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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatctctcttcatggctctgctagtattgttatgttatcattggctaatgttctacaatttgcagCTATTCATTCTTCTCTCATGTGGTCTAGCTGTGTTCTGCAACATAAGCCAGTACCTTTGCATCGGGCGGTTTTCAGCAGTATCGTTCCAAGTTATTGGTC

Basic information

species Arabidopsis thaliana
transcript AT5G42420.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42420.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g39280.1 (Oryza sativa), 3'ss of exon 4
-------------gtaagtatctctcttcatggctctgctagtattgtt---------------atgttatcattggcta--atgttctacaatttgcagCTATTCATTCTTCTCTCATGTGGTCTAGCTGTGTTCTGCAACATAAGCCAGTACCTTTGCATCGGGCGGTTTTCAGCAGTATCGTTCCAAGTTATTGGTC
              || | |  |||| |  | ||| |  || |  |  |               ||||| | |     |   |||||    | | ||||| | |||||  | || || ||     | ||||| ||||||||||| ||||||||||| |||||||| ||||| || |||   |||||||| ||  | || |
tctgttttaatcattatgcacttctccttgttgctttaatactcctactgggaattcttaaaacatgttctaacaacttgctatgttaataactctgcagTTCTTCATATTGCTTTCTTGCTCCTTGGCTGTCTTCTGCAACATGAGCCAGTACCTCTGCATCGGCCGGTTCTCTGCAACTTCGTTCCAGGTCCTGGGCC

upper sequence: AT5G42420.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: AC194970.5_FGT005 (Zea mays), 3'ss of exon 4
--------------------------gtaagtatc--tctcttcatggctctgctagtattgt-tatgttatcattggctaatgttcta-caatttgcagCTATTCATTCTTCTCTCATGTGGTCTAGCTGTGTTCTGCAACATAAGCCAGTACCTTTGCATCGGGCGGTTTTCAGCAGTATCGTTCCAAGTTATTGGTC
                           | ||| |    |   | |||  |  |   | |  || |||| | | |  |  ||   ||  | || | ||||| | ||||| || || || ||    || || |||||||||||||| ||||| ||||| |||||||||||||| |||||    || ||||| ||  | || |
cgaatgataatgaacgtagatgcatatttagtctaaaacgaattatgttttgggacggagagtgtatgatctaaccgcttaccttttaatcattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC

upper sequence: AT5G42420.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G00210.2 (Glycine max), 3'ss of exon 4
-------------------------------------------gtaagtatctctcttcatggctctgctagtattgttatgtta----tcattggctaatgttctacaatttgcagCTATTCATTCTTCTCTCATGTGGTCTAGCTGTGTTCTGCAACATAAGCCAGTACCTTTGCATCGGGCGGTTTTCAGCAGTATCGTTCCAAGTTATTGGTC
                                           ||  |||| | |||| |    | | | | || ||||   |||    |  |    |  |  | ||  || ||||| ||||||||||||| |||||    |||||||| || |||||  | ||||| ||||||||||| ||||| |||||||| || || ||||| ||| | || |
gtaagttccttttccccctattgacagtagtcttttatatcctgtgtgtatttatcttta--attatacaaatactgttggattaattcttttaaattttttctttaatatctgcagTTATTCATTCTTCTTTCATGCTCGCTAGCTGTATTTTGCAATGTGAGCCAATACCTTTGCATTGGGCGCTTTTCAGCTGTTTCCTTCCAGGTTTTAGGCC

upper sequence: AT5G42420.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G45700.1 (Glycine max), 3'ss of exon 4
-------------------------------------------gtaagtatctctcttcatggctctgctagtattgttatgttatcat--tggctaatgttctacaatttgcagCTATTCATTCTTCTCTCATGTGGTCTAGCTGTGTTCTGCAACATAAGCCAGTACCTTTGCATCGGGCGGTTTTCAGCAGTATCGTTCCAAGTTATTGGTC
                                           ||| ||||     || ||   | | | | || ||||   ||||  |  |   |  | || ||  ||  |||| ||| ||||||||| |||||    |||||||| || |||||  | ||||| ||||||||||||||||| |||||||| || || ||||| ||| | || |
gtaagttgctttttcccctattgacactagtcttttatattctgtatgtattatcttttat---tatacaaatactgttggattattcttttaattttttttttaatatccgcagTTATGCATTCTTCTTTCATGCTCACTAGCTGTATTTTGCAATGTGAGCCAATACCTTTGCATCGGGCGCTTTTCAGCTGTTTCCTTCCAGGTTTTAGGCC

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|86079446|gb|DR375203.1|DR375203
EST:     TCATTATGAAGTATAATATGTCTTCCGGTTGCTTT                         CTATTCATTCTTCTCTCATGTGGTCTAGCTGTGTTCTGCAACATAAGCCAG
genomic: TCATTATGAAGTATAATATGTCTTCCGGTTGCTTTgtaagtatct ... caatttgcagCTATTCATTCTTCTCTCATGTGGTCTAGCTGTGTTCTGCAACATAAGCCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggctctgctagtattgttatgttatcattggctaatgttctacaatttgcagCTATTCATTCTTCTCTCATGTGGTCTAGCTGTGTTCTGCAACATAAGCCAGTACCTTTGCATCGGGCGGTTTTCAGCAGTATCGTTCCAAGTTATTGGTC
                                ggctaat  putative branch site (score: 3)
              tattgttatgttat  TA-rich tract