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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaaaatttgcagcataaagagtatcttcttagatgagtctctttattttactgatcagactattacttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT

Basic information

species Arabidopsis thaliana
transcript AT1G79550.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 4
gtatttaaaatttgcagcataaagagtatcttcttagatgagtctctttattttac-tgatc-----agactatt------acttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT
 ||  |   ||  |||    |   |   | || ||   ||||  | |||    ||  | |||     | | | ||      |||    | |       |||||||||| || ||||| |||||||| || |||||||| || || ||||||||||||||||| || || ||||| |||||||||||||| || |||||| 
ttaaattgtatccgcaatgaattcaagctgtttttccttgagattttttgaaatatgtaatccttttaaaattttgtagtaactgtcctcaccaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCTGCCATTGTTGGTGGATCCAAGGTGTCAACAAAGATTGGGGTGATTGAGA

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 4
----gtatttaaaatttgcagcataa-----agagtatcttcttagatgagtctctttattttactgatcagactatt---acttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT
     | |||  ||| | ||   ||      | | ||| ||     |||  | | |     | |   ||   ||| |    |  || || ||| | |||||||||||| || ||||| |||||||| |||||||| |||||||| ||||| ||||| ||||| || || ||||| ||||| |||||||| || |||||||
taatatttttttaatcttcaatgtattctccaaaatatgttgcataatgcttatttcagaataaaaaatacaactgtactgatatggttaattatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCGGCCATCGTTGGTGGATCCAAGGTCTCAACTAAGATTGGGGTGATTGAGT

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G382914_T03 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------gtatttaaaatttgcagcataaagagta--tcttcttag---atgagtctctttatttt----actgatcagact--attacttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT
                                                                        | ||  |  |||  |     |  | ||  |||| |||     | ||| | || ||       |  |   ||| |  |  | |   |||||| | |||||||||||| |||||||| |||||||| || ||||| |||||||| ||||| ||||||||||| || || ||||| ||||| |||||||||||||||||||
gtaataaaatgtcacccatgctcatgatcttttaagtatatttaggtactgttcagtaggatggggtaaatattttctacctttcaaaagagaccaataaatctttttaacatttcagttttttcataaataaaaaaggaaagatttgacaaatgactttattatctcagGAACTTGACTACCTTGTTGGAGCTGTTGCCAACCCAAAGAAGCCATTTGCCGCCATTGTTGGTGGATCCAAGGTCTCAACTAAGATTGGTGTCATTGAGT

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G17600.1 (Glycine max), 3'ss of exon 4
gtatttaaaatttgcagcataaagagtatcttc-ttagatgagtctc---------------tttattttactgatcagactattacttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT
|| | ||  |  |      |||    || |||| ||| |||| | |                |||||     | ||    || ||| |||||| ||||| |||||||||||| || || || ||||||||| ||||||||||||  || |||||||| || ||||| || |||||||| ||  | |||||||| || |||||||
gtttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATCGTTGGTGGGTCAAAGGTGTCTTCCAAGATTGGAGTTATTGAGT

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 4
--------gtatttaaaatttgcagcataaagagtatcttcttagatgagtctctttattttactgatcagactattacttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT
        | | | |   || ||  ||| |    ||| ||     || |     |||||     ||||    ||  |   | ||| ||||| |||||| |||||||| || || || |||||| ||||||||||||  || |||||||| ||||| || || || ||||| ||  | |||||||| || ||||| |
gtttgtaggaagtaattgttagcttcattatatatatattgggtaattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 3'ss of exon 3
----------gtatttaaaat--ttgcagcataaagagtatcttct---tagatgagtctctttattttactgatcagactattacttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT
          | | |  ||||  | ||  ||   ||  | |||| |   ||||  | |   || | ||||||   ||   ||  | ||||||| | || | |||||||||| |||||||| ||||||||| |||||||||||| ||| |||||||| |||||||| ||||| ||||| ||| | || ||||| || ||||| |
cttaatgtatgaagtccaaatagtggctacacctaggttttcttttgtttagaatacttctttgagtttacttgaca---taacatttgttttctggttttagGAACTTGACTACCTTGTTGGAGCTGTGTCAAACCCCAAGAGGCCATTTGCTGCAATTGTTGGTGGCTCGAAGGTGTCATCGAAAATTGGAGTGATTGAAT

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|47831797|gb|CK121481.1|CK121481
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
EST: gi|47829445|gb|CK119129.1|CK119129
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
EST: gi|125004082|gb|EL076351.1|EL076351
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGC
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGC
EST: gi|164096547|gb|ES117934.1|ES117934
EST:     CCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
genomic: CCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
EST: gi|116434727|gb|EG477319.1|EG477319
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
EST: gi|116403251|gb|EG445843.1|EG445843
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
EST: gi|47831355|gb|CK121039.1|CK121039
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
EST: gi|47828442|gb|CK118126.1|CK118126
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
EST: gi|125191228|gb|EL206182.1|EL206182
EST:     GAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAG
genomic: GAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAG
EST: gi|116434726|gb|EG477318.1|EG477318
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
EST: gi|124902518|gb|EH976598.1|EH976598
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGT
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGT
EST: gi|47828962|gb|CK118646.1|CK118646
EST:     GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT
genomic: GAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaa ... attgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagatgagtctctttattttactgatcagactattacttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT
                    tactgat  putative branch site (score: 2)
                                         ttttatt  putative PPT
                                tattacttgttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttaaaatttgcagcataaagagtatcttcttagatgagtctctttattttactgatcagactattacttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG