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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattttgaaacgtatattcttcagttgttgagaacttactgactttactgtttacctttttctag

Basic information

species Arabidopsis thaliana
transcript AT1G10290.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 15
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcag-cattttgaaacgtatattcttcagttgttgagaacttactgactttactgtttacctttttctag--------------------------------------------------------------------
| ||| |  ||||||||||||||||||||||||| ||||||||| | |||||||| || ||||||||||  |||||||| |  ||   |  ||     ||  || |||| |      |||  ||   | || |      | |    |                                                                     
GTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAGgttaatcagagttcaatcatcatcttttagttttgtttgtctttttgcactaacaggaggaatatcaggataatttatttatgtattttccgatggacttctatgcatgggtggttggttaaccttctatttttatcag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os08g32920.1 (Oryza sativa), 5'ss of exon 15
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattttg---aaacgt---atattcttca--gttgttgagaactt--actga--ctttactgtttacctttttctag----------------
| | | |  | || ||| |||||||| ||||||  |||||||  || ||||||||||| ||||||| || |||||||||  || || ||   || | |   | || |   |  ||  ||   || ||  ||||    ||||||  ||   |  |   |                 
GTTTCCTTTTCAAAAAACGTGCAAAAGCAAATGACTGGAGTAACCGCTGGTTTGTTCTAAATGAGAGAAGTGGAAAGgttggctttctgtttaagcatcttacatcccgtaacgtcatttcaaattttcactgggtttttactactttgatcatgggacaatgaattttatccag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GRMZM5G811223_T01 (Zea mays), 5'ss of exon 3
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgt----cagcattttgaaacgtatattcttcagttgttgagaacttactgactttactgtttacct-----ttttctag---------------------------------------------------------------------------------------------
| ||| |  | |||||||| |||||||| |||||||||||||   | ||||||||||| |||||||| | |||||||||    |||   ||  |||| | | || |  | | ||       ||  | |||||  | | |   |        |   |                                                                                             
GTTACCTCTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGTAAAAGGTGGTTTGTTCTTAATGAGAAGAGTGGAAAGgttaatcagttcttcaaaacatttcttttatactcgtgatttgtttgat-actttgatatgtgtgtgaaagcccttcggttttcaaatgtttacttaatgattattgtatttcatggttcttgtttgatatgtgggtgtggtttgactcactatctgttgtttctatgccag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 15
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgt----cagcattttgaaacgtat-------attcttcagttgttgagaacttac-tga-----ctttactgtttacctttttctag----------------------------------------------------------
| ||| |  | |||||||| |||||||| ||||||||||| |   ||||||||||||| |||||||| | |||||||||    |||   ||   ||| | |       | |||| | |||||    |  ||  |||     |||   | || |  | | | |                                                            
GTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAGgttaatcagttcttcagaacatttcttttgaactcttgatttgtttgatatgtatgtgaaagcccttaggttttcaaatgtatttcatggttcttgtttgatatgtgggtgtggttttattcattatctgttgtttctatgccag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GRMZM2G485898_T01 (Zea mays), 5'ss of exon 15
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattttgaaacgta---tattcttcagttg--ttgagaacttactgactttactgtttacctttttctag-------------------------
| |  ||  | || ||| | |||||| ||||||  ||||| | ||||||||||||||| |||||||||| |||||||||  | | | | |    ||   || || ||  ||   || |  | |||  |    |  |        |||| | |                         
GTTTTTTGTTCAAAAAACGCGCAAAAGCAAATGATTGGAGCAAGCGATGGTTTGTTCTAAATGAGAAAAGTGGAAAGgttggtagtatcagcattaaaatactcatccattccttttaccatttatggtgcctcttaacatttgttttgtggccagcttggatacacaaagaaacaa

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GRMZM2G485898_T02 (Zea mays), 5'ss of exon 15
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattttgaaacgta---tattcttcagttg--ttgagaacttactgactttactgtttacctttttctag----
| |  ||  | || ||| | |||||| ||||||  ||||| | ||||||||||||||| |||||||||| |||||||||  | | | | |    ||   || || ||  ||   || |  | |||  |    |  |        |||| | |    
GTTTTTTGTTCAAAAAACGCGCAAAAGCAAATGATTGGAGCAAGCGATGGTTTGTTCTAAATGAGAAAAGTGGAAAGgttggtagtatcagcattaaaatactcatccattccttttaccatttatggtgcctcttaacatttgttttgtggccag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA12G37100.1 (Glycine max), 5'ss of exon 15
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattttgaaacgtatattcttcagttgttgagaac-ttactgactttactgtttacctttttctag------------------------------
| |  ||  | ||||||||||||||||| ||||| ||||| |||||||||||||| || |||||||| || ||||||||  | |  |     |  |  ||  | | || || | |   ||  | | | |  | |     || |||                                 
GATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAGgttggtaactgttggccga-gttgataaattatttacagtgttctttagtcttttatcattattattcctacatcaagttcactgtcttctgattaacaca

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA09G00430.2 (Glycine max), 5'ss of exon 15
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattt-----------tgaaacgta---tattcttcagttgttgagaacttactgactttac---tg--tttacctttttctag------------
| |  ||| | ||||||||||||||||| ||||| ||||| |||||||||||||| || ||||| || || ||||||||  |    |           ||| |  ||   | ||||| |||  || |  | ||| |     |||   ||  || ||  | ||||              
GATTTTTATTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAAAAGACAGGAAAGgttggtgactgttggccgagttgatatttacagtgttctttagtcttttatca-ttattattcctacatctggtttcactgtcttctgactgacatgctag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 15
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattttgaaacgtatattcttcagttgttgagaacttactgactttactgtttacctttttctag----------------------------------
| |  ||| |||||| ||| || ||||||||||| ||||||||||||||||||||| | |||||||||| | | |||||  | | | |   |  |  |     ||   ||   | | |||| |  ||   ||   || |||||  |                                   
GATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAGgtaggtaatgtagtatttccaccaaccaaaagt---gtaattacag-tttgcttgaacacatttttgaaatgaatcatgtaccatgtctttggtgcagtgatcc

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 15
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattttgaaacgtatattcttcagttgttgagaacttactgactttactgtttacctttttctag---------------------------------------------------------------------------------------
| |   || |||||||||||| |||||| ||||| ||||| ||||||||||||||| | ||||| || ||||| ||||| || |     ||   |   ||| ||| | | || |  |||  ||  ||   |  ||   | |||  |                                                                                        
GCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAGgttagta-----aagtatcagttcatcactggatgtgccctttttgtattctttcattggttctttgcaccatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgtatttcatcaatatggttgtctttttgtttcacag

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|124924966|gb|EL003011.1|EL003011
EST:     CAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAG                         CTTGGCTATACCAAAAAGCAAGAAGAAAGAAACTTTCGGGGCACG
genomic: CAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattt ... ctttttctagCTTGGCTATACCAAAAAGCAAGAAGAAAGAAACTTTCGGGGCACG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAGgtcagcattttgaaacgtatattcttcagttgttgagaacttactgactttactgtttacctttttctag

- - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - GTGGAG