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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttacttacactcgctcacttttgttgtcgattgtttgatactcttgctaatttgtgagttttgttattttttagATAAGAAGGTGTTCCCTGACTTCTACGTATTGGGATGGTATTCTACGGGAAGTGACGCTACCGAATCTGATATGCATATCCACAAAGCT

Basic information

species Arabidopsis thaliana
transcript AT4G26430.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------gtaagtttacttacactcgctcacttttgttgtcgattgtttgatactcttgctaatttgtgagttttgttattttttagATAAGAAGGTGTTCCCTGACTTCTACGTATTGGGATGGTATTCTACGGGAAGTGACGCTACCGAATCTGATATGCATATCCACAAAGCT
                                                         | |  | |  |  | |       ||| |  || | ||   |||| |      |  ||||| |    |||   | |  ||||||||||||||||||||||||||||||  | || ||||| || || ||||| || |    |||  | || ||||| ||||||||||| 
gtaagcttctacgtgaatctgcgggttctcttttaagatttcacctgtcacgacgcctgaaatcatatggaatgctagggtttcgcggtaggtttggtgatgc----agtgctttgttacgactgtggctatgcagATAAGAAGGTGTTCCCTGACTTCTACGTGCTCGGTTGGTACTCCACTGGAAGCGATGTGCACGACACCGACATGCAAATCCACAAAGCC

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------gtaagtttacttacactcgctcacttttgttgtcgattgtttgatactcttgctaatttgtgagttttgttattttttagATAAGAAGGTGTTCCCTGACTTCTACGTATTGGGATGGTATTCTACGGGAAGTGACGCTACCGAATCTGATATGCATATCCACAAAGCT
                                                      |  | ||      ||||    |||   |  ||| |||||||  |  || |  ||||| |     ||   | |  |||||||||||||||||| |||||||||||  | || ||||| || || ||||| || |    |||  | || ||||  ||||||||| | 
gtaagctggggcattttgttttttgtttcacggcttcatctttcacgacgcctggaatcctagggaacgctagggttt--cgcggatggtttgatgatgctggtgctttgttacggccgtggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 1
------------------gtaagtttacttacactcgctcacttttgttgtcgattgt-ttgatactcttgctaatttgtgagttttgttattt-tttagATAAGAAGGTGTTCCCTGACTTCTACGTATTGGGATGGTATTCTACGGGAAGTGACGCTACCGAATCTGATATGCATATCCACAAAGCT
                    |||||   || || |   ||| ||  ||| | |   || |||||  | |||  |  |  |  ||||| ||  || || ||||||||||||||||||  |||||||| || |||| |||||||| || || ||||| ||    ||||| ||||||||||| |||||||||
taagcattttttctctctcaaagttgtgtttcatttattcatttaagtttttggaggtgttgattttattggaagatgatttgtttttttccttcttcagATAAGAAGGTGTTCCCGCACTTCTACATACTGGGCTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGATATGCATATTCACAAAGCT

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|116443197|gb|EG485789.1|EG485789
EST:     TGCTCTTGATACTCTCGACAGATCCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCTGACTTCTACGTATTGGGATGGTATTCTACGGGAA
genomic: TGCTCTTGATACTCTCGACAGATCCTTCCTCGAGAAGAAGCAAGAACTCTgtaagtttac ... tattttttagATAAGAAGGTGTTCCCTGACTTCTACGTATTGGGATGGTATTCTACGGGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgtcgattgtttgatactcttgctaatttgtgagttttgttattttttagATAAGAAGGTGTTCCCTGACTTCTACGTATTGGGATGGTATTCTACGGGAAGTGACGCTACCGAATCTGATATGCATATCCACAAAGCT
                         tgctaat  putative branch site (score: 2)
                                       ttttgttatttttt  putative PPT
                                     agttttgttatttttt  TA-rich tract