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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtagcttaaaccttttgttttattgtaaaaaaaaaggaagcttcacctttaagcagaaagattagctgcatgagaccgatggtataaaatttgcaattcgagtttcttacgatgatcaaatgaattgctttggttcaaatggtggtgttaacgactctgattgcacattttattcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G12840.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 4
gtattgtagcttaaaccttttgttttattgtaaaaaaaaaggaagcttcacctttaagcagaaagattagctgcatgagaccgatggtataaaatttgcaattcgagtttcttacgatgatcaaatgaattgctttggttcaaatggtggtgttaacgactctgattgcacattttat-tcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG
                                                                  ||   | |    || | | ||   |||||    ||| |   |||   || ||| | || ||||||       ||| | |  |    | ||   || ||        |||||| ||||||||||||| |||| ||||||||||||||  |||| || |||||||| ||||||||||||| ||||||
----------------------------------------------------------------tgttctttactgatgaacaaagg---aaaatacagaatccccattttgcacaatg-taaattgaatt-------ttctatttttcccttaaat--ctttg------tgttttatgtcagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCCATCAACCGAAAGCAAACTGGAAG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 4
gtattgtagcttaaaccttttgttttattgtaaaaaaaaaggaagcttcacctttaagcagaaagattagctgcatgagaccgatggtataaaatttgcaattcgagtttcttacgatgatcaaatgaattgctttggttcaaatggtggtgttaacgactctgattgcacattttat-tcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG
                                                                  ||   |||    || | | ||   |||||    ||| |   |||   || |||  ||||| ||    | |  ||       |    ||||          |     |||||| ||||||||||||| | || ||||||||||||||  |||| || |||||||| ||||||||||||| ||||||
----------------------------------------------------------------tgttctttgctgatgaacaaagg---aaaatacagaatccccattttgcacaatg--caaattaaaatttctattt-------tccccttaa-------atctatgtgttttatgtcagGTTCGTGTTTCCGAGTATAACAATATCCGCAGTCAGCTTAATGCCATCAACCGAAAGCAAACTGGAAG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 4
gtattgtagcttaaaccttttgttttattgtaaaaaaaaaggaagcttcacctttaagcagaaagattagctgcatgagaccgatggtataaaatttgcaattcgagtttcttacgatgatcaaatgaattgctttggttcaaatggtggtgttaacgactctgattgcacattttat-tcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG
                                                                                || || ||  | ||| |        |     |  |  || | |  |    ||  ||| || |  |    || ||  |   |   | |     ||| ||  |||||||||||| |||| ||||||||||||||  |||| || ||||| || ||||||||||||| ||||||
------------------------------------------------------------------------------ccccaattgtgaataatatatcgaagaacaacatccc--tgcttattttgcatg--ttgattaattttcccgt-ttggccctttaaactttgtctttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACTGGAAG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 4
gtattgtagcttaaaccttttgttttattgtaaaaaaaaaggaagcttcacctttaagcagaaagattagctgcatgagaccgatggtataaaatttgcaattcgagtttcttacgatgatcaaatgaattgctttggttcaaatggtggtgttaacgactctgattgcacattttattcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG
                                                                  || | |   |||     ||    | ||       || |  | || ||  |     ||  |  |||  |||  | | | | |     ||||  ||| ||  | | |||      |||||||||||| |||| ||||||||||||||  |||| || ||||| || |||||||||||||  |||||
------------------------------------------------------------------tttgttttctgaa--taatctattgaagaacaacatccctgcttattttg-----catgttgattaattt--tcccatttggccctttaa--actttgtcttc-catgc----cagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACAGGAAG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 4
gtattgtagcttaaaccttttgttttattgtaaaaaaaaaggaagcttcacctttaagcagaaagattagctgcatgagaccgatggtataaaatttgcaattcgagtttcttacgatgatcaaatgaattgctttggttcaaatggtggtgttaacgactctgattgcacattttattcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG
                                                                           |||||   |    ||   ||    | ||  | ||  ||  | | |   | |   | |  |   ||   ||| | | || |  || ||  |||     || |  | |||||||  ||||||| ||||| ||| | ||  |||| |||||||| ||||| |||||||||||||||||
---------------------------------------------------------------------------tgagataaaaaaaattgtatacatatttttacttatttg-gtttac--agtttgtagactgtatttggatgtttgggt-attgaatc--attatttcttatgct-agGTTCGCATTGCTGAGTATAATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG

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|124725420|gb|EH816822.1|EH816822
EST:     TTGTGGACAATATTCAGTCTCAGGTTGCAAAAATTGAGGATGATCTCAAG                         GTTCGTGTTGCTGAATATAACAATA
genomic: TTGTGGACAATATTCAGTCTCAGGTTGCAAAAATTGAGGATGATCTCAAGgtattgtagc ... ttttattcagGTTCGTGTTGCTGAATATAACAATA
EST: gi|125221494|gb|EL235579.1|EL235579
EST:     TCTCAGGTTGCAAAAATTGAGGATGATCTCAAG                         GTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAGTGCCATT
genomic: TCTCAGGTTGCAAAAATTGAGGATGATCTCAAGgtattgtagc ... ttttattcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATT
EST: gi|125321551|gb|EL335636.1|EL335636
EST:     TTGTGGACAATATTCAGTCTCAGGTTGCAAAAATTGAGGATGATCTCAAG                         GTTCGTGTTGC
genomic: TTGTGGACAATATTCAGTCTCAGGTTGCAAAAATTGAGGATGATCTCAAGgtattgtagc ... ttttattcagGTTCGTGTTGC
EST: gi|125008326|gb|EL080595.1|EL080595
EST:     CAAAAATTGAGGATGATCTCAAG                         GTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATG
genomic: CAAAAATTGAGGATGATCTCAAGgtattgtagc ... ttttattcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgctttggttcaaatggtggtgttaacgactctgattgcacattttattcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG
                                             ttttattc  CT-rich tract
                                          acattttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtagcttaaaccttttgttttattgtaaaaaaaaaggaagcttcacctttaagcagaaagattagctgcatgagaccgatggtataaaatttgcaattcgagtttcttacgatgatcaaatgaattgctttggttcaaatggtggtgttaacgactctgattgcacattttattcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG