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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttgaatttcaaagcttatctatattgtgacgctgctaagtggatttcgaactgattgcttctccctctcttttaagGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTGGCACATCACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTG

Basic information

species Arabidopsis thaliana
transcript AT5G20000.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 4
gtacacttgaatttcaaagcttatctatattgtgacgctgc-taagtgg-atttcgaactgattgcttctccctct-------cttttaa----------gGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTGGCACATCACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTG
|||   |   ||||    |  |  ||| ||| || |  | | | ||  | |        || ||  || ||  | |       || || |          ||||||  || | || || |||||||| || || || ||| | |||||| |||| ||||| ||||| ||||||||||| |||||||| || ||||||||||
gtagtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGGGCAGTGGCTCATCATACTGACTGTACATTCATCAGGGTGTCTGGTTCTG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 4
gtacacttgaatttcaaagcttat-ctatattgtgacgctgc-------taagtggatttcga----actgattgct-----tctccctctcttttaagGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTGGCACATCACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTG
|||   |   ||||    | |  | ||| ||| || |  | |        |  ||| | | ||     ||| |||||     |||   || | |   |||||||  || | || || |||||||| || || || ||| | |||||| |||| ||||| ||||| ||||||||||| |||||||| || ||||||||||
gtagtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGGGCAGTGGCTCATCATACTGACTGTACATTCATCAGGGTGTCTGGTTCTG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
gtacacttgaatttcaaagcttatctatattgtgacgctgctaagtggatttcgaactgattgcttctccctctcttttaagGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTGGCACATCACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTG
|||   || | ||  |    ||  ||  |   | |   |  ||||    | |  |  |||||  ||       |  |   |||| ||  || |||| || |||||||| || ||||| ||  |  | ||  |||| || || ||||| |||||||||||||||||||| |||||||||||||
gta-gttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgatt--ttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------gtacacttgaatttcaaagcttatctatattgtgacgctg-ctaagtggatttcgaactgat-tgcttctcc-ctctcttttaagGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTGGCACATCACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTG
               |      |     ||  |    || |  |         ||  |   |  ||||  || |||| |||  |    || | | |  |||| || ||||||||||| || ||||||||||| ||||| ||  | || |||||||| || |||||||| |||||||| |||||| ||||||| || ||||
atgagttgtttcgtcgattttgtagtcatcggattccatgtcaacaacagaattgattggataaattttaaaatgatctgccacaaaactttgtctgcagGGGGTTTTGTTGTACGGCCCTCCTGGAACTGGAAAGACGCTTCTTGCCCGGGCTGTAGCTCATCACACAGACTGTACGTTCATCCGAGTTTCAGGATCTG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 3
gtacacttgaatttcaaagcttatctatattgtgacgctgctaagtggatttcgaactgattgcttctccctctcttttaagGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTGGCACATCACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTG
               |||  ||  |||       |   ||     |||     | |   ||| ||| ||     || |  |||| ||| |  |||| || || ||||||||||| |||||  |  |||||||||| ||||| || || ||||||||||| ||||| |||||||| || || |
-------------gtaaaattttgctaa--caaaagtttggcttttggtaccagcatctatt-cttgtcttctgctgtgcagGGAGTGCTACTGTATGGCCCTCCTGGAACTGGAAAGACTTTGCTGGCTCGGGCCGTGGCTCACCATACTGACTGTACATTCATAAGAGTTTCAGGGTCCG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ20576 (Selaginella moellendorffii), 3'ss of exon 4
gtacacttgaatttcaaagcttatctatattgtgacgctgctaagtggatttcgaactgattgcttctccctctcttttaagGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTGGCACATCACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTG
               |||  ||  |||       |   ||     |||     | |   ||| ||| ||     || |  |||| ||| |  |||| || || ||||||||||| || ||  |  |||||||||| ||||| || || ||||||||||| ||||| |||||||| || || |
-------------gtaaaattttgctag--caaaagtttggcttttggtaccagcatctatt-cttatcttctgctgtgcagGGAGTGCTACTGTATGGCCCTCCTGGAACTGGAAAAACTTTGCTGGCTCGGGCCGTGGCTCACCATACTGACTGTACATTCATAAGAGTTTCAGGGTCCG

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|164201077|gb|ES026000.1|ES026000
EST:     CATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG                         GGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGG
genomic: CATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAGgtacacttga ... ctcttttaagGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGG
EST: gi|164231170|gb|ES041092.1|ES041092
EST:     CAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG                         GGTGTGTTGTTGTACGGTCC
genomic: CAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAGgtacacttga ... ctcttttaagGGTGTGTTGTTGTACGGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtgacgctgctaagtggatttcgaactgattgcttctccctctcttttaagGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTGGCACATCACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTG
                           aactgat  putative branch site (score: 3)
                             ctgattgcttctccct  CT-rich tract
                                              tcttttaa  TA-rich tract