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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtttcctaatattttgagagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG

Basic information

species Arabidopsis thaliana
transcript AT1G51690.3
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
--------------------gtcagt--ttcctaatattttgagagagat--acatttggcga----gttggtgctttgctgaatggtat-tccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
                     | | |  | | || |  ||||||    ||  ||| |   | |      ||| |     |||| |  | | |  |||  ||   |  | ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| |||  ||| ||  |||| ||||||| ||| || |||||||||||
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctga--aactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
gtca-gtttcctaat----attttgagagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
|| | ||||| |||     ||  ||  | | ||     ||   ||      |       ||||   |     || |  || ||| |||||||||||| |||||||||||||||| || |||||||| || || |||||| | |||||  ||||  | || |  || || || ||||||||
gtgaagtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatt-tcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 10
---------------------gtcagt--ttcctaatattttgagagagatacatttggcgagttggtgcttt-gctgaa-tggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
                     || | |  ||  | ||  |||| |    || |||    |   ||  ||||   ||  || || |       ||      |  | ||| | |||||||||||||||||||| || || |||||||| || |||||||||  ||||||  |||| ||  ||| ||| || ||||| |||||
gtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatccatgtgttacttggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 10
gtcagtttcctaat--attttgagagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
||  | |   | ||  ||| |||      | |   ||    ||  | | | |      |  |  |   | | ||  | |   ||||| ||||||||||||||||||||||| ||||| || |||||||| |||||| |||||||  |||| ||||| | ||| || |||||||||||
gtttgataagtgatgaattatgaatttctttctactgttttgtctgagttataactggttatgctttttgtttgaacgtgc-cagCTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
gtcagtttcctaatattttga-gagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcatttt-----cagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
|| || |||| | | ||| || |||  ||  ||||       || ||||||    | |  || |  ||   |  |  ||||     ||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||| |||||||  |||| ||||| |   | || || ||||||||
gttagattccca-tgtttggatgagcaatgaattt------ctgctgctttatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
gtcagtttcctaatattttgagagagatacatt-tggcgagttggtgctttgctgaatggtattccctttgtggtcatttt-----cagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
|| || |||| |   || |   ||  ||      ||      || ||||||    | |  || |  ||   |  |  ||||     ||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||| |||||||  |||| ||||| |   | || |||||||||||
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
gtcagtttcctaatattttga-gagagatacatttgg-----cgagttggtgctttgctgaatggta------ttccctttgtggtcat---tttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
|| || |||||  | ||| ||  || |||  |||  |     |    |  |||||||  || |  ||      |    ||| || |      |  ||||| || ||||||||||||||||| || |||||||| |||||||| |||||| |||||||  |||| |||||   ||| || |||||||||||
gttagattcctg-tgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataactggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
gtcagtttcctaatattttgagagagatacatttggcgagttg---gtgctttgctgaatggtatt----ccctttgtgg------tcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
|| || || ||    |    | ||   ||||     | | ||     |   |  ||| ||| || |    |||| |||        |  | | ||| | ||||||||||||||||||||||| |||||||| || || || |||||| | |||||  ||||  |||| | ||||||||||||||||||
gtgagcttgctttcctcagaaaagtcttacacagaacaacttctacattactctctgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
-------------------gtcagtttcctaatattttgagagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
                   |   |      |      | ||   | ||  ||||    ||| ||  |   || |  |  ||| |  ||  | |  ||| |||||||||||| | ||||| || ||||| ||||| || ||||| ||||||||| | |||||| ||||| |||| | ||| || ||||| |||||
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattac--ttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG

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|125146872|gb|EL181375.1|EL181375
EST:     ACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG                         CTCTGTGATTTATATAGAAAATGATTCCATCTTTGACAAGTTCGA
genomic: ACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAGgtcagtttcc ... tcattttcagCTCTGTGATTTATAT-GAAAATGATTCCATCTTTGACAAGTTCGA
EST: gi|86070771|gb|DR366528.1|DR366528
EST:     ACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG                         CTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGT
genomic: ACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAGgtcagtttcc ... tcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGT
EST: gi|86070769|gb|DR366526.1|DR366526
EST:     ACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG                         CTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGT
genomic: ACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAGgtcagtttcc ... tcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGT
EST: gi|86070768|gb|DR366525.1|DR366525
EST:     ACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG                         CTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGT
genomic: ACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAGgtcagtttcc ... tcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatttggcgagttggtgctttgctgaatggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
                                             tcattttc  CT-rich tract
                                             tcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtttcctaatattttgagagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT