  |||||||||| |||||||| || ||||| |||||||||||      
aaaaagtaaacatgccataagttgtttagccaccttatactattaatggaatacttgtagttgatt---catgccttaat-tttgtggattttcatatat------gcagTTGGAGATTCT-TCAGTATCAA-----CTGGAACGGCTGAGGATGATGTGTTGAAAGCCTTGTCTCAGATCATTGATCCAGACTTTGGAACAGATATTGTTACTTG

upper sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 2
-gttataaagtttgttcct--ttgtctccgcctgaaaaattgttaacgttatacgcgaaggagactaagcaagttctgatattttttaacttatgcattttggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGTTGAAGGCTCTGTCTCAGATTATTGATCCTGATTTTGGGACAGATATTGT------
   || | |   ||       |||| |   |   | ||| | |||| |  ||||  | ||  || |   || |   | || ||| || | ||     | |       ||| | |   |  | |  ||   |      ||  |||  | ||  | ||||||||||| ||  |||||||||| |||||||| || ||||| |||||||||||      
aagtaaacaacatgccataagttgtttagccaccataaactattaatggaatacttgtagttgatt---catgccttaat-tttgttgattttcatgtat------gcagTTGGGGATTCT-TCAGTATCAA-----CTGGAACGGCTGAGGATGATGTGTTGAAAGCCTTGTCTCAGATCATTGATCCAGACTTTGGAACAGATATTGTTACATG
















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|86052775|gb|DR348532.1|DR348532
EST:     CAAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGCTCAAG                         CTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGT
genomic: CAAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGCTCAAGgttataaagt ... tggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGT
EST: gi|86052779|gb|DR348536.1|DR348536
EST:     CAAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGCTCAAG                         CTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGT
genomic: CAAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGCTCAAGgttataaagt ... tggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGT
EST: gi|86052777|gb|DR348534.1|DR348534
EST:     CAAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGCTCAAG                         CTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATTTGT
genomic: CAAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGCTCAAGgttataaagt ... tggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGT
EST: gi|86052776|gb|DR348533.1|DR348533
EST:     CAAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGCTCAAG                         CTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGT
genomic: CAAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGCTCAAGgttataaagt ... tggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGT
EST: gi|152035624|gb|BP859299.2|BP859299
EST:     AAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGCCTCAAG                         CTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTG
genomic: AAACGGGTCTCTCAGAATCTCTCTGTAGCTAAAGCTGCTTCAGC-TCAAGgttataaagt ... tggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaaggagactaagcaagttctgatattttttaacttatgcattttggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGTTGAAGGCTCTGTCTCAGATTATTGATCCTGATTTTGGGACAGATATTGT
                            ttttaac  putative branch site (score: 2)
                       atattttttaacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttataaagtttgttcctttgtctccgcctgaaaaattgttaacgttatacgcgaaggagactaagcaagttctgatattttttaacttatgcattttggaaaacagCTAGTAGTAGTGTTGGTGAGAGTGTTGCTCAAACATCAGAAAAAGATGTGTTGAAGGCTCTGTCTCAGATTATTGATCCTGATTTTGGGACAGATATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG