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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttttatttttccccttccttccctgtttctctctttcaattatcaatcatctgatttatattgtctggtatggattggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTTACATTTAGCAGCCCGCCAAAGGAGGTCTGATTGTGTTCATATCCTCCTA

Basic information

species Vitis vinifera
transcript Vv08s0007g00200.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G47310.1 (Glycine max), 3'ss of exon 4
-----gtaaggttttatttttccccttccttccctgtttctctctttcaattatcaatc-------------atctgatttatattgtctggtatggattggag--agcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTTACATTTAGCAGCCCGCCAAAGGAGGTCTGATTGTGTTCATATCCTCCTA
       |   || | | | || |  | | | |              | | |||| |||                ||| |  |  ||     | |  | ||||     |||||||||| |||||||||| || |||||||||||||| || || || ||  | ||| | ||||| ||||| ||  || | || ||| |||||  ||| |||
gttagacacaattctctctctctctcttcatacacacacaggcacacccaatatcgatccaagcatatacaagaatgactggtgatgctaattgttcaatggaattgtcagGGGATTTGCAAGATTTGTCAACATAAGAGATGGAAACGGTGCCACCCCTCTGCATCTTGCAGCTCGCCATAGATGGCCGGAATGTCTTCATGCCCTTCTA

upper sequence: Vv08s0007g00200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G38610.1 (Glycine max), 3'ss of exon 4
----gtaaggttttatttttccccttccttccctgt---ttctctctttcaattatcaatc-------------atctgatttatattgtctggt-atggattggag--agcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTTACATTTAGCAGCCCGCCAAAGGAGGTCTGATTGTGTTCATATCCTCCTA
    |  |  || | | |||| |  ||  ||| |         |     ||| ||||||||              | ||| |  |  ||  |  |  |  | ||||     |||||||||| |||||||||| || |||||||||||||| || || || ||  | ||| | ||||| ||||| ||  |||| || ||| |||||  |||  ||
gttagacacattctctctttctctctctctccatacacacatgcatgcccaaatatcaatccaagcatatgctggtatgaatggtgatgcttaattgttcaatggaattgtcagGGGATTTGCAAGATTTGTCAACATAAGAGATGGAAACGGTGCCACCCCTCTGCATCTTGCAGCTCGCCATAGACGGTCGGAATGTCTTCATGCCCTTTTA
















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|110700513|gb|EE078637.1|EE078637
EST:     TCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTG                         GGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
genomic: TCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTGgtaaggtttt ... tggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
EST: gi|18458145|gb|BM436423.1|BM436423
EST:     CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTG                         GGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
genomic: CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTGgtaaggtttt ... tggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
EST: gi|110413263|gb|EC979042.1|EC979042
EST:     CTCCATGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCGTG                         GGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
genomic: CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTGgtaaggtttt ... tggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
EST: gi|27583732|gb|CB006427.1|CB006427
EST:     CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTG                         GGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
genomic: CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTGgtaaggtttt ... tggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
EST: gi|161721280|gb|FC070033.1|FC070033
EST:     CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTG                         GGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
genomic: CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTGgtaaggtttt ... tggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
EST: gi|110412439|gb|EC978189.1|EC978189
EST:     CTCCATGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCGTG                         GGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
genomic: CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTGgtaaggtttt ... tggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
EST: gi|30125105|gb|CB910444.1|CB910444
EST:     CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTG                         GGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT
genomic: CTCCAAGCTATTCTTTCTGCTGCCCATTCCACCCCTATTGCAGTTTCTTGgtaaggtttt ... tggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttcaattatcaatcatctgatttatattgtctggtatggattggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTTACATTTAGCAGCCCGCCAAAGGAGGTCTGATTGTGTTCATATCCTCCTA
                  atctgat  putative branch site (score: 4)
                  atctgatttatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggttttatttttccccttccttccctgtttctctctttcaattatcaatcatctgatttatattgtctggtatggattggagagcagGGGATTTTCAAGATTTGTGAATATAAGAGATGGAAAGGGAGCAACTCCGTTACATTTAGCAGCCCGCCAAAGGAGGTCTGATTGTGTTCATATCCTCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG