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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcagGCATACGCTGAATCAGATGCATTTTTCTGTTTTGTTGAATTGATGAGTGGGTTTCGAGATAATTTCTGTCAACAACTAGATAACAGTGTTGTGGGTATAC

Basic information

species Arabidopsis thaliana
transcript AT4G13730.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 6
gtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcagGCATACGCTGAATCAGATGCATTTTTCTGTTTTGTTGAATTGATGAGTGGGTTTCGAGATAATTTCTGTCAACAACTAGATAACAGTGTTGTGGGTATAC
                              |   |   | | |  | | | | || | | |  |      |  ||  | |||   |     |  | | |||  |    | |||| |||| |  | | |||   | ||||||| |  |||||| |||||||||| || |||||||||||  |  ||||||||||||||||||| ||   ||||||||| || || ||||||||||| || |
------------------------------taggtggcaatatggtggaata-atgtagattcataatact--gtcatgtttaattg---tattattggttgac----tctgctcaacagttccctattattatttgcagGCCTCTGCTGAAGCAGATGCATTCTTTTGTTTTGTTGAGCTATTGAGTGGGTTTCGAGATAACTTTGTTCAACAACTCGACAATAGTGTTGTGGGAATCC

upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 6
gtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcagGCATACGCTGAATCAGATGCATTTTTCTGTTTTGTTGAATTGATGAGTGGGTTTCGAGATAATTTCTGTCAACAACTAGATAACAGTGTTGTGGGTATAC
                             |  |    || | ||  |  | | ||| |||  |    ||||   ||  | |||        |  | | |||  |    | |||| |||| |  | | |||   | ||||||| |  |||||| |||||||||| || |||||||||||  |  ||||||||||||||||||| ||   ||| ||||| || || ||||||||||| || |
----------------------------atggtggagtaatgtagattcata-atactgtcatgttcctttgtatttctattg-------tattattggttaac----tctgctcaacagttccctattataatttgcagGCCTTTGCTGAAGCAGATGCATTCTTTTGTTTTGTTGAGCTATTGAGTGGGTTTCGAGATAACTTTGTTCAGCAACTCGACAATAGTGTTGTGGGAATCC

upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcagGCATACGCTGAATCAGATGCATTTTTCTGTTTTGTTGAATTGATGAGTGGGTTTCGAGATAATTTCTGTCAACAACTAGATAACAGTGTTGTGGGTATAC
                         |   ||| ||||| |  |   |   |||    | | ||| ||    |   ||||          |  |   | |||   ||   ||| | | | |   | ||| ||||||||||||| |  || ||| | ||  ||||||| |||||||| || ||  | || || ||  | ||| |||||||||| ||||| |||||||||||||| ||||| |
-------------------------ctgatttcttcttgtgatgactaatcac----tatactatctagcctttatctt----------atgcttttggtttcactttgttgatcatctcccac-tttcaagttatgcagGCTTCTGCAGAAGCGGACACATTTTTTTGTTTTGTCGAGTTATTAAGCGGATTCAGGGATCATTTCTGTCAGCAACTCGATAACAGTGTTGTTGGTATCC

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|86076731|gb|DR372488.1|DR372488
EST:     TGTCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCA                         GCATACGCTGAATCAGATGCATTTTTCT
genomic: TGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtactt ... agttatgcagGCATACGCTGAATCAGATGCATTTTTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcagGCATACGCTGAATCAGATGCATTTTTCTGTTTTGTTGAATTGATGAGTGGGTTTCGAGATAATTTCTGTCAACAACTAGATAACAGTGTTGTGGGTATAC
                          gcttaac  putative branch site (score: 3)
                                       attttaagttat  TA-rich tract