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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgtccattccatataccgctggttgggttttcgtaccaaagtgcattgttttatttgcatactgaactaccatcttgactcatcacgatgtcatcgacgccaatagataataatgactgggtgaaaattttctgtgatttagccttgattgattttgtgactctttacattattgtttaagcagGGTATCATACATTATATGAGTGGTACAAATCAGTGGAGAATGAGCATTTCCCGGACCCTACTGGCCTTCGAGCCCGTATCGAACAATGGACATTTGGCTT

Basic information

species Arabidopsis thaliana
transcript AT4G11800.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA17G36310.1 (Glycine max), 3'ss of exon 12
gtcagtgtccattccatataccgctggttgggttttcgtaccaaagtgcattgttttatttgcatactgaactaccatcttgactcatcacgatgtcatcgacgccaatagataataatgactgggtgaaaattttctgtgatttagccttgattgattttgtgactctttacattattgtttaagcagGGTATCATACATTATATGAGTGGTACAAATCAGTGGAGAATGAGCATTTCCCGGACCCTACTGGCCTTCGAGCCCGTATCGAACAATGGACATTTGGCTT
                                                                                  |   |  | ||| ||| | ||      |  |   | ||  || |||  |   |  ||  |||| |  |  | || | | |||  | |||       |||  |  |||||||||| || |||||| ||||||| | ||||||||| | |||||| || || || || ||||| ||  |||| |||||||||||||||||||||||   
----------------------------------------------------------------------------------agagaaaaagatttcagc-actttgtaaagtgggattgtgtgtgtgtga---tgatgatatttggtttataatg-tctggtgtttttttgggggggtgta-atccaGGGTATCACACTTTATATCAGTGGTATAGATCAGTGGAAAGTGAGCACTTTCCTGATCCAACTGGACTCAGAGCTCGTATCGAACAATGGACATTTGGAC-

upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA14G08860.1 (Glycine max), 3'ss of exon 12
gtcagtgtccattccatataccgctggttgggttttcgtaccaaagtgcattgttttatttgcatactgaactaccatcttgactcatcacgatgtcatcgacgccaatagataataatgactgggtgaaaattttctgtgatttagccttgattgattttgtgactctttacattattgtttaagcagGGTATCATACATTATATGAGTGGTACAAATCAGTGGAGAATGAGCATTTCCCGGACCCTACTGGCCTTCGAGCCCGTATCGAACAATGGACATTTGGCTT
                                                                                         | ||| |||   ||      |  |   | ||  || ||||  ||  | | || ||||        ||||||| | | | |||    |     | |  |||||||||| || |||||| ||||||| | ||||||||| | |||||| || || || || ||||| ||  |||| ||||| |||||||||||||||||  |
----------------------------------------------------------------------------------------aaagatttcaat-actttgtgaagtgggattgtgtgtgtgatgatgatatttggtttataaagtcctgatttttttatttttttttatgggtgtaatccagGGTATCACACTTTATATCAGTGGTATAGATCAGTGGAAAGTGAGCACTTTCCCGATCCAACTGGACTCAGAGCTCGTATTGAACAATGGACATTTGGACT

upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 13
gtcagtgtccattccatataccgctggttgggttttcgtaccaaagtgcattgttttatttgcatactgaactaccatcttgactcatcacgatgtcatcgacgccaatagataataatga-ctgggtgaaaattttctgtgatttagcct--tgattgattttgtgactctttacattattgtttaagcagGGTATCATACATTATATGAGTGGTACAAATCAGTGGAGAATGAGCATTTCCCGGACCCTACTGGCCTTCGAGCCCGTATCGAACAATGGACATTTGGCTT
                                                                                          |  || || | |  |  ||  | | |||  | || | |  || |  |   |    ||   |  |  |||| |||| |  |  |       || |||   |||| |||||||| |||||| | ||||||  | ||||||||| ||| || || ||||| || || ||||||||||| ||||| |||||||||||||||||  |
----------------------------------------------------------------------------------------ttctgtgacaacaattctcattaaaattaaaaaactagtttcaagtaattgctaggctaatttgattgttgactttgag-ttgatggtggacttattt---cagGCTATCATACTTTATATCAATGGTACCGAACAGTGGAGAGTGAACACTTTCCGGATCCCACAGGCCTTCGAGCTCGTATAGAACAATGGACATTTGGTCT

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|163993455|gb|ES080123.1|ES080123
EST:     CTTGCAAATTCTG                         GGTATCATACATTATATGAGTGGTACAAATCAGTGGAGAATGAGCATTTCC
genomic: CTTGCAAATTCTGgtcagtgtcc ... gtttaagcagGGTATCATACATTATATGAGTGGTACAAATCAGTGGAGAATGAGCATTTCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtgatttagccttgattgattttgtgactctttacattattgtttaagcagGGTATCATACATTATATGAGTGGTACAAATCAGTGGAGAATGAGCATTTCCCGGACCCTACTGGCCTTCGAGCCCGTATCGAACAATGGACATTTGGCTT
                 gattgat  putative branch site (score: 4)
                                  tttacattattgttta  TA-rich tract