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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttcatgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcagATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTTGGGGTTGCCTTTCGTGCTAA

Basic information

species Vitis vinifera
transcript Vv04s0023g02940.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os10g36830.1 (Oryza sativa), 3'ss of exon 12
gtaagtttagaacacattttccctttatcttgtgcatatt-ctcaggatatatattttttcccct-gcaaatcagctttcatgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcagATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTTGGGGTTGCCTTTCGTGCTAA
                               ||||  ||| |||     |   |  | |     | |||||||     |           |     |||||||    ||  |      | | |||  ||  ||||||||| |||||| ||||||||||||  | ||| |||||||||||||  || ||  |  | ||||| || | 
----------------------------tgagtgctaattgctcgaagaaaccacctataattttagcaaatcttaccttgct------ccatgtcatcttctcactagtatggatggc-catgcatttccgcagATGGTTGCTGGACGATTTGTGAATGTTTACTCCACAAATGATTGGATTCTCGGTATCACTTTTCGAGCAAG

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 12
---gtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttc--atgaagtagtcccactatcttctatgcagcctta--tcacctcctgctatt--ttgcagATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTTGGGGTTGCCTTTCGTGCTAA
    |     |  ||    ||||  || |||  | |   ||      |   | |  |     |       | | |  || |   | |  |  |||||   |||||  |     ||||  ||||   ||  |  |  | ||||||||| |||||||||||||||||||  | ||| ||| |||| ||||  ||||| ||| | |||||||| | 
gtaatggcgatgaaatcatttttttctctattatctctgtaggaatggtgca-acgtaacaacaagaaacagtgaagttgctgttcattttatcccagcttcttccctcggcgcttaattcactcacttgtcctcatggcagATGGTTGCTGGAAGATTTGTGAATGTGTACTCCACAGATGACTGGATTCTTGGTGTTACTTTTCGTGCGAG
















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|110360866|gb|EC924300.1|EC924300
EST:     TTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA                         ATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTT
genomic: TTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttag ... tattttgcagATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTT
EST: gi|33401930|gb|CF207557.1|CF207557
EST:     TTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA                         ATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTT
genomic: TTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttag ... tattttgcagATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcagATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTTGGGGTTGCCTTTCGTGCTAA
                                     cctcctgctatttt  CT-rich tract
                                             tatttt  TA-rich tract