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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgtaatgcttatttggtagacaattccaggttccccagtagagttaggactttgcattttaatgtttcttcctgtccgacatttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGATGAACTTGTTGTCCCAATCATAGAGAACACAGCATATGAGAATGAACTAA

Basic information

species Arabidopsis thaliana
transcript AT5G53850.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53850.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 3
gtaagctgtaatgcttatttggtagacaattccaggttccccagtagagt-taggactttgc--attttaa--tgtttcttcctgtccg-acatttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGATGAACTTGTTGTCCCAATCATAGAGAACACAGCATATGAGAATGAACTAA
 | |||||||||  | | |   |  |  |      ||    |||||   | |    || |||  ||||| |  || ||||   ||||   |||  |   |||||||||||||||| ||||||||||| ||  | || || || || ||||||||||||||  |||| || |||||||||||||| || ||  |||| || |
-ttagctgtaattgtgactcattttattaaattgtgtgtttcagtaatttgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA

upper sequence: AT5G53850.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 3
-------gtaagctgtaatgc-ttatttggtag-acaattccaggttccccagtagagttaggactttgcattttaatgtttcttcctgtccgacatttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGATGAACTTGTTGTCCCAATCATAGAGAACACAGCATATGAGAATGAACTAA
        | |||| |  | | || | | ||   |   ||  |  | | |     |   ||  | ||| ||||| | |||   |  ||   | |||  |   |||| ||||||||||| ||||||||||| ||  | || || || || |||||||||||||||||||| || || |||||||| || || ||| || | || |
tagaaagtttagctctgcttcattgtcttgtcccatgcttttatttcctcttcctgtaatactatttt-catttgactgtggttgtct---ccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAACACGGCCTACGAGTATCAGCTCA

upper sequence: AT5G53850.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G35120.3 (Glycine max), 3'ss of exon 3
-gtaagctgtaatgcttatttggtagacaattccaggttccccagtagagttaggactttgc-attttaatgtttcttc--ctgtc-cgacatttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGATGAACTTGTTGTCCCAATCATAGAGAACACAGCATATGAGAATGAACTAA
   ||  | ||   ||  ||   |       |||| | |      |    ||   |   | | ||||| || |  |||   ||||| | |||  |   |||| ||||||||||| ||||||||||| ||  | || || || || |||||||||||||||||||| || || ||||| || || || ||| || | || |
tagaaagtttagctctgcttcattgtcttgctccatgcttttatttcctcttcctataatactattttcatttgactttggctgtctccacaaatggcagATCACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGCTATTATGATGAACTTGTTGTCCCCATAATTGAGAATACGGCCTACGAGTATCAGCTCA

upper sequence: AT5G53850.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 3
gtaagctgtaatgcttatttg---gta-gacaattcca----ggttccccagtagagttaggact--ttgcattttaatgtttcttcctgtccgacatttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGATGAACTTGTTGTCCCAATCATAGAGAACACAGCATATGAGAATGAACTAA
 |||  | | |  |||  | |   |||  | |||||      ||||| |   ||   ||     |  ||| |||||    | | ||  ||| | | |||  | |||| ||||| ||||| ||||||||||| |||||||| || || || |||||||| ||||| |||||||||||||||||||| ||  | || |  || || |
ataattttttacactttctagaatgtataataattctgttttggttctctgatatcttttaatttgcttgaatttt---ttatgtttttgtgcaaaatt--acagATCACTCATATGGAAATGATAAAAGGAATTCAAGGACATGGTTATTATGATGAGCTTGTGGTCCCAATCATAGAGAACACTGCCCACGAAAGGGAGCTCA

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|86071569|gb|DR367326.1|DR367326
EST:     TGGAATCTTGTCTTGTGACGATGCTGAATCCGCAAGCCAAAGAATTCCGT                         ATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGAT
genomic: TGGAATCTTGTCTTGTGACGATGCTGAATCCGCAAGCCAAAGAATTCCGTgtaagctgta ... catttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGAT
EST: gi|19876846|gb|AU237677.1|AU237677
EST:     TGGAATCTTGTCTTGTGACGATGCTGAATCCGCAAGCCAAAGAATTCCGT                         ATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGAT
genomic: TGGAATCTTGTCTTGTGACGATGCTGAATCCGCAAGCCAAAGAATTCCGTgtaagctgta ... catttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagtagagttaggactttgcattttaatgtttcttcctgtccgacatttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGATGAACTTGTTGTCCCAATCATAGAGAACACAGCATATGAGAATGAACTAA
                      ttttaat  putative branch site (score: 3)
                     attttaatgtttctt  TA-rich tract