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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgttttctatttctctacttctatcttgttctctctacattttgcctctctcttatgtttttggttaatacggtcag

Basic information

species Arabidopsis thaliana
transcript AT5G19990.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 5'ss of exon 6
CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgta-aagtgttttctatttctctactt-ctatcttgttctctctacattttgc-ctctctcttatgtttttggttaatacgg--tcag------------
 |||||||||||||| || || |||||||| ||||||||||| || |||||||||||||||||||||||||||||||| || || || || ||||| |||||     |  ||   | || |   |    | |||      ||   |||||    ||    |  || |  |    | | ||     |||            
TATCTTGAAGATTCATTCAAGAAAAATGAACTTGATGCGTGGCATTGATCTGAAAAAGATTGCAGAGAAGATGAATGGGGCATCTGGAGCAGAGCTTAAGgtgtgtatagttgacacttatgagccaattttctaaaatacttctcatttcaagctgatacaaatatcatgaactgaaacaaatccaggcccagttataa

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 5'ss of exon 8
CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgttttctatttctctacttctatcttgttctctctacattttgcctctctcttatgtttttggttaatacgg--tcag-------------------
 |||||||||||||| || || |||||||| ||||||||||| || |||||||||||||| || || ||||||||||| |||||||| || ||||| |||||    |||||  | |||   | | ||| |  |      | |  | | ||  | | ||| |      || ||| | ||   | ||                   
TATCTTGAAGATTCATTCAAGAAAAATGAACTTGATGCGTGGTATTGATCTGAAAAAGATCGCTGAAAAGATGAATGGGGCTTCAGGAGCCGAGCTCAAGgtt---tgtttagtctttactttcatctgttataaaacat-tgtactgtgtatttgtctcacacgagtgattattgcgagattagtttaaatccctccgctact

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 8
CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgttttctatttctctacttctatcttgttctct-ctacattttgcctctctcttatgttt-ttggttaatacggtcag----------------------
 ||  ||||||| || || ||||||||||| ||||||||||| ||||||||||||||||| ||||| ||||||||||| || ||||| |||||||| |||||      || |  | | | || | |||       | | | || | | | |  ||  |||| ||||  || |     ||| | |                       
TATTCTGAAGATCCATTCAAGGAAAATGAACTTGATGCGTGGTATCGATCTGAAAAAGATCGCAGAAAAGATGAATGGGGCCTCAGGAGCTGAGCTCAAGgt------ttgttaaatccacttcatctgatgaactgtttgctgcctctcgtttcaatcttgtgttgattcgaagtaacgtttaacattttttttttggctgttcag

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 8
CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgttttctatttctctact----tctatcttgttctctctacattttgcc-tctctcttatgtttttggttaatacggtcag------------
 ||||||||||| || || || |||||||| ||||||||||| || |||||||||||||| || || ||||||||||| || ||||| |||||||| |||||    |  || |  ||| |||  |    |   |  ||     | |  ||||||   | | |  | | || | | |  || |   |||            
TATCTTGAAGATCCATTCAAGAAAAATGAACTTGATGCGTGGCATTGATCTGAAAAAGATCGCGGAAAAGATGAATGGGGCCTCAGGAGCTGAGCTCAAGgtttgttaattccactttatctgatgaactgcgtgctgcctcatttcaattttgtgatgtttgctttcttgtcgttccattcaagcagaaaattatgttc

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 8
CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgttttctatttctctacttctatcttgttctctctacattttgcctctctcttatgtttttggttaatacggtcag---------------------
 || ||||| || || || || | ||||||||| |||||||| || |||||||| |||||||| |||||||||||||| || || |||||||| || |||||| | | |  | |   ||  || || |   ||   | |   |   |||     | | ||   | ||     |||  ||| ||                     
TATTTTGAAAATCCATTCAAGAAGAATGAATTTAATGCGTGGCATTGATCTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatatt-tcatttgcatccatatttttggttttaacacctga---tttaaaattgtattccatgttgaaacaatgtggtgagattgctgaactcctttgcttt

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 8
CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgttttc----tatttctctacttctatcttgttctctctacattttgcctctctcttatgt--ttttggttaatacggtcag------------
 || ||||| || || || || | ||||||||| |||||||| || ||| |||| |||||||| |||||||||||||| || || |||||||| || |||||| | | | ||      || | | |  || || |   |  |||  | ||| |    ||   | | |   |||  | |  ||  |                
TATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactctatttgcatcatatgtttggttttaacacctaatctaaa-attgtattccttgttgaagcaatttgtggtggtattgctgaactcctttgctt

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 5'ss of exon 8
CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgttttctatttctctacttctatctt--gttctctctacattttgcctctctcttatgtttt-tggttaatacggtcag-----------------
 || || || || ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| || || ||||| ||||| |||||    ||||| |  ||  | || || |   ||  | |       |||||  |||||     |    || | | ||    | ||                   
TATTTTAAAAATACACTCGAGGAAAATGAATTTGATGCGTGGGATCGATCTGAAGAAGATTGCAGAGAAGATGAATGGTGCATCTGGTGCAGAGCTCAAGgt---ctgtttccacttcatttattttttatttcagataaaaaggcatttctcctcttatgaacaagttgtaggtaggctgttcttttcaattggtcctcgtt

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 8
CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgttttct-atttctctactt---ctatcttgttctctctacattttgcctctctcttatgtt---tttggttaatacggtcag----------
 || ||||| || ||||| || |||||||| || |||||||| || |||||||| ||||| ||||||||||||||||| || || ||||| ||||| |||||| | |  |   | ||   |  | ||   ||||||   |         ||||||   |   || ||      ||| |||  | ||||            
TATTTTGAAAATCCACTCAAGAAAAATGAACTTAATGCGTGGGATTGATCTGAAGAAGATAGCAGAGAAGATGAATGGTGCATCTGGTGCAGAGCTTAAGgtatattaatcagtcatgcgtacagttactctatctgaatggtctcctgttttgctctttggttttgagagacttgcttatgatggtccatgattcttcc

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|86084788|gb|DR380547.1|DR380547
EST:     TGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAG                         GCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACAC
genomic: TGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgtt ... atacggtcagGCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACAC
EST: gi|125225984|gb|EL240069.1|EL240069
EST:     TGGCGCTTCAGGTGCTGAGCTGAAG                         GCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACAC
genomic: TGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgtt ... atacggtcagGCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACAC
EST: gi|86075404|gb|DR371161.1|DR371161
EST:     TGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCT-AAG                         GCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACAC
genomic: TGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgtt ... atacggtcagGCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACAC
EST: gi|124971086|gb|EL044876.1|EL044876
EST:     TGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAG                         GCTGTGTGCACGGAGGCGGGAATGTTTGCT
genomic: TGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgtt ... atacggtcagGCTGTGTGCACGGAGGCGGGAATGTTTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTGCTGAGCTGAAGgtaaagtgttttctatttctctacttctatcttgttctctctacattttgcctctctcttatgtttttggttaatacggtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG