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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgagatagcatctatgcttttgtccgattgttcttatcatctgagtctttcttctattaattgaggctgttgttcttctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTAT

Basic information

species Arabidopsis thaliana
transcript AT5G53120.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 4
----------gtttgagatagcatctatgcttttgtccgattgttc------ttatcatctgagtct-ttcttctattaattg---aggctgttgttcttctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTAT
             ||  |    | || ||    |     |||  |       | | || || | | | ||   |||||  |||   |  ||||  |  |||| | |||||||  | || || || || || || || || |||||||| || |||||||||||||| |||||||||||||| ||||| ||| |  | || || ||  | |
gtcattcttcacctgctaggctagctgtgtgcatactacattactttatacataaacaactaattttgttgaactattttttgtataacctgtc-tatttctgtatgcagTCCTCAACCTATGGGAATGTTCTGGTGCTTGATGGTATTGTGCAGCTGACCGAAAAGGATGAATGTGCATACCAGGAAATGGTTACTCACCTTCCACTGT

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------gtttgagatagcatctatgcttttgtccgattgttcttatcatctgagtctttcttctat------taattgaggctgttgttcttctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTAT
                                        ||||  |||  || ||  |||| ||    |||  |  || |||   ||||||||||||      ||  | | || |   ||||| | |||||||||  |  | || || || |||||||| || ||||| || || ||| ||| ||| |||||||||||||| |||||||||||||| || || || ||  | |
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccat-tttttatctatctgtcatgttcttcttt-tctttcttctatattagctagctaatgcag--attcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
















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|47829276|gb|CK118960.1|CK118960
EST:     AAGTCCTAGTGTTCGAG                         TCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
genomic: AAGTCCTAGTGTTCGAGgtttgagata ... ctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
EST: gi|86043708|gb|DR339463.1|DR339463
EST:     AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAG                         TCAGCCACGTACGGA
genomic: AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAGgtttgagata ... ctttttgcagTCAGCCACGTACGGA
EST: gi|86043711|gb|DR339466.1|DR339466
EST:     AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAG                         TCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
genomic: AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAGgtttgagata ... ctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
EST: gi|86043709|gb|DR339464.1|DR339464
EST:     AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAG                         TCAGCCACGTACGGAAAGGTGCTT
genomic: AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAGgtttgagata ... ctttttgcagTCAGCCACGTACGGAAAGGTGCTT
EST: gi|86043705|gb|DR339460.1|DR339460
EST:     AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAG                         TCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCCGTACAGCTGAC
genomic: AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAGgtttgagata ... ctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATC-GTACAGCTGAC
EST: gi|86043706|gb|DR339461.1|DR339461
EST:     AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAG                         TCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
genomic: A-GTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAGgtttgagata ... ctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
EST: gi|47831735|gb|CK121419.1|CK121419
EST:     AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAG                         TCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
genomic: AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAGgtttgagata ... ctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
EST: gi|86043707|gb|DR339462.1|DR339462
EST:     AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAG                         TCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
genomic: AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAGgtttgagata ... ctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
EST: gi|86043704|gb|DR339459.1|DR339459
EST:     AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAG                         TCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC
genomic: AAGTTCTGTTCAAAGACAAGTCGGATTTTCAGGAAGTCCTAGTGTTCGAGgtttgagata ... ctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatcatctgagtctttcttctattaattgaggctgttgttcttctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTAT
                      tattaat  putative branch site (score: 2)
                                  ctgttgttcttctttt  putative PPT
               tttcttctattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgagatagcatctatgcttttgtccgattgttcttatcatctgagtctttcttctattaattgaggctgttgttcttctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG