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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggaaatgatatctcttgaggatctgatttcatattattctcaaagtttcattgagctctgacttgttagaaatgtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG

Basic information

species Arabidopsis thaliana
transcript AT5G50950.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
gtttggaaatgatatctcttgaggatctgatttcatatt-attctcaaagtttcattgagctctgacttgttagaaatgtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
||     | | || |      |  || || ||| | | | ||   ||||  || | |||  |||||     ||    |   ||   ||||||| |||||||||||||| ||||| || || || ||||||||||||||
gtactacactaatgttc----aatatttgtttttagaatgatatgcaaaagttgaatgatttctgatca--tattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG

upper sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
gtttggaaatgatatctcttgaggatctgatttcatattattctcaaagtttcattgagctctgacttgttagaaatgtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
|| || || |   |  | || ||  | | | |     ||   |    || |  | ||| |   || |         ||||||   |||||||||||||||| |||||||| ||||| ||||| ||||| ||||||||
gtctgcaacttgaag-tattaagtttttaactgttctttcccccactaggtctaatgaacagggaat-------gttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG

upper sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ18116 (Selaginella moellendorffii), 3'ss of exon 6
gtttggaaatgatatctcttgaggatctgatttcatattattctcaaagttt-cattgagctctgacttgt-tagaaatgtttgtc-tagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
                                           |   ||    |  | |  ||||| |  | |  ||||  ||||   |||||||||||||||||||||| || || || ||  | ||||||||||||||
------------------------------------------gtaggagcgcgctcttacttctgattgctctctaaattcttgtggcagCTTGCACAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG

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|116422670|gb|EG465262.1|EG465262
EST:     TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG                         CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
genomic: TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAGgtttggaaat ... gtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
EST: gi|125311122|gb|EL325207.1|EL325207
EST:     TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG                         CTTGCACAAGGTGGAA
genomic: TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAGgtttggaaat ... gtttgtctagCTTGCACAAGGTGGAA
EST: gi|116467405|gb|EG509997.1|EG509997
EST:     TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG                         CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
genomic: TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAGgtttggaaat ... gtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
EST: gi|116443356|gb|EG485948.1|EG485948
EST:     TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG                         CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
genomic: TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAGgtttggaaat ... gtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
EST: gi|125268428|gb|EL282513.1|EL282513
EST:     CCGCATCTATCAG                         CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
genomic: CCGCATCTATCAGgtttggaaat ... gtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
EST: gi|116456305|gb|EG498897.1|EG498897
EST:     TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG                         CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
genomic: TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAGgtttggaaat ... gtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
EST: gi|125087477|gb|EL146591.1|EL146591
EST:     TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG                         CTTGCACAAGGTGGAACTGCTGTTGGGACCGGA
genomic: TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAGgtttggaaat ... gtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGA
EST: gi|125026225|gb|EL098494.1|EL098494
EST:     CCCCGCATCTATCAG                         CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
genomic: CCCCGCATCTATCAGgtttggaaat ... gtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
EST: gi|116428316|gb|EG470908.1|EG470908
EST:     TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAG                         CTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
genomic: TTGAGTATGGACTTAATAGAGTCGCATGTACTCTACCCCGCATCTATCAGgtttggaaat ... gtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatattattctcaaagtttcattgagctctgacttgttagaaatgtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG
                           ctctgac  putative branch site (score: 3)
                                              tttgtct  putative PPT
                                     ttagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggaaatgatatctcttgaggatctgatttcatattattctcaaagtttcattgagctctgacttgttagaaatgtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA