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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactctttctttctttctcatattatccctatactatttgcaccaattttttgtatttcaaatatatattattatctttgtgtag

Basic information

species Arabidopsis thaliana
transcript AT1G01050.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G061928_T02 (Zea mays), 5'ss of exon 5
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgt-attactctttctttctttctcatattatccctatactatttgc-accaattttttgtatttcaaatatatatta--------ttatctttgtgtag-
  | || |||||||||||||| ||||||||||| |||||||| |||||  | ||  | ||||||||||||||||| || ||||| |||||| | |||||||| | |  || || || |  |    | |      |     |||||  |  ||| |   |||||     | |  ||||        |||| | |||  || 
AGTCCTGTACTCATCAGTTGTATACCCTCACAATTATGGTTTCGTTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTAGTCCTGATGCAGgttagtcttcctttttccacttgtctgtgtcatgtggggcatttgtgaagaatgtagagtattcactctttggattacaaggtccttatttctgttcagg

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G104918_T03 (Zea mays), 5'ss of exon 5
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactctttctttctttctcatattatccctatactatttgcaccaattttttgtatttcaaatatatattattatctttgtgtag-------------
  | || |||||||||||||| ||||||||||| ||||||||  ||||  | ||  | ||||||||||||||||| || ||||| || ||| | ||||||||  || ||  |||| ||||  |   || ||  | |  | |  | ||   | |   | || |  | |||  | | ||    ||     |             
AGTCCTTTACTCATCAGTTGTATACCCTCACAATTATGGTTTCATTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTGGTCCTGATGCAGgt--tagtcagtcttccttttcccacttgtctgtgtcatgtggggacatttgtgaagaatgtagagtattcactctttgtattacaaggcccttgtttctgt

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G015418_T01 (Zea mays), 5'ss of exon 5
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactctttctttctttctcatattatccctatactatttgcaccaattttttgtatttcaaatatatattatt---atctttgtgtag---------------------------------------
  | || ||||||||||| || ||||| |||||||| |||||  |||| || |||||||||||||||   || || || |||||  | ||  | ||||||||   |   | |  ||    ||  | |  | | |  |       |||  | ||  |||| || | ||||||||   |     |||  | |                                         
GGTGCTATACTCATCAGTGGTCTACCCACACAACTACGGTTTCATTCCACGAACATTGTGTGAAGACGGAGATCCAATGGATGTGCTGGTGTTGATGCAGgt--cagcatgttcttacgacttgtttgtttcatcgatctagcccacttaattagtgtactt-agatatatataggttaagccttcatcttctggggttaattattcactgactggcttacaaccaaatag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G42280.1 (Glycine max), 5'ss of exon 5
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactctttctttctttctcatattatccctatactatttgcaccaattttttgtatttcaaatatatattattatctttgtgtag
  || | || ||||||||||| || ||||| |||||||||||| | ||||||||| |||||||||||||||| || |||||||| || ||  |||||||||||  | ||     | |  | |  |||| |   |||   ||  ||   || | ||| | |   || | | |  |    | |||   |||
GGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTCTCATGCAGgta--aatccagtgtacaatattctattttaattattgaataggcgataactatttatttaagaatttttttctgcattgttttgatag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA19G45050.1 (Glycine max), 5'ss of exon 4
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgta--ttactctttctttc--tttctcatattatccctatactatttgcaccaattttttgtatttcaa----atatatattattatctttgtgtag-------------------------------------------------------------------
  || | || ||||||||||| || || || |||||||||||| | ||||||||| |||||||||||||||| || |||||||| || ||  |||||||||||  ||| |     ||||   |||  ||||| | |    |  |||    ||  ||| |  ||||  |     || | ||  ||| | |   |||||                                                                   
GGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTCTCATGCAGgtaaattagtaccattttcaaattcatatattttacaagaagcattaaatcctgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgttttaaattgttgaatagacaatgactatttaattaagaattttttctacattgttatgatag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G18510.1 (Glycine max), 5'ss of exon 4
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgta--ttactctttctttctttctcatattatccctatactatttgcaccaa---ttttttgta-tttcaaatatatattattatctttgtgtag-------------------------------------------------------------------------
  || | || |||||| |||| || ||  | |||||||||||| | ||||||||| |||||||||||||||| || |||||||| || ||  |||||||||||  ||| |     ||||    ||||||  |   || || |   |||  ||   || ||| || | |   ||| | ||   ||   |||||||                                                                          
GGTTTTGTATTCATCATTTGTTTATCCATATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTCTCATGCAGgtaaattagtaccattttcaaattcatatattt--tacacaagaagcattaaatattgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgccttaaattgttgaataggcaatggctatttaattaagaattgtttctgcattgttttgatag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G05390.1 (Glycine max), 5'ss of exon 5
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactctttctttctttctcatattatccctatactatttgcaccaattttttgtatttcaaatatatattattatctttgtgtag------------
  || | |||||||||||||| || ||||| |||||||||||  | ||  | ||  |||||||||||||||| || ||||||||||| ||  |||||||||||  | | || |  | ||   |  ||      ||||| |   ||   ||| | |  ||   | || || |   ||  |  |    |              
GGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTCTCATGCAGgtaa-atttttaccattttaaactcatccaaattatacaagaggccttaatgtataataaaaccaaaatttgccatggttctctcttcatcagtagttaaa

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA14G16860.1 (Glycine max), 5'ss of exon 2
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgt--attactctttctttctttctcatattatccctatactatttgcaccaattttttgtatttcaaatatatattattatctttgtgtag
  || | || ||||||||||| || || || ||||||| |||| | ||||||||| ||||||||||||| || || |||||| | || ||  | ||||||||  |||| |     ||||    ||||||  |   || || |   |||  || |  |    |||  |||||    ||              
GGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGATTTTATCCCTCGCACACTGTGTGAAGACAACGATCCAATTGATATTTTGGTTCTTATGCAGgtaaattagtaccgttttcaaattcatatattt--tacacaagaagcattaaatact---gtttataatattctatag-------------

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ33488 (Selaginella moellendorffii), 5'ss of exon 4
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactctttctttctttctcatattatccctatactatttgcaccaattttttgtatttcaaatatatattattatctttgtgtag
  | || || || || || || || || ||||||||||| |||||||| |||||  |||||||||||||||||||  |||| ||  | || |||||||| ||     ||  ||| | ||| || | ||  ||   |  | | |     ||   | |           |  | | || | |         
AGTCCTTTATTCCTCGGTGGTTTATCCACACAACTATGGATTTGTTCCACGCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGATCATGCAAgtgagcttccatctctttttttcttttttccctggttttgtcttagtaaacgctctcggccaagtgaacttttcatgaacag-------

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|152033655|gb|BP561551.2|BP561551
EST:     GCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAG                         GAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
genomic: GCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactct ... ctttgtgtagGAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
EST: gi|86084748|gb|DR380507.1|DR380507
EST:     GCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAG                         GAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
genomic: GCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactct ... ctttgtgtagGAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
EST: gi|47828474|gb|CK118158.1|CK118158
EST:     GCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAG                         GAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
genomic: GCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactct ... ctttgtgtagGAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
EST: gi|86078040|gb|DR373797.1|DR373797
EST:     GCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAG                         GAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
genomic: GCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactct ... ctttgtgtagGAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
EST: gi|164137359|gb|ES036780.1|ES036780
EST:     GACCCCATTGATGTCTTAGTCATCATGCAG                         GAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
genomic: GACCCCATTGATGTCTTAGTCATCATGCAGgtattactct ... ctttgtgtagGAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
EST: gi|125092166|gb|EL149989.1|EL149989
EST:     TTGATGTCTTAGTCATCATGCAG                         GAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
genomic: TTGATGTCTTAGTCATCATGCAGgtattactct ... ctttgtgtagGAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATG
EST: gi|124711244|gb|EH802646.1|EH802646
EST:     CATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAG                         GAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCA
genomic: CATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactct ... ctttgtgtagGAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCATCATGCAGgtattactctttctttctttctcatattatccctatactatttgcaccaattttttgtatttcaaatatatattattatctttgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA