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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgatgttgatgactggaatttcatcacttcgtggattggttacaagatttaaggctttctaatagttgttgcttaattggacttcctctattgttccagGCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTGTTTACAACTTCTGGGATGCTTTTTCTGGAAGTAAGCTTGGTGGCCTTTT

Basic information

species Vitis vinifera
transcript Vv14s0030g00750.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G05010.1 (Arabidopsis thaliana), 3'ss of exon 1
ctgatgttgatgactggaattt-catcacttcgtgg---attggttacaagatttaaggctttctaatagttgttgcttaattggacttcctctattgttccagGCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTGTTTACAACTTCTGGGATGCTTTTTCTGGAAGTAAGCTTGGTGGCCTTTT
 |  |||||||  || |  |        |||    |   ||   ||||  |||||| | ||| ||     ||     || | |  ||||  |  ||   |  ||||||||||||||||||| | ||| | |||    |||||| | ||| | ||||| ||||| ||||| ||| | |||||||||||||||||||| |||||| 
-tagtgttgatttcttggttagatgctgcttaacaggaaatgttttacctgattta-gtcttactccagatttcgttttgaatttactt--ttcatgagtttagGCATGGGAATGCACTCCGGGGAAAGAAGTTATTTGGAATTTGTTAACTTTGTTCACAACATCTGGAATGTTGTTTCTGGAAGTAAGCTTGGTAGCCTTTC

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G27210.1 (Arabidopsis thaliana), 3'ss of exon 1
--ctgatgttgatgactggaatttcatcacttcgtggattggttacaagatttaaggctttctaatagttgttgcttaattggacttcctctattgttccagGCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTGTTTACAACTTCTGGGATGCTTTTTCTGGAAGTAAGCTTGGTGGCCTTTT
       ||| |||      |  |  | |          |  |||||   |   ||| |  ||  |  ||  || |||    |  | |   | |  ||  |||  |||||||| ||||||| ||| | ||| |  |||||| | ||| | ||||| ||||| ||||| ||| | ||||||||||||||||||||||| ||| 
aatcacggtttatggaaatgagctagtgatccttgtatctatttacatattcctaggttagcttttgatt--tgattatcatgtttccggatttgattatagGGTTGGGAATGTACTCCTGGGAAAGAAGTTGTTTGGAATCTGTTAACTTTGTTCACAACATCTGGAATGTTGTTTCTGGAAGTAAGCTTGGTGGCTTTTC
















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|22012612|gb|BQ797646.1|BQ797646
EST:     ATCTCGC-TGGTGCT-CCTTCAG                         GCAT-GGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTG
genomic: ATCTCGCTTGGTGCTCCCTTCAGgtttgtgttt ... attgttccagGCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTG
EST: gi|110366928|gb|EC930848.1|EC930848
EST:     GCTGTCTTTGGCTCGTTAGTTTGCTCAATCTCGCTTGGTGCTCCCTTCAG                         GCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTG
genomic: GCTGTCTTTGGCTCGTTAGTTTGCTCAATCTCGCTTGGTGCTCCCTTCAGgtttgtgttt ... attgttccagGCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTG
EST: gi|110380174|gb|EC945419.1|EC945419
EST:     GCTGTCTTTGGCTCGTTAGTTTGCTCAATCTCGCTTGGTGCTCCCTTCAG                         GCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTG
genomic: GCTGTCTTTGGCTCGTTAGTTTGCTCAATCTCGCTTGGTGCTCCCTTCAGgtttgtgttt ... attgttccagGCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTG
EST: gi|37185993|gb|CF605346.1|CF605346
EST:     GCTGTCTTTGGCTCGTTAGTTTGCTCAATCTCGCTTGGTGCTCCCTTCAG                         GCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTG
genomic: GCTGTCTTTGGCTCGTTAGTTTGCTCAATCTCGCTTGGTGCTCCCTTCAGgtttgtgttt ... attgttccagGCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttaaggctttctaatagttgttgcttaattggacttcctctattgttccagGCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTGTTTACAACTTCTGGGATGCTTTTTCTGGAAGTAAGCTTGGTGGCCTTTT
                                     cttcctctattgttcc  CT-rich tract
           tttctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgatgttgatgactggaatttcatcacttcgtggattggttacaagatttaaggctttctaatagttgttgcttaattggacttcctctattgttccagGCATGGGAATGCACTCCTGAGAAGGCAGTAGCATGGAATGTCTTATCGTTGTTTACAACTTCTGGGATGCTTTTTCTGGAAGTAAGCTTGGTGGCCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
ctgatgt
- - - - - tgactgg
- - - - - - - - - - - catcact
- - - - - - - - - - - - - - - - -ggattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct