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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttttcttcagtgttcctccttattcatctctattgatctctcaacaagtattagtttttccctttaactctaatatcttacag

Basic information

species Arabidopsis thaliana
transcript AT1G01050.1
intron # 7
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA07G05390.1 (Glycine max), 5'ss of exon 7
ATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctt-------tttcttcagt--------------gttcctccttattcatctc-tattgatctctcaacaagtattagtttttccctttaactct-aatatctta--cag
|||||||| |||| ||||||||| |||||||||||||| |||||| ||||||||||||| ||||| || |||   || || || || ||||| ||||| |||||||||       ||  | || |              ||| ||      | |  || || |  | ||  || ||  || |    ||   |  |  ||| ||||| ||   |||
ATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGATTCGCCGCTTCTTTGAAGATTgtatccttaaaaatcttattccaataacttgatacatgagtttctttaagattacttcatagtattttcataaaaaaaataaaaaattgagtgcatttcttaatatattgatcag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA19G45050.1 (Glycine max), 5'ss of exon 6
ATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttttcttcagtgttcctccttattcatctctattgatc-----tctcaacaagtattagtttttccctttaactctaatatcttacag-
||||||||||||| |||||| || |||||||||||||  ||||||   | ||||||| | ||||| ||  |||| || ||||| || ||||| ||||||||||||||| ||||| ||| ||     |||   || | || |  |      | | | | ||   |||   |     || ||  ||||   ||  |  
ATTGCAGTGTGTGCTGATGACCCAGAATATAAGCACTTTACTGACTATAGAGAACTTGCACCTCATCGCATCTCCGAGATCCGACGCTTCTTTGAAGACTgtatccttcttctt-agttttatatattaaatatatttactacttcattatttgagctagagctagcgctgtttcttgaca-taattcattctaag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA03G42280.1 (Glycine max), 5'ss of exon 7
ATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttttcttcagtgttcctccttattcatctctattgatctctcaacaagtattagtttttccctttaactctaatatcttacag
||||||||||||| |||||| || |||||||| ||||  || |||   | ||||||| | ||||| ||  ||||||| ||||| || ||||| |||||||||||||||  ||||      |  |   |||| |  | || |  |   | | |   | ||  ||       || | |||||          
ATTGCAGTGTGTGCTGATGACCCAGAATATAAACACTTTACAGACTATAGAGAACTTGCACCTCATCGCATCTCTGAGATCCGACGCTTCTTTGAAGACTgtatccttcgtcttag----ttttatatattaaatt-tactagttcattagcgc-tgtttcttgacataattcattctaag---------

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA14G16860.1 (Glycine max), 5'ss of exon 5
--------------------ATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttttcttcagtgttcctccttattcatctctattgatctctcaacaagtattagtttttccctttaactctaatatcttacag
                    ||||||||||||| |||||| || |||||||||||||  ||   |   | ||||||| | ||||| ||  ||||  | ||  | || ||||| ||||||   |  |                                                                                    
GAGAGAAAGATGATAAAATCATTGCAgtgtgtgctgatgacccagaatataagcactttaccagctatagagaacttgcacctcatcgcatctccaagatttgacgcttctttgaagacgcgacac------------------------------------------------------------------------------------

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 6
ATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatccttttt---cttcagtgttcctccttattcatctctattgatctc-tcaacaagtattagtttttccctttaactctaatatcttacag
||||| || || | ||| ||||| ||||||   |||||||||||||||||||| ||||| |||||  | ||  |||| ||||| || ||||| |||||||||||||||||     ||||||    |   | ||  |  | | || |     | |||||     |  ||||  ||| |   | || |  | |   
ATTGCTGTATGCGCTGACGATCCAGAATATCGACACTACACTGACATCAAAGAGCTTCCACCTCATAGACTAGCTGAGATCCGGCGATTCTTTGAAGACTgtatccttttcatctttcagttcaacctttcatgaaaatttgttaaggggatgaacaatagacaaattttttcttga---caaacaattcag--

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|86084748|gb|DR380507.1|DR380507
EST:     AGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACT                         ACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG
genomic: AGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttt ... tatcttacagACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG
EST: gi|164058901|gb|ES078505.1|ES078505
EST:     CTCTCTGAAATCCGTCGTTTCTTCGAAGACT                         ACAAGAGAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCC
genomic: CTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttt ... tatcttacagACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCC
EST: gi|47828474|gb|CK118158.1|CK118158
EST:     AGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACT                         ACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG
genomic: AGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttt ... tatcttacagACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG
EST: gi|86078040|gb|DR373797.1|DR373797
EST:     AGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACT                         ACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG
genomic: AGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttt ... tatcttacagACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG
EST: gi|125207259|gb|EL222213.1|EL222213
EST:     AGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACT                         ACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATT
genomic: AGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttt ... tatcttacagACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATT
EST: gi|125292094|gb|EL306179.1|EL306179
EST:     CCGTCGTTTCTTCGAAGACT                         ACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG
genomic: CCGTCGTTTCTTCGAAGACTgtatcctttt ... tatcttacagACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG
EST: gi|124704845|gb|EH796247.1|EH796247
EST:     CCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACT                         ACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG
genomic: CCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttt ... tatcttacagACAAGAAAAACGAGAACAAGGAAGTTGCAGTGAATGATTTTCTGCCATCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAATCCGTCGTTTCTTCGAAGACTgtatcctttttcttcagtgttcctccttattcatctctattgatctctcaacaagtattagtttttccctttaactctaatatcttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA