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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtag

Basic information

species Arabidopsis thaliana
transcript AT5G42270.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttacaactgaaa--ctgtactggttttgatttacaagagtagtctt--cgagtgttaaacaatgtttattgtgtttcacctatggtag
|||| ||||| || || ||||| ||||| |||||||| ||||| |||||||| ||||| |||||||| |||||||||||||| || || ||||||||||||| | ||  |    ||      ||   |  |  || | | |  || ||  |    ||| || |||  |||    | |   |    |   |   
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagct-tacatggtttgcag---

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G126361_T03 (Zea mays), 5'ss of exon 4
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttacaactg-aaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgtttca--cctatggtag-------
|||| ||||| || || ||||| |||||||| |||||||| || |||||||| ||||| ||||| |||||||||||||||||||| || |||||||| ||||  | |    ||| | ||| |  |  |||     |    || |  |  |   | |   |   |||     || | |  |  | ||||||         
GTGGACTCACATTCTTTGCTCCAAGCGAAGAAAGGCTAGAATCTGGATTGTACAGCAGGAGCTATCTTGAGAACCAAATGGCTGTAGCCCTTGGTGGCAGgtgctcttt--ctgcatactctgttcatttctgcatcattgactgttgctgctgcgcatattgatggactgtgagatgtaatcttatggtttgctgcag

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 3
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtag-----------
|||| ||||| ||||| ||||| |||||||||||||| ||||| |||||||| || ||||| |||||||| || || ||||||||||| || ||||||||||   |   |  || |    ||||   |||||| |   |   |    || |   || |  || | ||||      | ||| | | ||             
GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaacgtgcacaattactttgtttgatcttggattttgacatttgcaagtcattcattctttaacaaactccacttgttgtcaattggctaatg

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 3
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgt-agtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgttt-cacctatggtag---------
|||| ||||| ||||| ||||| || ||||||||||| ||||| |||||||| || ||||| |||||||| || || |||||||||||  | |||||||||| |||  |  ||   |     | |    ||| || |    ||   |   |   || ||  || |  || || | |   |||   |||            
GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaacacaacatgcacagttaccttgtttgattttagattttgacatttgctagtcattcattcttatatcaacactactggcctactcttgag

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 3
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttac--aa--------ctgaaactgtactggtt-ttgatttacaaga-gtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtag
|||| || |||||||| ||||| || |||||||| || ||||| ||| |||| || ||||| ||||| ||||| || |||||||||||||| ||||||||||   || |  ||        |    ||   || |||  |||  ||| |    ||||| |         |  |||| ||    |  |   | ||   |   
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgcttaatcccatctccaggaccccacaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat-

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ31931 (Selaginella moellendorffii), 5'ss of exon 3
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtag
| ||  | ||||||||||| || ||||| ||||| || ||||| || || || ||| |||||||| | |||||||| ||||| || || ||||||||||||||       |   |||||   |   || |    |  ||| ||    ||| ||                                    
GAGGTTTGACCTTTTTCGCACCCAGCGAGGAGAGACTTGAGTCAGGTTTATACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgta---cgtgatctaaacttcccattttctttgctttaagcgtgcgattccag------------------------------------

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|125017651|gb|EL089920.1|EL089920
EST:     TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCG
genomic: TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCG
EST: gi|125212703|gb|EL227657.1|EL227657
EST:     ATAGCAGAAGCTACCTTGAGAACCAAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACG
genomic: ATAGCAGAAGCTACCTTGAGAACC-AAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACG
EST: gi|125189404|gb|EL204358.1|EL204358
EST:     TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACGAGAAT
genomic: TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAAT
EST: gi|124889013|gb|EH967915.1|EH967915
EST:     TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGG
genomic: TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGG
EST: gi|125034754|gb|EL107023.1|EL107023
EST:     ATAGCAGAAGCTACCTTGAGTAACCAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAG
genomic: ATAGCAGAAGCTACCTTGAG-AACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG