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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctaccatgtactgttttttggtgcctcttaggcatgaaaagtttggtcccaaggcaaagaatttcttttgcatgttttagaggggctatacttttaaccggattttggaattattgaccatatcttcaaatgtgtttatgttaaccatttgtagATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGGCCTCGCCAAAAG

Basic information

species Vitis vinifera
transcript Vv04s0008g00520.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 3
gtgagttctaccatgtactgttttttggtgcctcttaggcatgaaaagtttggtcccaaggcaaagaatttcttttgcatgttttagaggggctatacttttaaccggattttggaattattgac-catatcttcaaatgtgtttatgttaaccattt--gtagATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGGCCTCGCCAAAAG
                                                                   | | |   || |     |  |  |  |     |  | | | | ||  | ||||   |    |||       | |  || ||||   | |||   ||| | |||  ||||||| ||||||||||||| | |||||| ||||| ||||||||||| ||||||
----------------------------------------------------------------gacaatacaaatgaaaaccgtgcattgatttcttatacatcagcaattcagcattaacaaggtgtattggtgtttatacttttgtttggcctttcaatagGTTGTTGTTCACAAGGATAGTCCAAGAGGTATACATTTTCGACGTGCAGGGCCTCGGCAAAAG

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 2
gtgagttctaccatgtactgttttttggtgcctcttaggcatgaaaagtttggtcccaaggcaaagaatttcttttgcatgttttagaggggctatacttttaaccggattttggaattattgaccatatcttcaaatgtgtttatgttaaccattt--gtagATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGGCCTCGCCAAAAG
                                                             ||||||| |        ||  |  |    | |   | | | | |   |||  | ||| |        |    |   | |  ||  |||   | |||   ||| | |||  ||||||| |||||||||||||   |||||| ||||| ||||||||||| ||||||
-----------------------------------------------------------aacaaagaagtaaga--agataatcaaacatgacctgaatctcagc--aattcagcaataacaaggtgcactggcgtttatactttcgtttggcttttcaatagGTTGTTGTTCACAAGGATAGTCCAAGAGGTGTACATTTTCGACGTGCAGGGCCTCGGCAAAAG
















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|161705826|gb|FC057103.1|FC057103
EST:     GCAGTACTTTGTTAATGTAGACGATTCTGTGGCTCAAAAG                         ATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGG
genomic: GCAGTACTTTGTTAATGTAGACGATTCTGTGGCTCAAAAGgtgagttcta ... ccatttgtagATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGG
EST: gi|161716176|gb|FC068064.1|FC068064
EST:     GCAGTACTTTGTTAATGTAGACGATTCTGTGGCTCAAAAG                         ATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGG
genomic: GCAGTACTTTGTTAATGTAGACGATTCTGTGGCTCAAAAGgtgagttcta ... ccatttgtagATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGG
EST: gi|110718348|gb|EE095077.1|EE095077
EST:     GCAGTACTTTGTTAATGTAGACGATTCTGTGGCTCAAAAG                         ATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGG
genomic: GCAGTACTTTGTTAATGTAGACGATTCTGTGGCTCAAAAGgtgagttcta ... ccatttgtagATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattttggaattattgaccatatcttcaaatgtgtttatgttaaccatttgtagATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGGCCTCGCCAAAAG
                                       tgttaac  putative branch site (score: 2)
                                   tttatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctaccatgtactgttttttggtgcctcttaggcatgaaaagtttggtcccaaggcaaagaatttcttttgcatgttttagaggggctatacttttaaccggattttggaattattgaccatatcttcaaatgtgtttatgttaaccatttgtagATCGTTTGTCACAAGAATAGTCCAAGAGGGACACATTTCCGACGGGCAGGGCCTCGCCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG