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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagtttattgtgacttatctttttaattattctgattggaatcgagttgttcacctttaatctcttctttgacag

Basic information

species Arabidopsis thaliana
transcript AT4G21660.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 5'ss of exon 9
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagtttattgtgacttatcttttta-----attattctgattggaa---tcgagttgttcacctttaatctctt-ctttgacag
 || || ||||||| ||| |||||  |  ||||    ||  | ||||| ||||||||||||||||| || || || || |||||||| || |||||||||||   ||| |   ||   || |   |        | ||||  |||  |   ||    |||  ||   |||  |     |||| |||
CAAGCTTAGGGAAATGAAGCCAGGCATGCTGTCGCGAGAACTTAAAGAGGCTCTTGGTATGCCTGATGGTGCGCCACCTCCATGGCTTATAAACATGCAGgtatttttctgaagaacaatttccatgtatccggtgttctagttgagaagttctctatgtcaactgataacattaaattttggcag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G132060_T01 (Zea mays), 5'ss of exon 8
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagtttattgtgacttatctttttaattattctgattggaatcgagttgttcacctttaatctc---ttctttgacag--------
|||||||||||||| ||| |||||  |  ||||    ||  | ||||| ||||||||||||||||| ||||| |||||||||||||| || |||||||||||  |||  ||    || |  ||   |  |  ||  ||||  |  |  |   | ||     | ||    |   |  |||         
TAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGCAGgtttgttcttttaatctgaatttcagatgttctcctattgataatgcctctgttactggataacttggatcaatgtacaatgttccag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G121354_T01 (Zea mays), 5'ss of exon 5
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagtttattgtgacttatctttttaattattctgattggaatcgagttgttcacc------tttaatctcttctttgacag-----
|||||||||||||| ||| |||||  |  ||||  | ||  | ||||| ||||||||||||||||| || || |||||||||||||| || |||||||||||  ||| |||    || |  |      || | ||  |   |||    ||||| ||        |||||    | | | |        
TAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGCAGgtttgttcatttaacctgaattcagctcttctcctattgataatgcctttgtttactggctaacttaattcaatttataatgtttcag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA13G25110.1 (Glycine max), 5'ss of exon 9
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagttta------ttgtgacttatctttttaattattctgattggaatcgagttgttcacctttaatctcttctttgacag
 ||  |||| || | |||||| ||  | || ||| | || |||||||||||||||||||||||||| || |||||||| |||||||| ||||| |||||||| |  | |      ||||| | | | | ||  ||| ||||| |      |   |  |  | | | ||| | ||  |   |||
AAAGTTGAGAGAGATGAAACCTGGCATGTTATCACATGAATTAAAAGAAGCTCTTGGTATGCCTGAGGGTGCTCCTCCACCATGGCTTATTAATATGCAGgtaatatcagtgtctttgtggcatgtatgttgtattcttctggtcttggccctttcat--aacatcaatttttt--tcaccag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA15G07760.1 (Glycine max), 5'ss of exon 9
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagtttattgtgactt-------atctttttaattattctgattggaatcgagttgttcacctttaatctcttctttgacag
 ||  ||||||| | |||||| ||  |  | ||| | || || |||||||||||||||||||||||||| |||||||| || ||||| ||||| |||||||| |  |||| |   |||       || |||   ||||||||| |      |   ||   | | || ||| | || ||| |   
GAAGTTGAGGGAGATGAAACCTGGCATGCTATCACAGGAATTGAAAGAAGCTCTTGGTATGCCTGAAGGTGCTCCTCCTCCTTGGCTTATTAATATGCAGgtaatattatagcctcttctgttgcatttttcatattattctgttcctggcctttttaccc-cattaaatatgttttttcag--

