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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGTTGATGATTTTGAGCTTGGTAAGGAAGAAGCTGTTGATGTTAAAGATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttttttttctgtgtgtgtatctatgtgtaaatgattcatcaagcttatacaacaatgtgcag

Basic information

species Arabidopsis thaliana
transcript AT4G06599.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G06599.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv12s0035g00640.t01 (Vitis vinifera), 5'ss of exon 2
AATTGTTGATGATTTTGAGCTTGGTAAGGAAGAAGCTGTTGATGTTAAAGATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttttttttctgtgtgtgtatctatgtg------taaatgattcatcaagcttatacaacaatgtgcag-------------------------
 ||  ||||||||||||| |||||  | || ||| ||  |||| | ||||||||||| || ||||| ||||| ||||||||| | ||| ||||||||||||| |||   | ||           | |  |  ||       | ||  |   | |   ||||  ||  | |||  |                         
GATAATTGATGATTTTGAACTTGGGCAAGATGAATCTACTGATATCAAAGATAAAGAGGTCAATAAGCAGAAATTGAGAAGACGTATTTATCAATACAAGgtcagtcactgttaatacaaaaaattttgaaatgaattgtcatattttgggttatcattatggaaataagtgtggaggtattaaatttttggctaagatt
















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|86041604|gb|DR337359.1|DR337359
EST:     ATAANGAAGTTAATAA-CAGAAGTTGAGAAGAAGAATTGATCAATACAMG                         NTAAATCTTCGAACGCCATGTCGTCAAGGCA-GAAACTTCTT
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTT
EST: gi|86041596|gb|DR337351.1|DR337351
EST:     ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAG                         ATAAATCTTCGAACGCCATGTCGTCAAGGCA-GAAACTTCTTGTTTTTAGA
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTT-AGA
EST: gi|86041594|gb|DR337349.1|DR337349
EST:     ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAG                         ATAAATCTTCGGACGCCATGTCGT
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGT
EST: gi|86041600|gb|DR337355.1|DR337355
EST:     ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAG                         ATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
EST: gi|86041593|gb|DR337348.1|DR337348
EST:     ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAG                         ATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
EST: gi|86041598|gb|DR337353.1|DR337353
EST:     ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAG                         ATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
EST: gi|86041607|gb|DR337362.1|DR337362
EST:     ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTAATCAATACAAG                         ATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
EST: gi|86041597|gb|DR337352.1|DR337352
EST:     ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAG                         ATAAATCTTCGAACGCCATGTCGTC
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGTC
EST: gi|86041595|gb|DR337350.1|DR337350
EST:     ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAG                         ATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
EST: gi|86041592|gb|DR337347.1|DR337347
EST:     ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGNNNTGATCAATACAAG                         ATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT
genomic: ATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttt ... caatgtgcagATAAATCTTCGAACGCCATGTCGTCAAGGCAAGAAACTTCTTGTTTTAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGTTGATGATTTTGAGCTTGGTAAGGAAGAAGCTGTTGATGTTAAAGATAAAGAAGTTAATAAACAGAAGTTGAGAAGAAGAATTGATCAATACAAGgtgagttttttttttctgtgtgtgtatctatgtgtaaatgattcatcaagcttatacaacaatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG