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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgtttgtttccttcccgatatctctttagtcttgtttggtttcgtaacacttgaaatttcctgattagttggtggcttctattgcaaacag

Basic information

species Arabidopsis thaliana
transcript AT2G34860.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G34860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G44020.2 (Glycine max), 5'ss of exon 4
GTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgtttg--tttccttcccgatatctctttagtcttgtttggtttcgtaacac--ttgaaatttcctgatt-agttggtggcttctattgcaaacag-------
|||||||||||||||| |||||||||||||||||||| ||||| || || || |||||||| ||||| ||||| || |||||||| ||||| ||| ||   | |  |  | |  |  ||  | | || ||| | |     |     |   |||  | || ||   || |  ||   | ||  ||   |       
GTGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACCGGAAGCGAGCTAAAGATGTTTATGAATTTACTGAGTGTCCAAATTGTTATGgtatgaactccagtttctacttgactccatttttttttagctataagaggtgatgataatggcatggtttgattcgaagcacttttt--aagttgctgttct

upper sequence: AT2G34860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G38750.1 (Glycine max), 5'ss of exon 4
GTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgtttg--tttccttcccgatatctctttagtcttgtttggtttcgtaacacttga-aatttcctgattagttggtggcttctattgcaaacag---------
 ||||||||||||||| |||||||||||||||||||| ||| | || || || |||||||| || || ||||| || |||||||| ||||| ||| ||   | |  |  | |  |  ||  | | ||||| | | |   |     ||| |||  | || ||  || |  ||   | ||  ||  ||         
ATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACAGGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATGgtatgaactccagtttctacttgactccatttttgttagctataagaggtgatgataatggcatggtttattcgaagcacttttt--aagtagctgttctga

upper sequence: AT2G34860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA14G27040.1 (Glycine max), 5'ss of exon 2
GTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgtttg--tttccttcccgatatctctttagtcttgtttggtttcgtaacacttga-aatttcctgattagttggtggcttctattgcaaacag---------
 ||||||||||||||| |||||||||||||||||||| |||   || || || |||||||| || || ||||| || |||||||| ||||| ||| ||   | |  |  | |  |  ||  | | ||||| | | |   |     ||| |||  | || ||  || |  ||   | ||  ||  ||         
ATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACATGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATGgtatgaactccagtttctacttgactccatttttgttagctataagaggtgatgataatggcatggtttattcgaagcacttttt--aagtagctgttctga

upper sequence: AT2G34860.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv06s0004g01100.t01 (Vitis vinifera), 5'ss of exon 4
GTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgt--ttgtttccttcc------cgatatctctttagtcttgtttggtttcgtaacacttgaaatttcctgattagttggtggcttctat-tgcaaacag-
||||||||||||||||||| ||||||||||||||||||||| ||||||| || |||||||| || |||||||| ||||| ||||| ||||| |||  ||  |||| | |      | |||| |||||  | |  |    | |  | |  |  | | ||   ||  ||  |       | ||| |   |   | 
GTGATATGTGTGGTGGTACGGGAAAATGGAAAGCTCTCAACAGAAAACGGGCTAAAGATGTTTACGAGTTTACTGAATGCCCAAATTGTTATGgtatttacttccattcatattcctatatttcttttatttgttgctatctgatgaagcaggcatttctttgtctatatatatatatatatatctcagtggc

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|86073324|gb|DR369081.1|DR369081
EST:     AAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG                         GTCGAGGTAAGCTTGTTTGTCCGGTCTGTTTAGGTACAGGTTTACCAAACA
genomic: AAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgtttgtttcc ... ttgcaaacagGTCGAGGTAAGCTTGTTTGTCCGGTCTGTTTAGGTACAGGTTTACCAAACA
EST: gi|125192222|gb|EL207176.1|EL207176
EST:     AAACTGTTACG                         GTCGAGGTAAGCTTGTTTGTCCGGTCTGTTTAGGTACAGGTTTACCAAACA
genomic: AAACTGTTACGgtttgtttcc ... ttgcaaacagGTCGAGGTAAGCTTGTTTGTCCGGTCTGTTTAGGTACAGGTTTACCAAACA
EST: gi|86073323|gb|DR369080.1|DR369080
EST:     ANNNCGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG                         GTCGAGGTAAGCTTGTTTGTCCGGTCTGTTTAGGTACAGGTTTAACAAACA
genomic: AAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgtttgtttcc ... ttgcaaacagGTCGAGGTAAGCTTGTTTGTCCGGTCTGTTTAGGTACAGGTTTACCAAACA
EST: gi|125059582|gb|EL128259.1|EL128259
EST:     AAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG                         GTCGAGGTAAGCTTGTTTGTCCGGTCTGTTTAGGTACAGGTTTACCAAACA
genomic: AAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgtttgtttcc ... ttgcaaacagGTCGAGGTAAGCTTGTTTGTCCGGTCTGTTTAGGTACAGGTTTACCAAACA
EST: gi|125029033|gb|EL101302.1|EL101302
EST:     AAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG                         GTCGAGGTATGCTTGTTTGTCCGGTCTGTTTAGGTACAGGT
genomic: AAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgtttgtttcc ... ttgcaaacagGTCGAGGTAAGCTTGTTTGTCCGGTCTGTTTAGGTACAGGT
EST: gi|125026132|gb|EL098401.1|EL098401
EST:     TTTACGGAATGTCCAAACTGTTACG                         GTCGAGGTAAGCTTTGTTTGTCCGGTCTGTTTAGGTACAGGTTTACCAAAC
genomic: TTTACGGAATGTCCAAACTGTTACGgtttgtttcc ... ttgcaaacagGTCGAGGTAAGC-TTGTTTGTCCGGTCTGTTTAGGTACAGGTTTACCAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACGgtttgtttccttcccgatatctctttagtcttgtttggtttcgtaacacttgaaatttcctgattagttggtggcttctattgcaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG