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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctatatagcttgagcatttattggttttcatctgatgtgctttatattttgtttctgaacaccacttgtttgtgtcaaattcagCTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGGTTGACGTTGAACGTGGTAGAACTGTTCCTAATTGGCGTCCCCGCAGACT

Basic information

species Vitis vinifera
transcript Vv04s0023g01580.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os10g02630.1 (Oryza sativa), 3'ss of exon 7
------------gtttgctatatagcttgagca----tttattggttttcatc--tgatgtgctttatattttgtttctgaacaccacttgtttgtgtcaaattcagCTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGGTTGACGTTGAACGTGGTAGAACTGTTCCTAATTGGCGTCCCCGCAGACT
            ||||   ||||  | |    |       ||| |   |||||  |||||   |   | | ||   | |   | |  ||  | |||||      ||| |||||| || ||||| ||||| || ||  | || || || |||||||| ||||| || || ||||||||||||||||| |||||||||||| | ||| |
gtaaagcttctggtttagcatatctcctctatacagtccaatttggcgtcatcactgatgaagtgc-tgtcttacatttt--ctctgctaatatgtgttct-cgcagATGCTTACAAGCAAGCAGATGGGAGAAAAGTGGACAATAGGAGGGTGCTAGTTGATGTGGAGCGTGGTAGAACTGTTCCAAATTGGCGTCCCAGGAGATT

upper sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G38120.1 (Glycine max), 3'ss of exon 7
gtttgctatatagcttgagcatttattggtt--ttcatctgatgt-gctttatattttgtttctgaacaccacttgtttgtgtcaaattcagCTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGGTTGACGTTGAACGTGGTAGAACTGTTCCTAATTGGCGTCCCCGCAGACT
              |||| || | |||  ||  ||  | |  | |  || |   ||||  |||   ||| |  | |||||| |      ||||||||||||||||||||||||| |||||  |||||   ||||||||||| || || ||||| ||||| || |||||||| |||||| | || ||| | ||
-------------gttga-cactgattacttaatttgtttattatcactatggcttttaattc---acatctttggtttgttttg----cagCTGCTTATAAACAAGCTGATGGTAGGAAAATTGATGGTAGAAGGGTGCTTGTGGATGTTGAGCGTGGGAGGACTGTTCCAAATTGGAGACCTCGCCGCCT

upper sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 7
gtttgctatatagcttgagcatttattggttttcatctgatgtgctttatattttgtttctgaacaccacttgtttgtgtcaaatt--cagCTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGGTTGACGTTGAACGTGGTAGAACTGTTCCTAATTGGCGTCCCCGCAGACT
              ||||| | | ||||   || || || | |  | |  | |  |  | | ||   ||| | |||| || || ||  ||||||||||||||||||||||||| |||||  |||||   ||||||||||| || || ||||| ||||| || |||||||| |||||| | |||||  |  |
-------------gttgag-actgattg--cttaatttgtt-tattat-cactacggcttttaat-tcacatctttg-gttaattttgcagCTGCTTATAAACAAGCTGATGGTAGGAAAATTGATGGTAGAAGGGTGCTTGTGGATGTTGAGCGTGGGAGGACTGTTCCAAATTGGAGACCCCGTCGCTT

upper sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S42_265V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------gtttgctatata-gcttgagcatttat-tggttttcatctgatgtgctttatattttgtttctgaacaccacttgtttgtgtcaaattcagCTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGGTTGACGTTGAACGTGGTAGAACTGTTCCTAATTGGCGTCCCCGCAGACT
                                                || |  |   | |||  |||  ||        || ||    |||   || |  |   ||| ||||  | | |  | |||||    | ||||||||||||| |||||||||||  | ||| | || ||  |  | || || |||||||||||||| ||| | ||||| |||||||||||||| || ||| |
gtatgtgaagttcttcgcttgtcttgtccttatccatatcatacatttttggtgaggcatgctgcagcgcttgcacaaacttgatagattgttgcttttggtagctttttgaa-gcta-tcatctgtgt-gtgtgcagCTGCTTATAAGCAAGCTGATGGTCGTAAGATAGACAATCGGCGAGTCCTTGTTGACGTTGAACGAGGTCGCACTGTACCTAATTGGCGTCCTCGAAGATT

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|37184757|gb|CF604111.1|CF604111
EST:     ACCTAGAGGTTATGCTTTCATTGAATATATGCATACACGGGATATGAAAG                         CTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGG
genomic: ACCTAGAGGTTATGCTTTCATTGAATATATGCATACACGGGATATGAAAGgtttgctata ... tcaaattcagCTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGG
EST: gi|56409078|gb|CX017330.1|CX017330
EST:     ACCTAGAGGTTATGCTTTCATTGAATATATGCATACACGGGATATGAAAG                         CTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGG
genomic: ACCTAGAGGTTATGCTTTCATTGAATATATGCATACACGGGATATGAAAGgtttgctata ... tcaaattcagCTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgatgtgctttatattttgtttctgaacaccacttgtttgtgtcaaattcagCTGCTTATAAACAAGCTGATGGAAGGAAGCTTGATAACAGAAGGGTGCTGGTTGACGTTGAACGTGGTAGAACTGTTCCTAATTGGCGTCCCCGCAGACT
 atctgat  putative branch site (score: 4)
           tttatattttgtttct  TA-rich tract