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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttaccagctaccaaggactgtatttgcataagccaactatttattttataaataatgtttttattctggaacttttaatactgaagattttgttgtagGTTGGACAAATACGAGAGGCATCTAACAAGGCAAACAATGCTGAGCTAAAGCTGTTTTTGGAAATAGAGCGTGGACCG

Basic information

species Arabidopsis thaliana
transcript AT3G11910.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 12
-gtttaccagctaccaaggactgtatttgcataagccaactatttattttataaataatgttt-ttattctggaacttttaatactgaagattttgttgtagGTTGGACAAATACGAGAGGCATCTAACAAGGCAAACAATGCTGAGCTAAAGCTGTTTTTGGAAATAGAGCGTGGACCG
 ||||     ||  ||| ||   |  |||  |        | ||||||   |   |  | ||| ||||  |      || | |  |  |  | |      |||| |||||| |  | |||| ||| || |||||| ||||||||||||| ||| ||||||||||| |||| | ||| |||
cgtttttt--ctttcaatgagcttgcttgtttccattgtgtgtttattgcttctgttctctttcttatcatctccagttcatttttatatgtatctgcacagGTGGGACAACTGAGGGAGGTATCGAATAAGGCACACAATGCTGAGCTGAAGTTGTTTTTGGAAGTAGAACTTGGCCCG

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 16
gtttaccagctaccaaggactgtat-ttgcataagccaactattta-ttttataaataatgtttttattctggaacttttaatactgaagattttgttgta--gGTTGGACAAATACGAGAGGCATCTAACAAGGCAAACAATGCTGAGCTAAAGCTGTTTTTGGAAATAGAGCGTGGACCG
    |  | |    ||  ||  | |  | ||||    | |  |||| || | ||  |  ||    |    | |   |||||||  |     |||  ||| |  ||| || ||  |  | || |  || || |||||| ||||||||||||| ||||||||||||||| | || | |||||||
---cagaaacagtgaaaaacaatctgcttcatatcttagccttttacttctttagtttgtgccaatccatttgtcattttaat-ttatttctttcattgcacagGTCGGGCAGCTTAGGGAAGTCTCAAATAAGGCACACAATGCTGAGCTGAAGCTGTTTTTGGAAGTTGAACTTGGACCG
















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|124995660|gb|EL067929.1|EL067929
EST:     CCTATCACCTAATGAAGAATTACAGACG                         GTTTGGACAAATACGAGAGGCATCTAACAAGGCAAACAATGCTGAGCTAAA
genomic: CCTATCACCTAATGAAGAATTACAGACGgtagctgtta ... tttgttgtagG-TTGGACAAATACGAGAGGCATCTAACAAGGCAAACAATGCTGAGCTAAA
EST: gi|124905146|gb|EH979226.1|EH979226
EST:     ATACTTACCGCCCCAATCGTCCCCTATCACCTAATGAAGAATTACAGACG                         GTTGGACAAATACGAGAGGCATCTAACAA
genomic: ATACTTACCGCCCCAATCGTCCCCTATCACCTAATGAAGAATTACAGACGgtagctgtta ... tttgttgtagGTTGGACAAATACGAGAGGCATCTAACAA
EST: gi|163994589|gb|ES045389.1|ES045389
EST:     TACTTACCGCCCCAATCGTCCCCTTATCACCTAATGAAGAATTACAGACG                         GTTGGACAAATACGAGAGGCATCTAACAAGGCAAACAATGC
genomic: TACTTACCGCCCCAATCGTCCCC-TATCACCTAATGAAGAATTACAGACGgtagctgtta ... tttgttgtagGTTGGACAAATACGAGAGGCATCTAACAAGGCAAACAATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttataaataatgtttttattctggaacttttaatactgaagattttgttgtagGTTGGACAAATACGAGAGGCATCTAACAAGGCAAACAATGCTGAGCTAAAGCTGTTTTTGGAAATAGAGCGTGGACCG
                             ttttaat  putative branch site (score: 3)
                                            ttttgtt  putative PPT
     taaataatgtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaccagctaccaaggactgtatttgcataagccaactatttattttataaataatgtttttattctggaacttttaatactgaagattttgttgtagGTTGGACAAATACGAGAGGCATCTAACAAGGCAAACAATGCTGAGCTAAAGCTGTTTTTGGAAATAGAGCGTGGACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - -ctaccaa
- - - - - - - - - - - - - - - -aagccaa
- - - - - - - - - - - - - - - - - - - - - - - - - -aaataat