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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttccctttttgatatttctcttctctcatgtagtgttgtgtttgtttctcaatctcatgctaatatcttctcttctcttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC

Basic information

species Arabidopsis thaliana
transcript AT3G08710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G40970.1 (Glycine max), 3'ss of exon 3
gtaatttttccctttttgatatttctcttctctcatgtagtgttgtgtttgtttctcaatctcatgc---------taatatcttctcttctc-ttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC
    | ||||| |  |   | |        ||| |  |||  ||    |  ||| |    ||   |          |||||   |   | ||  || ||||||||| ||||||| |||||||| |||||||||||||| ||||| ||  | || |||| || || |||| | || |||||| |  | ||| | |||||| |  
---ttgtttccttgataagtgtcctcagggtcttagttagaatttgactaatttgttttccttgggtacaataatttaatactataaatccttgttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCGCCATATTACAGCGAGTTATCTGAGAAATACACATCTATGATGTTCTTGT

upper sequence: AT3G08710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G34660.1 (Glycine max), 3'ss of exon 3
------gtaatttttccctttttgatatttctcttctctcatgta-gtgttgtgtttgtttctcaatctcatgctaatatcttctcttctcttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC
       |  ||||   |        |   |  |||| |||||    |  ||| |||  ||      |    | ||||       ||||  ||  |||||||  ||||||| |||||||| |||||||||||||| |||||  |  | ||||||  ||    |||| | || | |||| |  | ||| | |||||| |  
cttaaatttcttttaaacccccacccagcccctttctttcatgagtatactgtatttcctttgggtgcaatagttaattctaaagcttcatttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCACCACATTATTGCGAGTTGTCCGTGAAATACCCGTCTATCATGTTCTTAT

upper sequence: AT3G08710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G00410.2 (Glycine max), 3'ss of exon 3
----gtaatttttc--cctttttgatatttctcttctctcatgta-gtgttgtgtttgtttctcaatctcatgctaatatcttctcttctcttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC
       |||||||    | | |  | || | |  || || ||   ||  ||| |||  ||      |    | ||||       ||||   |  |||||||  ||||||| |||||||| |||||||||||||| ||||| ||  | ||||||| ||    |||| | || |||||| |  | ||| | |||||| |  
cttgaagatttttcagtatatctttttttacccccctttcctgagtgtactgtatttcctttgggtgcaatagttaattctaaagcttcatgtttaacagGTTATTGCAAATTTCAGTGCCACATGGTGTGGTCCTTGTAAGATGATTGCACCATATTATTGCGAGTTGTCCGAGAAATACCCATCTATCATGTTCTTAT

upper sequence: AT3G08710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G44840.1 (Glycine max), 3'ss of exon 3
gtaatttttccctttttgatatttctcttctctcatgtagtgtt---gtg-tttgtttc---tcaatctcatg--ctaatatcttctcttctcttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC-
    | ||||| |  |   | |        ||| |  |||  ||   ||  ||| |||    ||  |   ||    |||||   |   | |   |  |||||||| ||||||| ||||||||  ||||||||||||| ||||| ||  | ||||||| || |   ||| | || |||||| |  ||||| | |||||| |   
---ttgtttccttgataagtgtcctcggggtcttagttagaatttgagtaatttattttccttcggtacaataatttaatactatgaatccatcttcaacaggTGATTGCAAATTTCAGTGCAGCATGGTGTGGTCCTTGTAAGATGATTGCACCATATTACTGTGAGTTATCTGAGAAATACACTTCTATGATGTTCTTGGT

upper sequence: AT3G08710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 3
------gtaatttttccctttttgatatttctcttctctcatgtagt--gttgtgtt-tgtttctcaatctcatgctaatatcttctcttctcttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC
         | ||   | |  |||  ||||   || |||  ||   |  |||||    | ||| || |  |    |||||     ||      | ||  |||||| ||||||| || ||||| |||||||||||||| ||||||||  | |||||||| | |  ||| || || |||  |||  ||||||| ||||| ||  
tgcttgaggaattgctcttcattgcaatttgatttatctggtgagttcagttgtacaatatttttccaattttcactaattggagctgcatattcga--cagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA

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|86077308|gb|DR373065.1|DR373065
EST:     AAGAGAGTTGGGATGACAAATTAGCTGAAGCTGATCGTGATGGCAAAATC                         GTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAGATTGTGGCA
genomic: AAGAGAGTTGGGATGACAAATTAGCTGAAGCTGATCGTGATGGCAAAATCgtaatttttc ... cttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgttgtgtttgtttctcaatctcatgctaatatcttctcttctcttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC
                          tgctaat  putative branch site (score: 2)
                                tatcttctcttctctt  CT-rich tract
                             taatatctt  TA-rich tract