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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacggcttttgttcttttgtgtcttttgttatattgttcaagtttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA

Basic information

species Arabidopsis thaliana
transcript AT1G52360.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
gtatacggcttttgttcttttgtgtcttttgttatattgttcaagtttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA
                                |||  |   | |  |||     | ||| ||   |   ||||    ||||  |  | || ||  | ||  |||  |  | ||  ||||||| || || || ||| | ||||| |||||||||||||| || || || ||||||||||  |||||||| ||||| || ||||| ||||||||||| ||
-------------------------------gtatgctcacccaactttc----tgtgtgcttcttgtccgtga--ggtttact--tcatgctaatattcaata--acaattt--cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
gtatacggcttttgttcttttgtgtcttttgttatattgttcaagtttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA
                                  ||| |  |||    || |      | ||   | ||| |  ||    | |   | || ||| | ||  |||  |  | ||  ||||||| || || || ||| | ||||| |||||||||||||| || || || || |||||||  |||||||| ||||| || ||||| ||||||||||| ||
---------------------------------gtat-gcacaaccaattttc-----tgcttgcttctcttcccttaggtttacatcatgctgatattccata--acaattt--cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 5
gtatacgg-cttttgttcttttgtgtcttttgttatattgttcaagtttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatat----tatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA
||    || | ||| ||  | | | || ||  |  |||   ||    | ||| |  || | ||   |     | |||   ||  ||  | |  ||   | | ||||     |||| ||||||||| |||||||||||||| | ||||| || || |||||||| ||||| || |||||||||| ||| |||||||| ||||||||||| ||||| || |||||
gtgggtggacgttttttagtctatttcattgatcgtata--tctgcctcttgattcatttgcttgatgtcattttctttctttatatatttcatggggtctcatatgcagcatgattttgcagTTAGGTCAGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCAGGGGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTTAA

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 5
----gtatacggcttttgttcttttgtgtcttttgt-tatattgttcaagtttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA
    ||  |||  || |  ||| ||   |   |||| ||| |   |   | ||   |||  || | | | |  |  | | | || | ||  | ||    ||  | || |  |||| ||||||||| |||||||||||||| | ||||| || || |||||||| ||||| || |||||||||| ||| |||||||| ||||||||||| ||||| || |||||
gtgggtgaacgttttatagtctatttcattggttgtgtatctgccttttgattcatttgcttgaagtcattttttttcttt-gtatatt--tcatgggtctcatatacagcatgattttgcagTTAGGTCAGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCAGGGGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTTAA

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 5
---------------------gtatacggcttttgttcttttg--tgtcttttgttatatt--gttcaag------tttttgttgtatgtactaagtactcgtgtctagtttgttact-----tattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA
                      | |    | ||||||  | |   |  || ||| |  |||   || |||      ||||  |||||| |   | |   || |   |||    | |||     | || | |   | || |  |||| ||||||||| | || ||||||||| | ||||| || || |||||||| || ||||| |||||||||| |||||||||||| ||||||||||| ||||| || || ||
gtacttgaagacgtgaaccttttttggtccatttgtttgtatatctacctcttgatgcatttgcttgaagacacacttttctttgtatatttcatgatttcttacttagaagatcactggagctcttatacaagtatacaacatgattttgcagTTAGATCGGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCTGGAGCAGATGATATGTTTATCCGTGTATATAATTACAACACAATGGATAAAGTCAA

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 5
-----------------------gtatacggcttttgttcttttgtgtcttttgttatattg--ttcaag----tttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA
                        |   |   || | |   | | | ||| ||| |  |||   || |||    ||||  |||||| |   | |   || |   |||      ||| |    ||| || || |  |||| ||||||||| | || ||||||||| | ||||| || || |||||||| || ||||| |||||||||| ||| |||||||| ||||||||||| ||||| || || ||
gtacatgaagtcatgaaccttttctggtccatttgtttgtctatatatctcttgatgcatttgcttgaagacacttttctttgtatatttcatgatttcttacttagaagaccactgaa---gctcttatacaacatgattttgcagTTAGATCGGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCTGGAGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTCAA

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 5
--------gtatacggcttttgttcttttgtgtcttttgttatattgttcaagttt-ttgttgtatgtactaagtactcgtgtctagtttgttac-ttattctgcttttttatatta---tgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA
         | |||    | ||||    | ||   | | |  | |  || || |   ||| |  || |       | |  | |||  || || |  |||||     |||  || |||   |  | |||||||| ||||||| |||||| ||||||| |||||||||||||| || |||||||||||||||| ||| |||||||||||||| ||||| ||||| ||||||||
gtatgtacatgtactttatctgtttccatatgctctatttggtgtgattgaattcccttgatccatttttactcaatttctctcttattggtaaggttattacatgtttcaattttacattatcattgcagTTAGGTCAGCGAAGTTTATAGCACGCAAGCAATGGGTTGTTGCTGGAGCTGATGATATGTTTATTCGTGTATACAATTATAACACAATGGATAAGGTTAA

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 5
gtatacggcttttgttcttttgtgtcttttgttatattgttcaagtttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA
                                ||| || ||||    |   || ||  | ||     |  || |     | || | ||  | | | |   ||    ||    ||||||| |||||||| || ||| |||| || ||||| ||||| || || ||||||||||| |||| ||||||||||||||||||||| || ||||| ||||||| 
-------------------------------gtatgttattcatacatgacttttaatttct-----ccagtcttggcatggtaatttcatttacatc--taaggcatctgcttgcagTCCGGTCAGCAAAATTTATAGCTCGTAAGCAGTGGGTGGTTGCTGGAGCTGATGACATGTTTATCCGTGTATACAATTACAATACTATGGATAAGGTTAC

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|164047583|gb|EL981896.1|EL981896
EST:     CAAAATCCTTTGAGGTGACTGAATTACCAG                         TTCGGTCAGCCAAGTTTATAGCACGAAAGCAATGGGTTGTCGCAGGAGCTG
genomic: CAAAATCCTTTGAGGTGACTGAATTACCAGgtatacggct ... gactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTG
EST: gi|124919533|gb|EH993287.1|EH993287
EST:     ACGCAGGTGATGGCAAAATCCTTTGAGGTGACTGAATTACCAG                         TTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTG
genomic: ACGCAGGTGATGGCAAAATCCTTTGAGGTGACTGAATTACCAGgtatacggct ... gactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA
                       ttattctgctttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacggcttttgttcttttgtgtcttttgttatattgttcaagtttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA