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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtgcttaaaattcccccttattctgtatcttatttttcaaactaattctgtgacatttccgtacagtcacttccttacatgattaaaatatttgcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTTCCTGTTGTGCAACCCTACCGCAAATTAGGAAGGCATCTT

Basic information

species Vitis vinifera
transcript Vv01s0010g00690.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g00690.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S256_41V6.1 (Physcomitrella patens), 3'ss of exon 15
ttggtgcttaaaattcccccttattctgtatcttatttttcaaactaattctgtgacatttccgt--acagtcacttccttacatgattaaaatattt---gcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTTCCTGTTGTGCAACCCTACCGCAAATTAGGAAGGCATCTT
     ||||||  | |    ||    || || | | |  |  |  |   || |      ||| ||  | ||  | |   | |   ||||  |   |||   |||| | || || ||  |     |  | |||  ||||| ||||||| | |||||||| ||||||||||| ||||||||    || || ||| | 
----agcttaacgtactattttcaagtg-atttcactgctagatttctctcagatttcattcagtctaaaggaattgagtgaatcgattggatgtttttgagcagATCATTGCCTCAAATGGAGAAACTGTGAAGTGGACTACTCCTCTTGGACTTCCCGTTGTGCAACCTTACCGCAAGCCTGGCAGACATTTG

upper sequence: Vv01s0010g00690.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ32457 (Selaginella moellendorffii), 3'ss of exon 14
ttggtgcttaaaattcccccttattctgtatcttatttttcaaactaattctgtgacatttccgtacagtcacttccttacatgattaaaatatttgcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTTCCTGTTGTGCAACCCTACCGCAAATTAGGAAGGCATCTT
                                                |      |  |||  ||  ||  ||| |  |    || |   |   |||||||| || ||    ||   | |  | ||| ||||||  |||||||||||||||||||| |||||||| |||||||     || || ||| | 
-----------------------------------------------gtatctccaggtttttgttaagagactcctct---cgagttccactgttgcagGTAATTGCCAACGACGGTGACTCCGTGAGGTGGATCACTCCTTTGGGACTTCCTGTCGTGCAACCATACCGCAGGCCCGGGAGACATGTG

upper sequence: Vv01s0010g00690.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ20792 (Selaginella moellendorffii), 3'ss of exon 14
ttggtgcttaaaattcccccttattctgtatcttatttttcaaactaattctgtgacatttccgtacagtcacttccttacatgattaaaatatttgcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTTCCTGTTGTGCAACCCTACCGCAAATTAGGAAGGCATCTT
                                                |      |  |||  ||  ||     ||||  |  || |   |   |||||||| || ||    ||     |  | ||| ||||||  |||||||||||||||||||| |||||||| |||||||     || || ||| | 
-----------------------------------------------gtatctccaggtttttgttaagaggactcct--ctcgagttccactgttgcagGTAATTGCCAACGACGGCGACTCCGTGAGGTGGATCACTCCTTTGGGACTTCCTGTCGTGCAACCATACCGCAGGCCCGGGAGACATGTG

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|27581209|gb|CB003904.1|CB003904
EST:     TGTTTGAAGCTGCACGTAGTATCATGAGCTGGCTTGGTGACTGTGCAAAG                         GTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTT
genomic: TGTTTGAAGCTGCACGTAGTATCATGAGCTGGCTTGGTGACTGTGCAAAGgtgagtttaa ... atatttgcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTT
EST: gi|27581087|gb|CB003782.1|CB003782
EST:     TGTTTGAAGCTGCACGTAGTATCATGAGCTGGCTTGGTGACTGTGCAAAG                         GTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTT
genomic: TGTTTGAAGCTGCACGTAGTATCATGAGCTGGCTTGGTGACTGTGCAAAGgtgagtttaa ... atatttgcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTT
EST: gi|27579010|gb|CB001705.1|CB001705
EST:     TGTTTGAAGCTGCACGTAGTATCATGAGCTGGCTTGGTGACTGTGCAAAG                         GTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTT
genomic: TGTTTGAAGCTGCACGTAGTATCATGAGCTGGCTTGGTGACTGTGCAAAGgtgagtttaa ... atatttgcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattctgtgacatttccgtacagtcacttccttacatgattaaaatatttgcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTTCCTGTTGTGCAACCCTACCGCAAATTAGGAAGGCATCTT
                             tccttac  putative branch site (score: 2)
                                ttacatgattaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtgcttaaaattcccccttattctgtatcttatttttcaaactaattctgtgacatttccgtacagtcacttccttacatgattaaaatatttgcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTTCCTGTTGTGCAACCCTACCGCAAATTAGGAAGGCATCTT

- - - cttaaaa
- - - - - - - -ccccctt
- - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - catttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatt