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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGATTTTGTGATGGACGATTATACAAGAGAGATGATGGATCTCAAGACTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccctctacttctctaccatacattattcgcagaaatttttgagtggaaatgagaacagagaagtgattcgtttgaaatacatacattactctttttctagggttcctgctattcagatcgaaatgctcgatattgttaattgcctatgcatctggaatcttgctgatagtttatttgtgtttgtag

Basic information

species Arabidopsis thaliana
transcript AT3G55000.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55000.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 1
ATTTGATTTTGTGATGGACGATTATACAAGAGAGATGATGGATCTCAAGACTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccctctacttctctaccatacattattcgcagaaatttttgagtggaaatgagaacagagaagtgattcgtttgaaatacatacattactctttttctagggttcctgctattcagatcgaaatgctcgatattgttaattgcctatgcatctggaatcttgctgatagtttatttgtgtttgtag
    ||    | ||||||||| ||  |  | ||||||||||| ||||||||  | ||||| || ||||| |||||||| || |||||||| |||||| ||||| |   || | |   |||| |    | |   | ||  |  ||| || |         || | ||      | | |   | |   ||   ||  |       |  |  || ||                                                                               
GGCGGAAGGGGGGATGGACGACTACGCGCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATCAGGgtacaaatcccccatccctcttcttctcttctcttgctcacctttctgcg---------gatctgactcactacttgc--ggatctca---atctccggcccgccggaattgct-------------------------------------------------------------------------------

upper sequence: AT3G55000.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G099980_T03 (Zea mays), 5'ss of exon 1
ATTTGATTTTGTGATGGACGATTATACAAGAGAGATGATGGATCTCAAGACTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccctctacttctctaccatacattattcgcagaaatttttgagtggaaatgagaacagagaagtgattcgtttgaaatacatacattactctttttctagggttcctgctattcagatcgaaatgctcgatattgttaattgcctatgcatctggaatcttgctgatagtttatttgtgtttgtag
|||| |    | ||||||||| ||  |  | ||||||||||| ||||||||  | ||||| || ||||| |||||||| || |||||||| |||||  ||||   | |   | |||| | | |  | | || | |||    ||   |   | ||   |    |  |     |  ||       ||  |  | || |      || ||  |                                                                                   
ATTTCAGGCCGGGATGGACGACTACGCCCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtacttccaacttattttc--ttcgtt-tccgcc---atcccttcattgatccggtgcctcacccacgcctcac---ggatcta-gcttttcatcccctccagttt-----------------------------------------------------------------------------------

upper sequence: AT3G55000.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA10G44070.2 (Glycine max), 5'ss of exon 1
ATTTGATTTTGTGATGGACGATTATACAAGAGAGATGATGGATCTCAAGACTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccctctacttctctaccatacattattcgcagaaatttttgagtggaaatgagaacagagaagtgattcgtttgaaatacatacattactctttttctagggttcctgctattcagatcgaaatgctcgatattgttaattgcctatgcatctggaatcttgctgatagtttatttgtgtttgtag
     |    |  ||||||||||| || || || |||||||| || |||||  |||||||||| || || ||||||||||| |||||||| | |||||| ||| || | | |        ||   |    | ||| ||   |||  | |  | | ||     ||      |  |    ||    |   ||   | |  ||||  |   ||  | |                                                                              
GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacacc------ttagggtttcctcttccca---attcctcaccgtagatccattcaa-----ttctcaacttagggt---tattcttccgttttctttttgtctcag------------------------------------------------------------------------------

upper sequence: AT3G55000.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
ATTTGATTTTGTGATGGACGATTATACAAGAGAGATGATGGATCTCAAGACTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccctctacttctctaccatacattattcgcagaaatttttgagtggaaatgagaacagagaagtgattcgtttgaaatac---atacattactctttttctagggttcctgctattcagatcgaaatgctcgatattgttaattgcctatgcatctggaatcttgctgatagtttatttgtgtttgtag
|  || |   | ||||||||| || ||  ||||||||||||| ||||||||  | |||||||||||||||||||||||||| |||||||| |||||||||||  |||  |  | | | | |||| |   ||     ||     ||  |  |          | |     | | || |||| ||||     ||||   |  |                                                                                               
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgt--attttcctttcctttttacc-tctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaaattttcaatacgagaaacga---------------------------------------------------------------------------------------------

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|164009212|gb|ES080511.1|ES080511
EST:     GTGTCCTCGCTAAGATCCGG                         GCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAGAGGATGGAGTG
genomic: GTGTCCTCGCTAAGATCCGGgtaaattccc ... gtgtttgtagGCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAGAGGATAGAGTG
EST: gi|124882698|gb|EH961600.1|EH961600
EST:     CTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGG                         GCTGAGCTCCGTGCAAGTGTGTTTG
genomic: CTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccc ... gtgtttgtagGCTGAGCTCCGTGCAAGTGTGTTTG
EST: gi|164160175|gb|ES161391.1|ES161391
EST:     GTGTCCTCGCTAAGATCCGG                         GCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTTGAAGAAGAGGATGGAGT
genomic: GTGTCCTCGCTAAGATCCGGgtaaattccc ... gtgtttgtagGCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATT-GAAGAAGAGGATAGAGT
EST: gi|19877291|gb|AU238122.1|AU238122
EST:     CTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGG                         GCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAGAGGATAGAGTG
genomic: CTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccc ... gtgtttgtagGCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAGAGGATAGAGTG
EST: gi|164219019|gb|ES110081.1|ES110081
EST:     GTGTCCTCGCTAAGATCCGG                         GCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAGAGGATGGAGTG
genomic: GTGTCCTCGCTAAGATCCGGgtaaattccc ... gtgtttgtagGCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAGAGGATAGAGTG
EST: gi|164010189|gb|ES128031.1|ES128031
EST:     GTGTCCTCGCTAAAGATCCGG                         GCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAGAGGATGGAGT
genomic: GTGTCCTCGCT-AAGATCCGGgtaaattccc ... gtgtttgtagGCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAGAGGATAGAGT
EST: gi|164194931|gb|ES107711.1|ES107711
EST:     GTGTCCTCGCTAAGATCCGG                         GCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAAGAGGATGGAGT
genomic: GTGTCCTCGCTAAGATCCGGgtaaattccc ... gtgtttgtagGCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAA-GAGGATAGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGATTTTGTGATGGACGATTATACAAGAGAGATGATGGATCTCAAGACTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccctctacttctctaccatacattattcgcagaaatttttgagtggaaatgagaacagagaagtgattcgtttgaaatacatacattactctttttctagggttcctgctattcagatcgaaatgctcgatattgttaattgcctatgcatctggaatcttgctgatagtttatttgtgtttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA