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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacag

Basic information

species Arabidopsis thaliana
transcript AT1G59610.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 5'ss of exon 19
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgt--------ggactagtcacttttcttgtgaat--tcttaaattcccatgccaatatcgcttttcattactcgatcacattactaa-atctgtgacttcaacag
||| || |  || || ||||| ||| | ||||||||||| |||||||| || |||||||| || |||||| | |||||| | || || ||||||||||||||        | ||    || || | |    | |  |  ||  ||   |   |||| |  | |     || | |      ||| ||   ||| |  | | | |||
GAAGCCTGCTGATCCTGAAGAAGAACTTCGGTGGATGTCTCAAGAAGTTCGTGGTTATGTAGAGGCTGTTTTGAACAGTTTGGCAGCAAATGTTCCAAAGgtttacatttgaacctcacaattgtttcaacagtcatactattttttaaactcaatttaacatggtcatagttgcaattgttattattgtctttttcatgatcag

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattact-cgatcacattactaaatctgtgacttc----aacag
|| ||| |  || || ||||| ||| |  | ||||||||||| ||||| || ||||||||||| |||||| | || ||||| || || ||||| ||||||||       | || ||       |  |   |  | | |||  || |    | | |||||    | ||    ||| |   | |    ||||    | |||
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgt-------ttacattaaaaaaaagctagcat-tgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GRMZM5G870253_T01 (Zea mays), 5'ss of exon 3
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgt--ggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacag
||  || |  || || ||||| ||| | || |||||||| |||||||| || |||||||||||||||||| | |||||| | ||||| ||||||||||||||  | ||| ||  |||   |||    ||   |  ||   ||      |      ||| ||  ||  |  ||| || |                  
GAGGCCTGCTGATCCTGAAGAAGAACTTCGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTTTGAACAGTTTGGCTGCAAATGTTCCAAAGgtttgtactcgtagcttcagttgattctttgaaccttgtgatttgtggagtaacgttcttttgtcttttgcatgaccag-----------------

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GRMZM5G811223_T01 (Zea mays), 5'ss of exon 7
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgc-ttttcattactcgatcacattactaaatctgtgacttcaacag
|| ||| |  || || ||||| ||| |  | |||||||| |||||||| || ||||||||||| |||||| | || ||||| || || |||||||| |||||  |    |   | |  |  | | ||   |    |   |     | ||   |||||||| || |     | |  | |                 
GAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcat--attgttctgttaatcagtttaaatggccttgtatttgtgtcaaattttcattgcttgtctgtacttgttag----------------

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 19
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgc-ttttcattactcgatcacattactaaatctgtgacttcaacag
 | ||| |  || || ||||| ||| |  | |||||||| |||||||| || |||||||| || |||||| | || ||||| || || ||||||||||||||  |    |   | |       | ||   |    |   |     | ||   || | |||  | |     | |  | |                 
TAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcat--attggtctgtcaaccagtttaaatggccttttatttgtgtcaaattcttattgtttgtctgtacttgttag----------------

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA07G40300.1 (Glycine max), 5'ss of exon 19
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacag
 ||||| |  || || ||||||||  |  | |||||||| |||||||| || |||||||||||||||||||| ||||| || ||||| ||||||||||| |||   |       | | || | || |   | | | |    |   | |   ||  |     | | | | || | |  |  | |||||  | |||
AAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTGCAAATGTTCCAAAAgtgagtt-------tattttatcaactaccatagttcttctct--tctgatttgacgcggtttg-tgagatgatttcactt-tgactg-agcag

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA17G00480.1 (Glycine max), 5'ss of exon 19
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtga--attcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacag
|||||| |  || || || |||||  |  | |||||||| |||||||| || |||||||||||||||||||| ||||| || || || ||||||||||| |||   |  |    |    |   |   |||||   |||  ||    || | | || | |  |     |||| ||  |  | | |            
GAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAGCTAATGTTCCAAAAgtgagtttattttatcaactaccatagttcttctcttctgat-ttgatgtggtttgtgag-atcatttcactttggttgagcag------------

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA12G37100.1 (Glycine max), 5'ss of exon 19
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacag
 | ||| |  ||||| || || ||| | || |||||||| |||||||| || || ||||||||||| ||| | || ||| ||||||| ||||||||||||||   ||  |   |||     |      ||  ||     | ||| | |  |   | | |  | |||    || ||   |   ||  ||  ||||
AAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAGgtaagcttctgtttttagcatttgccatttttataatttttccagttttcccagttaatttttgatgcattttctggttgcttggttt--acag

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttt----tcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacag
 | ||| | ||| || ||||| ||  | || |||||||| |||||||| || |||||||||||||||||||| ||||| || ||||||||||| ||||| || |  | ||    ||     | |    |||| |  |||    |||   | | | | |     | ||      |||||    ||||    || | |||
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctg--agtcttctttattacctgttctgg---ttgagcag

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 19
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacag
 | ||| | |||||| ||||| ||| | || |||||||| |||||||| || || ||||||||||| ||| | |||||||| ||||| ||||| || || ||   |   |  |  |   |    ||| ||  ||    |   |    || |||   | | || ||  |  | |   | |   || |        
AAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAAgtaagcacttgtccctgaattctcatttttgcatctttacatctg-gtcacttacaaatgcttgaatatgtgatcgattggttggcag------

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|164200292|gb|ES066203.1|ES066203
EST:     ACAGTCTAGCTGCCAATGTTCCAAAG                         GCTGTTGTTCTTTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAG
genomic: ACAGTCTAGCTGCCAATGTTCCAAAGgtggactagt ... acttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC