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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtagaccatatcatgttatactcgtcttagctattgttattgtctgcattctgataccccattttttcttggcagGATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCGTACAGCGGGGGCTGTCGCCCAT

Basic information

species Arabidopsis thaliana
transcript AT3G03960.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 6
-------------------------gtatgtgtagaccatatcatgttat--actcgtcttagctattgttattgt--------ctgcattctgataccccattttttcttggcagGATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCGTACAGCGGGGGCTGTCGCCCAT-
                         |   || |  |   | || |  |||  | |     |    ||| | | ||          ||  |||| |   |  | ||  |  |   ||| | |||||  |||||||||||||||||||||||||  | || |||||||| ||| | ||  |||| ||| || 
gtatgtgaagtctttatccatgtttggtggttttaattgtctcttactattgaattaatatgaacattataactgcacattagattgttttctaacttcaaaattcctgcttttagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACCGGCTCTGTTGCC-ATG

upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 6
-------------------------gtatgtgtagaccatatcatgttat--actcgtcttagctattgttatt-----gtctgcatt------ctgataccccattttttcttggcagGATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCGTACAGCGGGGGCTGTCGCCCAT-
                         |   || |  |   | || || |||  | |     |    ||| | | |     ||   ||||       | |   |  | |   |  | ||||| | |||||  |||||||||||||||||||||||||  | || |||||||| ||| | ||  |||| ||| || 
gtatgtgaagtctttattcatgtttggtggttttaattgtctcttgctattaaattaatatgaacattataacttacaagtgcacattagattgttaacttcaaaatccctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACTGGTTCTGTTGCC-ATG

upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 6
-------------gtatgtgtagac-catatcatgttatactcgtcttagctattgttat-----tgtctgcattctgataccccattttttcttggcagGATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCGTACAGCGGGGGCTGTCGCCCAT
               ||     ||  ||||||     | |    |||  ||   || |||     ||| || | |     |     ||| ||  | ||||  | ||||| ||||||||||||||||||||||||||| |||| |||||||||||| | || ||||| ||   |
ttgcatcttttcttcatcaagggatgcatatccaagaagaacaatctatgcatgtggtatggcgatgtatgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT

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|86064113|gb|DR359870.1|DR359870
EST:     AGTGGAGGATCAATTGGAGAAATGGCATTGCATTTCTGTGAGCGCTACAA                         GATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCG
genomic: AGTGGAGGATCAATTGGAGAAATGGCATTGCATTTCTGTGAGCGCTACAAgtatgtgtag ... ttcttggcagGATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCG
EST: gi|47831127|gb|CK120811.1|CK120811
EST:     AGTGGAGGATCAATTGGAGAAATGGCATTGCATTTCTGTGAGCGCTACAA                         GATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCG
genomic: AGTGGAGGATCAATTGGAGAAATGGCATTGCATTTCTGTGAGCGCTACAAgtatgtgtag ... ttcttggcagGATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtcttagctattgttattgtctgcattctgataccccattttttcttggcagGATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCGTACAGCGGGGGCTGTCGCCCAT
                            ttctgat  putative branch site (score: 3)
                                  taccccattttttctt  CT-rich tract
           tattgttatt  TA-rich tract