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA07G31350.1 (Glycine max), 5'ss of exon 5
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagttta------ttgtgacttatctttttaattattctgattggaatcgagttgttcacctttaatctcttctttgacag
 ||  ||||||| | |||||| ||  | || ||| | || |||||||||||||||||||| ||||| || |||||||| |||||||| ||||| |||||||| |  | |      ||||| | | | | ||  ||| ||||| |      |   |  |  | | | ||| | ||     | ||
AAAGTTGAGGGAGATGAAACCTGGCATGTTATCACATGAATTAAAAGAAGCTCTTGGTATACCTGAGGGTGCTCCTCCACCATGGCTTATTAATATGCAGgtaatatcagtgtctttgtggcatgtatgttgtattcttctggtcctggccctttcat--aacatcaatttttttcaccagag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA13G31550.2 (Glycine max), 5'ss of exon 9
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagtttattgtgacttatctt----tttaattattctgattggaatcgagttgttcacctttaatctcttctttgacag
 ||  ||||||| | |||||| ||  | || ||| | || || ||||||||||||||||||||||||||  ||||||| || ||||| ||||| |||||||| |  |||| | | ||| | ||    |||   ||||||| ||     |   |||  | | || ||| |  | |||  |||
GAAGTTGAGGGAGATGAAACCTGGCATGTTATCACATGAATTGAAAGAAGCTCTTGGTATGCCTGAAGGTTCTCCTCCTCCTTGGCTTATTAATATGCAGgtaatattatagcgtcttctgttgcatttttcatattctg-ttactggccttttgaccccattaaatatgatttttt-cag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv00s0818g00010.t01 (Vitis vinifera), 5'ss of exon 1
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagtttattgtgacttatctttttaattattctgattggaatcgagttgttcacctttaatctcttctttgacag----------------
 || || ||||| | ||| || ||  | |||||| | ||  |||||||||||||||||||||| || ||||| |||||||||||||| || ||||||||||| || | |   | | ||  ||    | | ||| |||     |  ||    |||| ||||  | | | ||||  | |                
AAAGCTAAGGGAGATGAAGCCGGGTATGTTGTCACAGGAGCTAAAAGAAGCTCTTGGTATGCCAGAGGGCGCACCTCCCCCATGGCTTATCAACATGCAGgtcagatgagc-taattt--ctcgcaattgattttgacctttacagaacc-ttcaactttgttttttcctttagctgactgtttatttttcag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 5'ss of exon 9
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagt----ttattgtgacttatctt--tttaattattctgattggaatcgagttgttcaccttta-atctctt-ctttgacag------------------------------------------------------
 ||| | ||||| | |||||| ||     | ||  | ||  | || ||||||||||| ||||| || || || |||||||| ||||| || |||||||||||| ||    ||  |   | || |  |  |||||  |  |   |  |  ||   |   ||  | ||| ||||||  | |||||                                                        
CAAATTAAGGGAGATGAAACCTGGCCAGCTATCCCAGGAACTTAAGGAAGCTCTTGGCATGCCAGATGGTGCGCCTCCCCCTTGGCTTATCAACATGCAGgtgcgtggctttgcttaaatttcttgtgctttaaggaagcatgtctgtttcttttgagtcgtcattatatctctaaccttgacgtttgtaatacgtctgaaatgcaaatcttagtttttattcctctgttttactgcag

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|164072760|gb|ES211967.1|ES211967
EST:     TGGCTGATTAACATGCAG                         AGATATGGTCCGCCTCCTTCTTACCCACATCTGAAAATTCCTGGTTTGAAT
genomic: TGGCTGATTAACATGCAGgtgagtttat ... tctttgacagAGATATGGTCCGCCTCCTTCTTACCCACATCTGAAAATTCCTGGTTTGAAT
EST: gi|164178671|gb|EL997991.1|EL997991
EST:     TCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAG                         AGATATGGTCCGCCTCCTTCTTACCCACATCTGAAAATTCCTGGTTTGAA
genomic: TCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagtttat ... tctttgacagAGATATGGTCCGCCTCCTTCTTACCCACATCTGAAAATTCCTGGTTTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGCAGgtgagtttattgtgacttatctttttaattattctgattggaatcgagttgttcacctttaatctcttctttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT