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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttataacatatattttatgtatactttgctttcaaagctccaccttgtgaatcctaaacttgggtgttgtattttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTG

Basic information

species Arabidopsis thaliana
transcript AT4G28470.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 22
gtaagtta-taacatatattttatgtatactttgctttcaa-agctccaccttgtgaatcctaaacttgggtgttgtattttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTG
|| ||| | |  || |  | ||   | | |||   | | |   |  |||| ||     | ||||    | ||    | ||   |    || |  |||||||||||| | |||||  |  ||||||| |||||||||||||||||||| || |||||||| || || ||  |||| ||  ||||||   | 
gtgagtaacttgcaaagttgttgaatctccttcaatcttattggaaccacatt-----ttctaaga--gagtccattcttcacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTA

upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os06g48640.2 (Oryza sativa), 3'ss of exon 22
----gtaagttataacatatattttatgta-tactttgctttcaaagctccaccttgtgaatcctaaacttgggtgttgtattttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTG
    |||| ||||||  | | ||  || |  | |  |  | |   | |  ||  || | |      || |    |||| |    | | |  || |  |||||||||||| | |||||  |  ||||||| || ||||||||||||||||| || |||||||| || || ||  |||| ||  |||||    | 
gtgagtaacttataaagt-tgttgaatctccttcaatcttattggaaccacattttctaagagtataagtccattgttcttcacttttc--agCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGTCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTACCCTA

upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 22
---------------gtaagttataacatatattttatgtatactt----tgct-ttcaaagctccacctt---gtgaatcctaaacttgggtgttgtattttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTG
                 |   | |   |   |  |  ||   ||||    || | || | | ||  ||  |    | | |    ||      |  |||||  | |    || || |||||||||||  || | ||  |||||||||| ||||| ||||||||| | ||| | ||||| |||||||||||||| ||||||||||| ||||||
gtaagcaaacctttatcagcctttctgactgagctggtggtgacttaaaatgatgtttacatctttactgtaatattattttctaatccacattctgtatcatttttacagGACAGCACTTGCTGGATTAATTACCATGTTGCATGCTTGCCTAGACATGAAAGCTATTGTGCTGGGAAAATATCACTATGTTCTCTACTTCCTCGTTTTG

upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 22
---------------------------gtaagtta-taacatatattttatgtatactttgctttcaaagctccaccttgtgaatcctaaacttgggtgttgtattttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTG
                            | ||||  | || |  |  | |||| ||| |   |     |   | |  |||| |||||  |  ||  ||||   ||||| |||  || || |||||||||||  || | ||  ||||||| |||||||| ||||||||| | ||| |  |||| |||||||||||||| ||||||||||| ||||||
gtaagcaacctttatcagccttttggactgagttggtgactttaaagtgatgtttacatctttactgtaatactattttgt-aatcc--actttctgtgtatcatttt-tac--agGACAGCACTTGCTGGATTAATTACCATGTTGCACGCATGCCTAGACATGAAAGCTATTGTGTTGGGAAAATATCACTATGTTCTCTACTTCCTCGTTTTG

upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 22
--------gtaagttataacatatattttatgtatactttgctttcaaagctccaccttgtgaatcctaaact-tgggtgttg----tattttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTG
          | | |  || | |||| | |   | |     | | |||     |        || ||||   | |   | |||    | |||||     ||| | || |||||||| ||||| || ||| ||||||||||||||||||||||  |||| ||  |||||||||| || ||||| || ||  |||||||||||
atataacaagagggtgcaagagatatct-acaaacagccatcctccaacatgtctagcctcaaagcctattttctaaatcttgcttctcttttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAAGGCCATCATCTTGGGGAAATACCATTATGTTCTTTATGTCCTTGTTTTG

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|125145454|gb|EL180651.1|EL180651
EST:     GGTCTCTTAACTCTCAATCCTTTCCACTCCGAACGGCTCTTGCTATCGCC                         AACCGCACTTGCTGGTATAGTGA
genomic: GGTCTCTTAACTCTCAATCCTTTCCACTCCGAACGGCTCTTGCTATCGCCgtaagttata ... ttgtacctagAACCGCACTTGCTGGTATAGTGA
EST: gi|116376321|gb|EG418913.1|EG418913
EST:     GGTCTCTTAACTCTCAATCCTTTCCACTCCGAACGGCTCTTGCTATCGCC                         AACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAA
genomic: GGTCTCTTAACTCTCAATCCTTTCCACTCCGAACGGCTCTTGCTATCGCCgtaagttata ... ttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcaaagctccaccttgtgaatcctaaacttgggtgttgtattttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTG
                       tcctaaa  putative branch site (score: 2)
                                      ttgtatttt  TA-rich tract