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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTGGATTTAACGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttcgaagaatgtgttcgaacgcattaaactttgaatttgaagtagtagaaatgatttttggtattatatggaagggatattcgaaatctacaa...

Basic information

species Arabidopsis thaliana
transcript AT2G24765.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G24765.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 3
CTATTGGATTTAACGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttt---tcgaagaatgtgttcgaacgcattaaactttgaatttgaagtagtagaaatgattt-ttggtattatatg-gaagggatattcgaaatctacaa
| ||||| || ||||| ||||| |||||||||||||| |||||||| || ||||||||| | |||  || |    | |||  | || |  |           || || |||   |     || |  |||| |  |||  || |  ||    ||    ||   | |   
CGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgcccccaagtctctgattcacgaggactggtttagatttttccgc----gagacaatttataagtacaatttacgacaatatccatgaggccaatt-

upper sequence: AT2G24765.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G147726_T05 (Zea mays), 5'ss of exon 2
-------------------------------------CTATTGGATTTAACGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttcgaagaatgtgttcgaacgcattaaactttgaatttgaagtagtagaaatgatttttggtattatatggaagggatattcg-----aaatctacaa
                                     | |||||||| ||||||||||| |||||||||||||| |||||||| || || |||||| | |||  |||      | || |   ||  | | ||    ||   |||   |  |||   ||||   | | |    ||  | |  | |  ||||     |||  || | 
TTGTTGGATTTGATGTGGTGCCCCGCGTGTGTTGCAGCAATTGGATTCAACGTTGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTATGGGATCTTGgtgagttactt--ggatctcgccgccctcttttgcattcctatt--gatgagtgataatgggctgttgagcgatcagaagtgcaatttcgtcccaaaacgtaga-

upper sequence: AT2G24765.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G147726_T01 (Zea mays), 5'ss of exon 3
CTATTGGATTTAACGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttcgaagaatgtgttcgaacgcattaaactttgaatttgaagtagtagaaatgatttttggtattatatggaagggatattcg-----aaatctacaa
| |||||||| ||||||||||| |||||||||||||| |||||||| || || |||||| | |||  |||      | || |   ||  | | ||    ||   |||   |  |||   ||||   | | |    ||  | |  | |  ||||     |||  || | 
CAATTGGATTCAACGTTGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTATGGGATCTTGgtgagttactt--ggatctcgccgccctcttttgcattcctatt--gatgagtgataatgggctgttgagcgatcagaagtgcaatttcgtcccaaaacgtaga-

upper sequence: AT2G24765.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S78_17V6.1 (Physcomitrella patens), 5'ss of exon 3
CTATTGGATTTAACGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgtttt-cgaagaatgtgttcgaacgcattaaactttgaatttgaagtagtagaaatgatttttggtattatatggaagggatattcgaaatctacaa-
||||||| ||||| || ||||||||||| ||||||||||| || ||||| || |||||| |||||  || |  |||  |  |  ||        ||  | ||  ||||||  ||| |  || |  ||| |  | | || || | |  |   | |      |  | 
CTATTGGCTTTAATGTGGAGACTGTGCAATACAACAATATTAAATTTCAAGTTTGGGATCTAGgttcgtgtcgcgagcacaggatttttttattttttatttataatttg--gtaatttaagttttttattctctcatgtgaatgtcacccttgtgtgtcaggac

upper sequence: AT2G24765.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S271_49V6.1 (Physcomitrella patens), 5'ss of exon 3
CTATTGGATTTAACGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttcgaagaatgt---------gttcgaacgc----attaaactttgaatttgaagtagtagaaatgatttttggtattatatggaagggatattcg---aaatctacaa-------------------------------------------------------------------
||||||| ||||| || |||||||||   ||||||||||| |||||||| |||||||||||||||  || ||   || ||||          || | | |     ||| |   || ||| | || | | |   ||| |||| || ||  |     ||   |||||    || | |||                                                                     
CTATTGGTTTTAATGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAGgttcgtgttatcagcatgttaattttttatttgtaggttcctattgagtatttaatgtcaa-tggcacctatg-ttttaggcatactgcttcagttgtattctctcaattatactcttatattttatccgttgatatgttatctgtaatatcttgtatttctaactacttgtgatgatggcag

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|86084655|gb|DR380414.1|DR380414
EST:     CGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAG                         GTGGACAAACAAGCATCAG
genomic: CGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttc ... cctatgacagGTGGACAAACAAGCATCAG
EST: gi|125249151|gb|EL263236.1|EL263236
EST:     CGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAG                         GTGGACAAACAAG
genomic: CGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttc ... cctatgacagGTGGACAAACAAG
EST: gi|125296023|gb|EL310108.1|EL310108
EST:     CGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAG                         GTGGACGAACAAG
genomic: CGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttc ... cctatgacagGTGGACAAACAAG
EST: gi|124933836|gb|EL010958.1|EL010958
EST:     CAACAATATCAAGTTTCAGGTCTGGGATTTAG                         GTGGACAAACAAGCATCAG
genomic: CAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttc ... cctatgacagGTGGACAAACAAGCATCAG
EST: gi|124708200|gb|EH799602.1|EH799602
EST:     CGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAG                         GNGGACAAACAAGCATC
genomic: CGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttc ... cctatgacagGTGGACAAACAAGCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATTGGATTTAACGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttcgaagaatgtgttcgaacgcattaaactttgaatttgaagtagtagaaatgatttttggtattatatggaagggatattcgaaatctacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtagaaa