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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA

Basic information

species Arabidopsis thaliana
transcript AT1G54270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G00950.1 (Glycine max), 3'ss of exon 4
------------gtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
               |   || ||  |  |  | || |          |   ||  | ||  |     ||||   |||||    |||  | ||   ||||||||||||||||| || ||||| || ||| | || ||||||||||||||||||||||| |||||||| || |||||  | ||||| |||||||| |||||||
agttataagaagaaatacaatatttattta--tctggacaggatacaagaatttccccctcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G20300.3 (Glycine max), 3'ss of exon 4
-------gtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattg---acttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
        |     |  |||   |||   |   | |      |||     | | || | ||     ||||   |||||    |||  | ||   ||||||||||||||||| |||||||| || ||| | || ||||||||||||||||||||||| |||||||| || |||||  | || || ||||| || |||||||
ggacaggatacaagaatttcccaaaacaatttctgtgagaaatgtaacagtttatgttcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G42360.1 (Glycine max), 3'ss of exon 4
--------------gtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
               | | ||   || || |||  |   || |   ||   ||      |||  | |||||    |||| | || ||      |||| | ||||||||||||||| ||||||||||| ||     | ||||||||||||||||||||||| |||||||| || || || |||||||| || || || |||||||
tttattttgttgaaatatttttctttatttaaaactcacatatgtgctagatgaagtcatcttgtgttgac---attttatatttttcgtgcatgaaat-gcagATCTATGACATCTTCCAGCTTCTGCCGGGTCAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCTGAGGCCTTGGAGATTACGAGGAAGTTCATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G03020.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------------------gtttgttatcttcttcaaagtttgaat-ctaccctctgtggt--tatctctgatattgacttggt--tttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
                                                                                          |  |   || || |||   ||  | |||      ||  |  | | |  ||||   |  |     ||| | || ||      |||| | ||||||||||||||| |||||||| || |||    | ||||||||||||||||||||||| |||||||| || || ||  ||||||| ||||| || |||||||
gtttgatggttttccatgttttgtctaaaactttgaattgtttttcttttccttgagtgtcatctaaacattctttcatgcatgttgaaataattctttatttaaaacctgtgtgctagatgaagtcatcttgtgttagatagatagctaacagtttatatttttcgtgcatgaaat-gcagATCTATGACATCTTCCAGCTACTGCCAGGTCAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCTGAGGCCCTGGAGATTACAAGGAAGTTCATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 4
--gtttgttatcttcttcaaag---tttgaatctacc--ctctgtggttatctctgatat---tgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
  ||||  |||    | ||||    |   | | || |  |  | |||||   |  ||| |   |  ||   || ||  ||  | | |    |  || ||||||||||| || || ||||| || ||||| ||||| |||||||| || |||||||| ||||||||||| |||||  |||| |||||||| || || ||||
atgtttaatatgaaatacaaatacctacaactttatctgccttttggttcattaagatgtatctttctgaattctgactttctcttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G05580.1 (Glycine max), 3'ss of exon 4
---gtttgttatcttcttcaaa---gtttgaatctacc--ctctgtggtt-atctctgatattgacttgg-ttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
   ||||  |||    | ||||    ||  | | || |  |  | ||||| ||      |||     ||  |||||  ||  ||| |    |  || ||||||||||| || || ||||| || ||||| ||||| |||||||| || |||||||| ||||||||||| |||||  |||| |||||||| || || ||||
catgtttaatatgaaatacaaataccttcaactttatctgccttttggttcataaagtgtatccttctgaattttgactttgttttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G18760.3 (Glycine max), 3'ss of exon 4
gtttgttatcttcttcaaagtttgaat----ctaccctctgtggtta-tctctgatattgacttggttttgtgttgttttctggtgaatttg-------cagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
  |||   | | ||  | | |||   |     |  ||| | || ||| | ||  | |   | ||  |  |  ||  |||     | | ||         ||||||||||| ||||||||| | || ||| | |||||||| || ||||| |||||||| ||||||||||| || ||  | ||||||||||| || |||||||
--ttgaattatcctggagattttatttattattggcctatttgtttagtttcccaaacaaatttattcataagtgctttaaccttaatttcatttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCTGAGGCACTTGAGATCACAAGGAAGTTCATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 4
gtttgttatcttcttcaaagtttgaatctac---cctctgtggtta-tctctgatattgacttggttttgtgttgttttctggtgaatttg-------cagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
 ||||   | | ||  | | |||   | ||    ||| | || ||| | ||  | |   | ||  |  |  ||  |||     | | ||         ||||||||||| ||||||||| | || ||| | |||||||| || ||||| |||||||| ||||||||||| || ||  | ||||||||||| || |||||||
-tttgaattatcctggagattttatttatattggcctatttgtttagtgtcccaaacaaatttattcataagtgctttaaccttaatttcatttttatcagATCTATGATATATTCCAGTTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCCGAGGCACTTGAGATCACAAGGAAGTTCATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 4
--gttt---gttatcttcttcaaagt---ttgaatctaccct-ctgtggttatct-ctgatattgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
  ||||    | |  || ||| |||    |||  | |    | ||      ||    | || |  |  || | |    ||| |||       ||   |||||||| || ||||| ||||| || ||| | |||||||| || ||||| |||||||| ||||||||||| || ||  | |||||||| || || || ||||
aagtttcaattgacttttttccaagcctattgggtttgtagtgctaaaagaattgatttatgtataactgctctaaccttggttttattgttatcatcagATCTACGATATATTTCAGCTGCTTCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCCACAATGCCTCCTGAGGCCCTTGAGATCACCAGGAAGTTTATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G16570.1 (Glycine max), 3'ss of exon 4
gtttgttatcttcttcaaagttt---gaatctaccc--tctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttg-------cagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
   ||   |    || ||  |||   ||  |||     | ||| ||  |    || ||||| ||   | |   |  | |     ||  |||        |||||||| || ||||| ||||| || ||| | |||||||| || ||||| |||||||| ||||||||||| || ||  | |||||||| || || || ||||
-agtgcctttgaattgaattttttctgagcctattgggtttgtagtgctaaaaga-attgatttatgtataaatactctaaccttggctttattgttatcagATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTCTCTGCTACAATGCCTCCTGAGGCCCTTGAGATCACTAGGAAGTTTATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 3'ss of exon 3
gtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgtt-ttctggtgaatt-----------tgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
 ||  || | |   ||   |||  | || |    |       | || | |  || | | |  ||| | |   | ||||  | ||||           ||||||||||||| || ||||| || || ||| ||||  |||| ||||||||||||||||| |||||||| || || ||  | ||||| ||||| || || ||||
-ttatttttttaactctgtgttgtattccaagaacctcaacaacctttcaactttaat-gcgtttatatcactgttctaataaattagtttcttccttgcagATCTATGATATTTTCCAACTCCTGCCATCAAAAGTTCAAGTTGGAGTGTTCTCTGCCACAATGCCACCCGAGGCCCTTGAGATTACAAGGAAGTTTATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g01760.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------------------------------------------------gtttgttatcttcttcaaagttt----gaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttg-cagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
                                                                                               | |  ||   |  | |    |||      || | |    | ||  |  || || | ||    || |  |   ||  ||| |  ||    || |||||||||||||| |||||||| || ||| | ||  | |||||||||||||||||||| |||||||| || || ||  | ||||||||  |||| |||||||
gtctgttctattatatctctgtttctttactagttgtaatatttttgcatacttcatggtgaagaacattattttgctaattgttagaagttcatgctcattgcttattgctggatttttcaatatgtgcaagttttgactggctttgttgtttttctgataattcattaattttttttgctgctgtcagATCTATGACATTTTCCAGCTGCTGCCATCTAAAGTCCAGGTTGGAGTGTTCTCTGCCACAATGCCCCCTGAGGCCCTTGAGATCACTCGAAAGTTCATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0008g01000.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtttgt---tatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
           | |||     || || ||    ||||   |||  | |   ||   || ||| ||  ||| ||  | |  || |  |      | | || |||||||||||| || |||||| | || ||| |||||||||||||||| ||||||||||| || ||||| || || ||  | ||||||||||| ||||||||||
tttagctatgtggttgcaagcattttgttgtgggttt---tctgactttcatgtgcat-tctaatgctgatttcttgtcttgatactgaaatttcatttggcagATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTCTCTGCCACGATGCCACCTGAGGCCCTTGAGATCACAAGGAAATTCATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------gtttgt-tatcttcttcaaagtttgaatc-taccctctgtg-gttatctctgatattgacttggttttgtgttgtt--ttctggtgaatt-tgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
                                                              |||||| |  ||  ||||    |  |||  | | |  | |  | |||    |||||||        |   |   ||  ||| ||    || ||||||| |||||||| ||||||||||| ||||  ||| |||| || || ||||| ||||| |||||||| || |||||  | |||||||| || || |||||||
gtttgttcggagagtcctggaatggtagaagaaatttgtttttactcccaagaaaactaattgtttgtgtgactatttcagttctctaattatcctccttataagctatgagagatattgctcaacgctaacgaaattgattcgggcatcttctgcagATTTATGACATCTTCCAGCTTCTTCCACAGAAGCTTCAAGTGGGTGTGTTTTCTGCCACAATGCCACCCGAAGCGCTTGAGATCACCAGGAAGTTCATGA

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S136_29V6.4 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------gtttgttatcttcttcaaagtttgaatctaccctctgtggttatct--ctgatattgac-ttggttttg--tgttgtttt---------ctggtgaatt-tgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
                                          || || | | ||  |   |  | |  |   || | |  ||      | | | |  |  |||||  ||  | |||  ||           ||||| || ||||||| |||||||| ||||||||||| || |  ||| |||| ||||| ||||||||||| || ||||| || |||||| | || ||||| |||||||||||||
gtgtgtaaaggatttttcaagttcagtagaacttgcatgatcttattgt-tcctggatgataaggaagtgatctttatacttgctcgacagctgtgaaagttggtgctgcttattgacttaggtcagattgggtgagttgtgcagATTTATGACATTTTCCAGCTTCTTCCCCAGAAGCTTCAAGTTGGTGTGTTCTCTGCCACCATGCCACCCGAAGCTCTTGAAATCACCAGAAAATTCATGA

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|163980587|gb|EL987789.1|EL987789
EST:     CTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTC
genomic: CTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTC
EST: gi|125082358|gb|EL143274.1|EL143274
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGG-TTCAAGGATCAG                         ATCTATGACATATTCCAGCTTCTCCCACCAAAGATTC
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTC
EST: gi|125052397|gb|EL124200.1|EL124200
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATT
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATT
EST: gi|125305970|gb|EL320055.1|EL320055
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATTCCAGCTTCTCCCACCAAAGATT
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATT
EST: gi|125267915|gb|EL282000.1|EL282000
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATTCC
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCC
EST: gi|125287338|gb|EL301423.1|EL301423
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGG
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA
               tattgac  putative branch site (score: 2)
            tgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA