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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgctctatgcagaactctgtttctaatgtccttttcgttgttacttcatcttaattgatgtactaatgaaatgtattgtttagCTATATGTTGGGATCAGTGGTTTCCTGAGGCAGCTCGAGCTATGGTTCTACAGGGTGCTGAAATACTGTTTTATCCCACTGCTATTGGTTCTGAACCTCA

Basic information

species Arabidopsis thaliana
transcript AT2G27450.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 6
---------------------------------gtaagatgctctatgcagaactctgtttctaatgtccttttcgttgttacttc-atcttaattgatgtactaatgaaatgtattgtttagCTATATGTTGGGATCAGTGGTTTCCTGAGGCAGCTCGAGCTATGGTTCTACAGGGTGCTGAAATACTGTTTTATCCCACTGCTATTGGTTCTGAACCTCA
                                  | |  |  | || | | |       |  || |      | ||   | |  || ||| ||| |    |   |      |  |   | |||  || || ||||||||||||||||| |||   ||  |||| ||||  || | ||| |||||||||||||||||||||||||| ||||| || ||||| ||
gtaagttatttatgttctgcagtgttataggctcttatttagtttaagtacagtagcactaatagtaattaatacgacttaatatcgatcataactctaatgtcatcattcttgaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTCTGGGGGCTGAAATACTGTTTTATCCCACTGCAATTGGATCCGAACCCCA

upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G31100.2 (Glycine max), 3'ss of exon 7
----gtaagatgctctatgcagaactctgtttctaatgtccttttcg---------ttgttacttcatcttaattgatgtactaatgaaatgtattgtttagCTATATGTTGGGATCAGTGGTTTCCTGAGGCAGCTCGAGCTATGGTTCTACAGGGTGCTGAAATACTGTTTTATCCCACTGCTATTGGTTCTGAACCTCA
       | |  |  | || | | ||   ||| | || |   |  |           ||     | |||||  ||  | |  |||| || | |  |||  |||||| || |||||||||||||||||||||||||| ||||| ||||| || || |||||||| || || |||||||| ||||||||||| |||||||||||
agcaaccaaacacattttgga-agctgcatttttcatctttctcccagataggaaactgaagaattatcttttttactattttaattaattttcatgtc-agCTATTTGCTGGGATCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTCAAGGTGCTGAGATTCTATTTTATCCTACTGCTATTGGGTCTGAACCTCA

upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 6
gtaag-atgctctatgcagaa-ctctgtttctaatgtccttttc--gttgttacttcatcttaattg--------atgtactaatgaaatgtattgtttagCTATATGTTGGGATCAGTGGTTTCCTGAGGCAGCTCGAGCTATGGTTCTACAGGGTGCTGAAATACTGTTTTATCCCACTGCTATTGGTTCTGAACCTCA
| ||  || | |  |   ||| ||   ||| | || |   || |   | |  |  | |  ||||           || |  |||| || | |  |||  |||||| || ||||| |||||||||||||||||||| ||||| ||||| || || |||||||| ||  | |||||||||||||||||||| |||||||||||
gcaaccatacacattttggaagctgcatttttcatctttcttccagataggaaactgaagttaaccaaaaaaaaaatattttaattaattttcatgtc-agCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTCAAGGTGCTGAGATTTTATTTTATCCCACTGCTATTGGGTCTGAACCTCA

upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 6
------gtaagatgctctatgcagaactctgtttctaatgtccttttcgtt-----gttacttcatcttaattga-tgtactaatgaaatgtattgtttagCTATATGTTGGGATCAGTGGTTTCCTGAGGCAGCTCGAGCTATGGTTCTACAGGGTGCTGAAATACTGTTTTATCCCACTGCTATTGGTTCTGAACCTCA
         | |  |  | || |     |  |||  | | | |||   | |       |     || ||  || | | |  |||| || | |  |||  |||||| || |||||||||||||||||||||||||| ||||| ||||| || || |||||||| || || |||||||| || |||||||| |||||||||||
caagcaaccaaacacattttggaagctgcatttttcatttttcttccagataggaaactgaacaattttttttaactattttaattaattttcatgtc-agCTATTTGCTGGGATCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTCAAGGTGCTGAGATTCTATTTTATCCTACCGCTATTGGGTCTGAACCTCA

upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 6
---gtaagatgctctatgcagaactctgtttctaatgtccttttcgttgttacttcatcttaa----ttgatgtactaatgaaatgtattgt----ttagCTATATGTTGGGATCAGTGGTTTCCTGAGGCAGCTCGAGCTATGGTTCTACAGGGTGCTGAAATACTGTTTTATCCCACTGCTATTGGTTCTGAACCTCA
       | |   | ||||| |  |   | | | |  | |    | | |   |   || || |    ||| |  || | |  | |||||| |    | ||| ||||| ||||||||||||||||| ||||||||||||||||||||||| || ||||| || || || || || || ||||||||||| |||||||||||
ggctctggctttacaatgcaaacatgaatgtgttaatttcacagcttagaagcaggatttttagtgtttgcttcaccatttcattgtattttaatgtcagCAATATGCTGGGATCAGTGGTTTCCAGAGGCAGCTCGAGCTATGGTTCTTCAAGGTGCAGAGATTCTTTTGTACCCTACTGCTATTGGGTCTGAACCTCA

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|125216416|gb|EL230499.1|EL230499
EST:     GTTTTCCAGACGAAGTTTGCTAAAATTGGAGTGG                         CTATATGTTGGGAT
genomic: GTTTTCCAGACGAAGTTTGCTAAAATTGGAGTGGgtaagatgct ... tattgtttagCTATATGTTGGGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttcgttgttacttcatcttaattgatgtactaatgaaatgtattgtttagCTATATGTTGGGATCAGTGGTTTCCTGAGGCAGCTCGAGCTATGGTTCTACAGGGTGCTGAAATACTGTTTTATCCCACTGCTATTGGTTCTGAACCTCA
                                tactaat  putative branch site (score: 1)
                                   taatgaaatgtatt  TA-rich tract