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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaatgcagaattttctctcaagccttgagaattgtccttattcttcaatgagcggtttatttatttttgtttgtaaaaattctgtatcaggtaaggatgtgagaatgttgattcccatattctttttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAAT

Basic information

species Arabidopsis thaliana
transcript AT5G03406.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03406.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g01360.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------gtaactaatgcagaattttctctcaagccttgagaattgt----ccttattcttcaatgagc---ggtttatttatttttgtttgtaaaaattctgtatc-aggtaaggatgtgagaatgttgattcccatattctttttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAAT
                           | | |  | | |  || |   | | |   ||  || |        | | | ||||| ||     |||| ||| |||| | | | || || || |||||| |||||  ||||  ||||| |||||  |||| || ||||  ||||||||||||||| || ||||||||||| ||||||||||| || ||||||||| | ||||||||||||||| | ||| | || |||||||| ||||| ||||||
gtactaagatactagttcttctgtatttcattgcttctgctttctgaatgatgtagtgtcaactaaaaaatttgactgttcaaagaattttggttcattcatttatctatttataatttttgtatccaggtacagatgccagaat-ttgatctccatgtttttttctgtccagAAAATCTGTATCTCTTCCATTGAAATGGTTTGCTGTAGGACAGTGTTGGCGTTATGAGAGAATGACAAGGGGACGCCGTCGTGAGCACTACCAATGGAAT
















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|116436932|gb|EG479524.1|EG479524
EST:     TTGAGGCCTGAGCTTACACCTTCTTTAGCGAGGCTTGTCATACAGAAAGG                         AAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG
genomic: TTGAGGCCTGAGCTTACACCTTCTTTAGCGAGGCTTGTCATACAGAAAGGgtaactaatg ... tttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG
EST: gi|116436934|gb|EG479526.1|EG479526
EST:     TTGAGGCCTGAGCTTACACCTTCTTTAGCGAGGCTTGTCATACAGAAAGG                         AAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG
genomic: TTGAGGCCTGAGCTTACACCTTCTTTAGCGAGGCTTGTCATACAGAAAGGgtaactaatg ... tttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG
EST: gi|116436933|gb|EG479525.1|EG479525
EST:     ATACAGAAAGG                         AAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG
genomic: ATACAGAAAGGgtaactaatg ... tttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG
EST: gi|116437263|gb|EG479855.1|EG479855
EST:     TTGAGGCCTGAGCTTACACCTTCTTTAGCGAGGCTTGTCATACAGAAAGG                         AAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG
genomic: TTGAGGCCTGAGCTTACACCTTCTTTAGCGAGGCTTGTCATACAGAAAGGgtaactaatg ... tttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG
EST: gi|116436940|gb|EG479532.1|EG479532
EST:     TTGAGGCCTGAGCTTACACCTTCTTTAGCGAGGCTTGTCATACAGAAAGG                         AAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG
genomic: TTGAGGCCTGAGCTTACACCTTCTTTAGCGAGGCTTGTCATACAGAAAGGgtaactaatg ... tttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtatcaggtaaggatgtgagaatgttgattcccatattctttttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAAT
                          tgttgat  putative branch site (score: 4)
                                ttcccatattcttttt  CT-rich tract
                                     atattcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactaatgcagaattttctctcaagccttgagaattgtccttattcttcaatgagcggtttatttatttttgtttgtaaaaattctgtatcaggtaaggatgtgagaatgttgattcccatattctttttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA