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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAAgtaagagattatctaccttcttcttatgactgaatttgttccatttttgtgactggaggtcttatctattgttgtaaatgtctttctatcag

Basic information

species Arabidopsis thaliana
transcript AT1G20110.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20110.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G02550.1 (Glycine max), 5'ss of exon 2
ATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAAgtaagagattatctaccttcttcttatgactgaatttgttccatttttgtgactggaggtcttatcta---ttgttgtaaatgtctttctatcag---------
||||||||||||||  |||||||||| ||||||| ||| ||||| || |||||||| ||||||||||||||||| |||||||| || ||  ||| || |  |  | ||||  |  |||    |  ||||||    |  | |     || ||   |   |  || ||| | | |    ||            
ATTGGTTTGGATGGAATTCGTATGCTGGATCCAAATACCAGCCGGACATTGAGAATTTATCCTCTTGAGAACATAACAAGATGTGATgt--gagcttcttgatttccttcagaaaacttctctacttccat----gaaattaattttcctagtcaatctcattataattttttgctaattgaatcatgcag

upper sequence: AT1G20110.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA17G37890.1 (Glycine max), 5'ss of exon 2
ATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAAgtaagagattatctaccttcttcttatgactgaatttgttccatttttgtgactggaggtcttatctattgttgta-aatgtctttctatcag------------------------------------------------------
|| |||||||||||  |||||||| | ||||||| |||||| ||||| |||||||||||||| ||||||||||| |||||||| || |||||   || | ||  | |||  |   | |   ||   |  || |||   | |  |  | |  || ||     || ||||| ||   ||                                                         
ATCGGTTTGGATGGAATTCGTATGTTGGATCCAAATACTAGTCGAACATTGAGAATATATCCACTTGAGAACATAACAAGATGTGATgtaagc--ttgtttatttactttgtgaaatt---ttgaatagatattttgaaattaatttgtagtcaatctcaatataatgttttctaattgatttatggctttatgcatgaaattcgattcaattacctttgcattttggtcgaag

upper sequence: AT1G20110.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA14G40250.1 (Glycine max), 5'ss of exon 2
ATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAAgtaagagattatctaccttcttcttatgactgaatttgttccatttttgtgactggaggtcttatctattgttgtaaatgtctttctatcag
||||||||||||||  |||||||| | ||||||| |||||| ||||| ||||||||||||||  |||||||||| |||||||| || |||||        |    | ||| | ||    ||||||       |||||            |||    | || ||| ||  ||     |||
ATTGGTTTGGATGGAATTCGTATGTTGGATCCAAATACTAGTCGAACATTGAGAATATATCCAATTGAGAACATAACAAGATGTGATgtaag------cttgttgttttcctttgtgaaaatttgaaattaatttgtagtcaatctcaatataacattttctaattgaattatg--cag

upper sequence: AT1G20110.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G02510.1 (Glycine max), 5'ss of exon 3
ATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAAgtaagagattatctaccttcttcttatgactgaatttgttccatttttgtgactggaggtcttatctattgttgta-aatgtctttctatcag----------
||||||||||||||  |||| ||||| ||||||| ||| ||||| || |||||||| ||||||||||||||||| |||||||| || ||  ||| || |  |  | ||||  |  |||  | |   |||||     | | |      ||  || ||     |  ||||| || |||   |          
ATTGGTTTGGATGGAATTCGCATGCTGGATCCAAATACCAGCCGGACATTGAGAATTTATCCTCTTGAGAACATAACAAGATGTGATgt--gagcttcttgatttccttcagaaaacttcactgcatccatcaaattaatttt---cctagtcaatctcaatgtaatgttttgctaattgaatcatgcag

upper sequence: AT1G20110.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv18s0001g14750.t01 (Vitis vinifera), 5'ss of exon 2
ATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAAgtaaga-gattatctaccttcttct---tatgactgaatttgttccatttttgtgactgga----ggtcttatctattgttgtaaatgtctttc--tatcag------------------------
||||||||||||||  ||||||||||||| || || ||||| ||||| |||||||||||||| |||||||  || |||||||| ||||| ||  | ||   | |||| || |   | |  ||  | |   |   |||||   |||  |    | | |  | || | | ||  || | |  |  ||||                          
ATTGGTTTGGATGGAATTCGTATGCTTGAACCCAGCACTAGTCGAACATTGAGAATATATCCACTTGAGACAATAACAAGATGTGAAgtgagttggttgcttccctttttttggatttccctctactgtcttagtttttagcactatattttgttatggtatactatggtggatatgtagcattatcttgaaatgttttctctttttgttcag

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|86015833|gb|DR311579.1|DR311579
EST:     CTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA                         AAACTAGATTCGTCTATTCTGGCTTTCTGGTCTAAGACTCCGGTAGACATT
genomic: CTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAAgtaagagatt ... tttctatcagAAACTAGATTCGTCTATTCTGGCTTTCTGGTCTAAGACTCCGGTAGACATT
EST: gi|125059919|gb|EL128596.1|EL128596
EST:     TCACAAGATGCGAA                         AAACTAGATTCGTCTATTCTGGCTTTCTGGTCTAAGACTCCGGTAGACATT
genomic: TCACAAGATGCGAAgtaagagatt ... tttctatcagAAACTAGATTCGTCTATTCTGGCTTTCTGGTCTAAGACTCCGGTAGACATT
EST: gi|86068172|gb|DR363929.1|DR363929
EST:     CTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA                         AAACTAGATTCGTCTATTCTGGCTTTCTGGTCTAAGACTCCGGTAGACATT
genomic: CTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAAgtaagagatt ... tttctatcagAAACTAGATTCGTCTATTCTGGCTTTCTGGTCTAAGACTCCGGTAGACATT
EST: gi|86079507|gb|DR375264.1|DR375264
EST:     CTCTTGAGAACATCACAAGATGCGAA                         AAACTAGATTCGTCTATTCTGGCTTTCTGGTCTAAGACTCCGGTAGACATT
genomic: CTCTTGAGAACATCACAAGATGCGAAgtaagagatt ... tttctatcagAAACTAGATTCGTCTATTCTGGCTTTCTGGTCTAAGACTCCGGTAGACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAAgtaagagattatctaccttcttcttatgactgaatttgttccatttttgtgactggaggtcttatctattgttgtaaatgtctttctatcag

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