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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTCTTGAACTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtcacatacgaatttgctccacattcctcaaaaactaaactgtggtcataatcttttacttttgcttcgtatgcag

Basic information

species Arabidopsis thaliana
transcript AT4G12590.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G08370.1 (Glycine max), 5'ss of exon 4
-GTACTTCTTGAACTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtcacatacga----atttgctccacat---tcctcaaa--aactaaac-----tgtggtcataatcttttacttttgcttcgtatgcag-----------------------------------------------------
 ||||||| | ||  |||||||||||||||| ||||| ||||||||  | || || |||||||||||| | | ||||   |    ||||  |  | ||   |  |  ||  || | | |       ||   || || |||||||  |  |   ||||  |                                                     
GGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGGGTGAAGAAAATggttagttataacatgaaagctgatttcttttatatgtatatttgaattaattcatcaatttcatgaatatgat-ttttactacttttcattatgttgtcatttttccatgtaagctggaatttgttgtgatgtgtgctgttttttatgca

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv00s0187g00220.t01 (Vitis vinifera), 5'ss of exon 6
GTACTTCTTGAACTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtcacatacgaatttgctccacattcctcaaa-aactaaactgtggtcat--aatct---tttacttttgcttcgtatgcag------------------------------------------------------------------------------------------
||||||| | ||| |||| |||||||| || || || ||||||||||| ||||| |||||||||| |   |    ||  || |        || | | |   ||||      |    ||   || |   | |  |||  | || | | ||                                                                                           
GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATGgtttgtattggtttataaactctaagatgatgctttagccaactgtgtgataactatttgatttgtctctcttttctcctccttttcaaagtactctttagactttatatgtttttttaagaaaaaaataataaaccctctttcaattcatgagaggctgatatgatgttttgatacag

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 6
GTACTTCTTGAACTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtcacatacgaatttgctccacattcctcaaa-aactaaactgtggtcat--aatct---tttacttttgcttcgtatgcag------------------------------------------------------------------------------------------
||||||| | ||| |||| |||||||| || || || ||||||||||| ||||| |||||||||| |   |    ||  || |        || | |     ||||      |    ||   || |   | |  |||  | || | | ||                                                                                           
GTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATGgtttgtattggtttataaactctaagatgatgctttggccaactgtgtgataactatttgatttatctctcttttctcctccttttcaaagtactctttagactttatacgtttttttaagaaaaaaagattaaaccctctttcaattcatgagaggctgatatgatgttttgatacag

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|164192835|gb|EL981742.1|EL981742
EST:     CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAACGTA
genomic: CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAACGTA
EST: gi|164163679|gb|ES170176.1|ES170176
EST:     TTGTTTGGATTAAGAGGCTTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAA
genomic: TTGTTTGGATTAAGAGGC-TTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAA
EST: gi|164175339|gb|ES109634.1|ES109634
EST:     CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAA
genomic: CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAA
EST: gi|86079343|gb|DR375100.1|DR375100
EST:     CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAACGTATGATGCAAATGGGTGGGTTTGGATTTGATG
genomic: CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAACGTATGATGCAAATGGGTGGGTTTGGATTTGATG
EST: gi|124903664|gb|EH977744.1|EH977744
EST:     CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATG                         CCATTGATGACACACAACGTATGATGCAAA
genomic: CTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtc ... tcgtatgcagCCATTGATGACACACAACGTATGATGCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTCTTGAACTTGTTTGGATTAAGAGGCTTGTTCAGTCTCATTCTCGGAGATGAAAATGgttagctgtcacatacgaatttgctccacattcctcaaaaactaaactgtggtcataatcttttacttttgcttcgtatgcag

- - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG