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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatgaaaaccaatgattttctctatcgtttacacataacttagtttttgaagtattcaagtttagttgcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG

Basic information

species Arabidopsis thaliana
transcript AT3G20050.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 10
gtgagaatgaaaaccaatgattttctctatcgtttacacataacttagtttttgaagtattcaagtttagttgcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG
                       |     | || |    ||   |   | | |    | || | | ||  | ||   | | |||   ||  | | |||  |  ||| |        | | |||||||||||| || ||||| ||||| |||||||| ||||||||||| || || ||  |||| |||||||||||||| || || || ||| ||
-----------------------tggtgtttgtgtgttaatctttgtatatgtatgatgttgatgattcctggctactgtctttaaatctgctttatgactgttcaatgg----aatatcatttcagTACTTCGTTGAGGCTGGAGCAATTGCTGTAAGGCGTGTGCGTAAGGAGGATTTGCGCCATGTTGCCAAGGCTACTGGTGCAACTATG

upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 10
--------------------gtgagaatgaaaaccaatgattttctct-atcgtttacacataact-tagtttttgaagtattcaagtttagttgcgtttat-gtttggttcaccgtaatggattctcatttctcttgtttt--------tatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG
                    |    ||   |  |  ||||| | || | | | | ||   | |||| | | | ||    |  |    | |      |    |  |   | | || || || || || | ||  | |||| |         |||||||||||||||| ||||| ||||||||||| || |||||||||||||| |||||  |||| ||||||||||| || || || || ||| ||
gtatgtttttcatcattcaagcagaaagtgattctgatgatgtccttttaacatctattgagaactcttgatcttcccatgctagtatctgtacaggcaactcatcctgatgactgtcattgaatcactttgttattgtgtcatggaacatatttcagTACTTTGTTGAGGCTGGAGCTATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATG

upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 10
gtgagaatgaaaaccaatgattttctctatcgtttacacataacttagtttttgaagtattcaagtttagttgcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG
                   |||    || |  | |   | |       ||| |  || | ||   |   | ||    | |   ||  ||||   | |  ||| |  | |      |||||    ||||||||||| ||||| || || ||||| || |||||||||||||| |||||  |||| ||||||||||| || || || || ||| ||
-------------------attaggactttgatctttccgtgctaatatttgtacagaaatctcatcctgatga--ctgtcactgaatcactccatt--attgtgctatgcaacattttt----cagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG

upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 10
gtgagaatgaaaaccaatgattttctctatcgtttacacataacttagtttttga-agtattcaagtttagttgcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG
           |     || || | | | |    ||  | |   ||| |  || |  | ||  ||  | |  ||  ||||||  |  ||            |||| | |  |  | || || |||||||||||||| ||||| || || |||||||| || |||||||| ||||| |||||||| |||||||||||||| || || || ||  ||
-----------attttgtggttctgtgtttaagatatgc-tcttttactgattaatggcataaaaagtca--tgaatttatgcattttt------------ttctgactatt--tattcttgtttcagTACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG

upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 10
gtgagaatgaaaaccaatgattttctctatcgtttacacataacttagtttttgaagtattcaagtttagttgcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG
                     |||     | || |  |    || | ||| ||  | |  | ||    |       | |||     || |  | | |   |||| | |  | |  || || |||||||||||||| ||||| || || |||||||| || |||||||| ||||| |||||||| |||||||||||||| || || || ||  ||
---------------------ttttgtggttgtgtttaagatacat-gttcttttactgatgaatgacataaaaagtcatg---aatttat-gcattttgttctgactatt-taattcttgtttcagTACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG

upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 10
gtgagaatgaaaaccaatgattttctctatcgtttacacataacttagtttttgaagtattcaagtttagttgcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG
                     |||    |||||      |||  |   | |   ||||      |||   |   ||  ||      ||  || |  |  ||| |   | | ||   | ||||| ||||||||||| ||||| || || |||||||| |||||||| || ||||| |||||||| |||||||||||||| || || || ||| ||
--------------------gttttgtaatcgtgccttgatatatccatatgcaaagtt-----gttccttcatgtggataacaaattt-cctttttctattttggctac-ctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG

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|164039847|gb|ES197242.1|ES197242
EST:     GGGCCAATGTAATTCTGACCAAAAAGGGGATTGACGACATGGCACTTAAA                         TACTTTGTAGAGGCAGGAGCTATTG
genomic: GGGCCAATGTAATTCTGACCACAAAGGGGATTGACGACATGGCACTTAAAgtgagaatga ... tttatttcagTACTTTGTAGAGGCAGGAGCTATTG
EST: gi|125112154|gb|EL163347.1|EL163347
EST:     GGGATTGACGACATGGCACTTAAA                         TAC-TTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAA
genomic: GGGATTGACGACATGGCACTTAAAgtgagaatga ... tttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG
                            ttctcatttctcttgt  CT-rich tract
                                      tcttgtttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaatgaaaaccaatgattttctctatcgtttacacataacttagtttttgaagtattcaagtttagttgcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG