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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgattctatctcaagtttctagatttcatctttatgattttttcttgacggtcttgctttgtgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAG

Basic information

species Arabidopsis thaliana
transcript AT2G04550.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G04550.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g20340.2 (Oryza sativa), 3'ss of exon 1
---------------gtatgtt----gattctatctcaagtttctagatttcatctttatgattttt-----tcttgacggtct--tgctttg---tgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAG
               | |||||     ||  |||   | ||||    |||   ||  |||||  |||     |||   | || |  |  |||    |  ||| || || || |  || || ||||||||||| || ||||||||||| |||||||||||
aacattcttcgctctgaatgttccaaaatattataataggttta-gcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG

upper sequence: AT2G04550.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g48840.1 (Oryza sativa), 3'ss of exon 2
-----------------------------gta-tgttgattctatctcaagtttctagatttcatctttatgattttttcttgacggtcttgctttgtgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAG
                             | | || | |        ||| |        ||  | ||| |    |||  ||     |||  | |||   ||| || ||||| | ||| |   ||||||||||||| |||||||||||||| ||||  ||
tagtaggaattatgctgtagtttgcttgggcagtgctaaactagaaacaaatggtggatgtttttgtttttatcatttgtttcgttatctgccattgc--agAACAGTGTGAAAGGGAGACATCACGTGTTCTTGTCCATTGCATGTCTGGAAAAAACAG

upper sequence: AT2G04550.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G174170_T02 (Zea mays), 3'ss of exon 2
---------------gtatgttgattctatctcaagtttctagatt--tcatctttatgatt--ttttcttgac--ggtcttgctttg---tgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAG
                  | ||   | || ||   | || ||  ||   ||| |   || |   || || | |     |  | |||||   |  ||| |||||||||| ||| || ||||| || || || |||||||||||||||||||||||
gtatgcacactattttcttcttctgtgtacctgttgattgtaagttaaccatttccctggtaagttctcctaattaaatgctcctttgaacttcagAGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG

upper sequence: AT2G04550.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G43410.1 (Glycine max), 3'ss of exon 2
--------------------------gtatgttgattctatctcaagtttctagatttcatcttt-atgattttttcttgacggtct-tgctttgtgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAG
                          | |      || | ||  |  | |||   | | | | || || ||    |     | || |      | || ||| |||||||||||||||||||  |||||||| || ||||||||||| || || |||||
tgattagtttcttcattttactattggcaatacttttttctccaatatgtcttcctattacccttgataatgaagtgagtgctgtgtgcttcctttgcagAGCAATGTGAGAAGGACAAGGAGCGTGTTCTGGTTCATTGCATGTCAGGAAAGAGTAG

upper sequence: AT2G04550.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0059g01650.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtatgttgattctatctcaagtttctagatttcatctttatgattt-------tttcttgacggtcttgctttgtgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAG
                     ||  | || |  | |||  |  || |  | || |  ||  | | |        | |  ||   || ||  ||| || ||| |||||||| ||||||||||| ||||||||||| ||||||||||| || |||| |||
tgtctggatgttcacaagttggttagctgttgatgtcttcatattgtgaactttaatttgcttactgggcatagtgtaatgcatgtgtttgtttttgcagAGCAATGTGAAAAGGACAAGGCTCGTGTTCTTGTACATTGCATGTCGGGAAAAAATAG

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|124803536|gb|EH891849.1|EH891849
EST:     TCTTGATAATGAAAAAGTTTTACAGTTTGATGATGCTATTAAGTTCTTAG                         ACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTG
genomic: TCTTGATAATGAAAAAGTTTTACAGTTTGATGATGCTATTAAGTTCTTAGgtatgttgat ... ctttgtgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTG
EST: gi|164115330|gb|ES068537.1|ES068537
EST:     TTACAGTTTGATGATGCTATTAAGTTCTTAG                         ACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGA
genomic: TTACAGTTTGATGATGCTATTAAGTTCTTAGgtatgttgat ... ctttgtgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGA
EST: gi|124711706|gb|EH803108.1|EH803108
EST:     TTTGATGATGCTATTAAGTTCTTAG                         ACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGA
genomic: TTTGATGATGCTATTAAGTTCTTAGgtatgttgat ... ctttgtgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGA
EST: gi|164066239|gb|ES155669.1|ES155669
EST:     ATGAAAAAGTTTTACAGTTTGATGATGCTATTTAAGTTCTTAG                         ACCAATGTGAGAAGGACAAGGCAC
genomic: ATGAAAAAGTTTTACAGTTTGATGATGCTA-TTAAGTTCTTAGgtatgttgat ... ctttgtgtagACCAATGTGAGAAGGACAAGGCAC
EST: gi|19876233|gb|AU237064.1|AU237064
EST:     TCTTGATAATGAAAAAGTTTTACAGTTTGATGATGCTATTAAGTTCTTAG                         ACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGA
genomic: TCTTGATAATGAAAAAGTTTTACAGTTTGATGATGCTATTAAGTTCTTAGgtatgttgat ... ctttgtgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtttctagatttcatctttatgattttttcttgacggtcttgctttgtgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAG
                               tcttgac  putative branch site (score: 3)
                                        tcttgcttt  putative PPT
           atttcatctttatgat  TA-rich tract