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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtccttatctcttttgctttgtttctgtttatgttttagtgcttttcctcttttctcatttgatattgttttggtgtggaaacagATTAACATGAAAGGTCTTGATGGGATACAAGGACCGATATATGTCGGGACAGGTTGTGTGTTTAGAAGACAGGCTCTTTATGGTTTTGATGCACCAAAGA

Basic information

species Arabidopsis thaliana
transcript AT4G39350.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G840940_T01 (Zea mays), 3'ss of exon 1
--gtatgtgtccttatctcttttgctttgtttctgtttatgttttagtgcttttcctcttttctcatttg-atattgttttggtgtggaaacagATTAACATGAAAGGTCTTGATGGGATACAAGGACCGATATATGTCGGGACAGGTTGTGTGTTTAGAAGACAGGCTCTTTATGGTTTTGATGCACCAAAGA
   | | || | | |  || ||     | | ||||   |    ||   | |  |  |||   |   |||    ||| | |   | |     ||||||||||||||||||||||||||||| |||||||| |||||||| ||||| |||||||| || |||||||| ||| | ||||||| |||||| ||||   
gtatgtatggcatgaattcattctaactttatctgaa-agacattgaagatagtattctgaacaagtttctgcattatctacttctctttgcagATTAACATGAAAGGTCTTGATGGGATCCAAGGACCAATATATGTTGGGACTGGTTGTGTTTTCAGAAGACATGCTTTGTATGGTTATGATGCCCCAACTG

upper sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 10
gtatgtgtccttatctcttttgctttgtttctgtttatgttttagtgcttttcctct--tttctcatttgatattgttttggtgtggaaacagATTAACATGAAAGGTCTTGATGGGATACAAGGACCGATATATGTCGGGACAGGTTGTGTGTTTAGAAGACAGGCTCTTTATGGTTTTGATGCACCAAAGA
||| || | ||  ||   |||  |||| || | |   || |||  |     |||| |  | |  ||  |  ||         | || ||||||||||||||||||||  | |||||||||||||| || ||||||||||| || || ||||| || |||||  | || |||||||| | |||||||||    |
gtaagttttctcttcctcttt-ttttgcttgtttgactgcttttctttcagtcctttaatatggcaactactaactccccaat-tgaaaacagATTAACATGAAAGGATTGGATGGGATACAAGGTCCAATATATGTCGGAACTGGATGTGTTTTCAGAAGGTACGCACTTTATGGATATGATGCACCTGCCA

upper sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 10
gtatgtgtccttatctcttttgctttgtttctgtttatgttttagtgcttttcctct--tttctcatttgatattgttttggtgtggaaacagATTAACATGAAAGGTCTTGATGGGATACAAGGACCGATATATGTCGGGACAGGTTGTGTGTTTAGAAGACAGGCTCTTTATGGTTTTGATGCACCAAAGA
||| || | ||  ||   ||| ||||| || | |   || |||  |  |  | || |  | |  ||  |  ||         | || ||||||||||||||||||||  | |||||||||||||| || ||||||||||| || || ||||| || |||||  | || |||||||| | |||||||||    |
gtaagttttctcttccaattttctttgcttgtttgactgcttttcttttggttctttagtatggcagcttctaactccccaat-tgaaaacagATTAACATGAAAGGATTGGATGGGATACAAGGTCCAATATATGTCGGAACGGGATGTGTTTTCAGAAGGTACGCACTTTATGGATATGATGCACCTGCCA

upper sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0031g02060.t01 (Vitis vinifera), 3'ss of exon 10
gtatgtgtccttatctcttttgctttgtttctgtttatgttttagtgcttttcctcttttctcatttgatattgttttggtgtggaaacagATTAACATGAAAGGTCTTGATGGGATACAAGGACCGATATATGTCGGGACAGGTTGTGTGTTTAGAAGACAGGCTCTTTATGGTTTTGATGCACCAAAGA
|||||| | | | | ||||||  ||| ||||  |||||           |||| | | |  |      |  |  ||||    | ||||||||||||||||| |||  | ||||| |||||||||||||||||||| || || |||||||| || ||||| || || |||||||||| |||||| ||    |
gtatgtatacctttttcttttcttttttttccctttat---------tgtttcttatatcattgggaaagctgatttttcaattgaaacagATTAACATGAGAGGCTTAGATGGTATACAAGGACCGATATATGTTGGAACCGGTTGTGTCTTCAGAAGGCAAGCACTTTATGGTTATGATGCTCCTGTCA

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|164201551|gb|ES068565.1|ES068565
EST:     GGATTGATAGACATGATAGATACTCAAACCGTAACGTTGTGTTCTTTGAT                         ATTAACATGAAAGGTC
genomic: GGATTGATAGACATGATAGATACTCAAACCGTAACGTTGTGTTCTTTGATgtatgtgtcc ... gtggaaacagATTAACATGAAAGGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttttagtgcttttcctcttttctcatttgatattgttttggtgtggaaacagATTAACATGAAAGGTCTTGATGGGATACAAGGACCGATATATGTCGGGACAGGTTGTGTGTTTAGAAGACAGGCTCTTTATGGTTTTGATGCACCAAAGA
                           atttgat  putative branch site (score: 5)
                           atttgatattgtttt  TA-rich tract