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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttccctttctcagagcatttctttcttatttatctattgagtactatgtgcaaaaaagggggaaaaatggctagaagcttcttgcttgcccatcaaagcttatggagcctttttaagttttttgatggctatttataaaaaatttatcagtatgtcatattcatttctcaatttgcagACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGAAAGTCCTCCTTGATTCTACTGGGGTACGCTTTGAAAAGGATTCATTTGG

Basic information

species Vitis vinifera
transcript Vv08s0007g00930.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g62810.2 (Oryza sativa), 3'ss of exon 3
gtaccttccctttctcagagcatttctttcttatttatctattgagtactatgtgcaaaaaagggggaaaaatggctagaagcttcttgcttgcccatcaaagcttatggagcctttttaagttttttgatggctatttataaaaaatttatcagtatgtcatattcatttctcaatttgc-agACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGAAAGTCCTCCTTGAT---TCTACTGGGGTACGCTTTGAAAAGGATTCATTTGG
                                                                                       |      | |    | |  |   ||| |  || ||       |  |||  | ||       |||  ||||  |    |  || ||  | |   | |||  |||| || |  || ||||||||||||||||||||||||||  | || |  ||| |   |||    ||| |||| | |   || ||||| |||  |     
--------------------------------------------------------------------------------------gtatactactagttgaacacacatagcgtactttaggacagcaagagctcataatttttgtgttactagta-atttcgtaaatgtcatactggaccagATGAAGGGGATGTCTATACATGGGGTTGGAAAGAATGTGTTCCAACAGGAAGGGTCATTTCTGACCAATCTTCTGGTGGAACTTTGGAAAAAGATGAAAG---

upper sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g38270.2 (Oryza sativa), 3'ss of exon 3
gtaccttccctttctcagagcatttctttcttatttatctattgagtactatgtgcaaaaaagggggaaaaatggctagaagcttcttgcttgcccatcaaagcttatggagcctttttaagttttttgatggctatttataaaaaatttatcagtatgtcatattcatttctcaatttgcagACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGAAAGTCCTCCTTGATTCTACTGGGGT--ACGCTTTGAAAAGGATTCATTTGG
                                                                                                        || || |     |  | |  ||||  ||   | |   | | || ||  || ||      ||| | |||       ||||  |||||||| |  ||||||||||||||||||||||| |||||  |||| |  ||| |    ||   | |||        ||| || |  |   | |     
-------------------------------------------------------------------------------------------------------gttgtgta-ttgatccatgcattttagtgaaaact-gcacataactttgcattacactg-attgaattccactcaagcagGTAAAGGTGATGTCTACACATGGGGTTGGAAAGAATGCGTTCCAACTGGAAGGGTCATTGCAGACCATTCTGCAACTGGGGCTATGGATTGTGATAAAAG--

upper sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 3
gtaccttccctttctcagagcatttctttcttatttatctattgagtactatgtgcaaaaaagggggaaaaatggctagaagcttcttgcttgcccatcaaagcttatggagcctttttaagttttttgatggctatttataaaaaatttatcagtatgtcatattcatttctcaatttgcagACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGAAAGTCCTCCTTGAT---TCTACTGGGGTACGCTTTGAAAAGGATTCATTTGG
                                                                                       |  ||  | ||| |||    |    |||     |||||     |    | | ||||  |   |||   | |   ||| |  |||  |      ||||  ||  ||| |  || ||||||||||||||||||||||||||  |||| |  ||  |    ||    ||| | |  | |  | | |||||||||  |     
--------------------------------------------------------------------------------------gtatttagcaatccaagtccctactccct-----agtttcgatctaaacaatcataattatggtattgttct--tataattgttttgctgga-acagATGAATATGATGTTTATACATGGGGTTGGAAAGAATGTGTTCCAACTGGAAGGGTTATTGGAGACCAGTCTTCAGTTGGAACCATGGAAAAGGATGAAAG---

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|161715939|gb|FC067136.1|FC067136
EST:     TCCAATAGTGAAGGCTGCTGCTGGTTGGGCACATTGTGTTTCACTTACAG                         ACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGA
genomic: TCCAATAGTGAAGGCTGCTGCTGGTTGGGCACATTGTGTTTCACTTACAGgtaccttccc ... caatttgcagACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGA
EST: gi|110373916|gb|EC938364.1|EC938364
EST:     GCTGGTTGGGCACATTGTGTTTCACTTACAG                         ACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGA
genomic: GCTGGTTGGGCACATTGTGTTTCACTTACAGgtaccttccc ... caatttgcagACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggctatttataaaaaatttatcagtatgtcatattcatttctcaatttgcagACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGAAAGTCCTCCTTGATTCTACTGGGGTACGCTTTGAAAAGGATTCATTTGG
 ttttgat  putative branch site (score: 4)
                                    ttcatttctc  putative PPT
      tatttataaaaaattt  TA-rich tract