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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgttttcttgctgtctatagtactttactctaatttcggcaagagatgggaattctggacttaactctaatttcctcatttgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCATTGGAGGAAGCAGGAGTGAGAGGAATACTTGGT

Basic information

species Vitis vinifera
transcript Vv01s0150g00320.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G12880.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatctgttttcttgctgtctatagtactttactctaatttcggcaagagatgggaattctggacttaactctaatttcctcatttgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCATTGGAGGAAGCAGGAGTGAGAGGAATACTTGGT
      || || ||      |  |  |   | ||||    |    |  |  ||  | | ||    |||| |     ||    || | ||| |||||| ||||||||  ||||||||||||||    ||||||| | |||||||||  | || ||||||||||| | |||||||||| | 
------gtctttttttgaattgaaaaatcatcctctgtact----atcatttgtaattgctcatgttaatttg---ttgtgtatattattatcagGGAGGATGGGAAGATGATGAGACTGTTCTTGAAGCTGCTTCTCGTGAAGCCATTGAAGAAGCAGGAGTTAAAGGAATACTTAGA
















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|110379149|gb|EC944326.1|EC944326
EST:     TTGTCCTCATGATTTCTTCACCAAATCGCCATGACCTTGTGTTTCCTAAG                         GGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA
genomic: TTGTCCTCATGATTTCTTCACCAAATCGCCATGACCTTGTGTTTCCTAAGgtatctgttt ... tgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA
EST: gi|110428236|gb|EC994702.1|EC994702
EST:     TTGTCCTCATGATTTCTTCACCAAATCGTCATGACCTTGTGTTTCCTAAG                         GGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA
genomic: TTGTCCTCATGATTTCTTCACCAAATCGCCATGACCTTGTGTTTCCTAAGgtatctgttt ... tgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA
EST: gi|110385476|gb|EC950008.1|EC950008
EST:     TTGTCCTCATGATTTCTTCACCAAATCGCCATGACCTTGTGTTTCCTAAG                         GGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA
genomic: TTGTCCTCATGATTTCTTCACCAAATCGCCATGACCTTGTGTTTCCTAAGgtatctgttt ... tgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA
EST: gi|110362042|gb|EC925549.1|EC925549
EST:     TTGTCCTCATGATTTCTTCACCAAATCGCCATGACCTTGTGTTTCCTAAG                         GGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA
genomic: TTGTCCTCATGATTTCTTCACCAAATCGCCATGACCTTGTGTTTCCTAAGgtatctgttt ... tgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA
EST: gi|351014144|gb|FQ434733.1|FQ434733
EST:     TTGTCCTCATGATTTCTTCACCAAATCGCCATGACCTTGTGTTTCCTAAG                         GGTGGATGGGAGAATTATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA
genomic: TTGTCCTCATGATTTCTTCACCAAATCGCCATGACCTTGTGTTTCCTAAGgtatctgttt ... tgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggcaagagatgggaattctggacttaactctaatttcctcatttgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCATTGGAGGAAGCAGGAGTGAGAGGAATACTTGGT
                                   tttcctcattt  CT-rich tract
                              tctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgttttcttgctgtctatagtactttactctaatttcggcaagagatgggaattctggacttaactctaatttcctcatttgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCATTGGAGGAAGCAGGAGTGAGAGGAATACTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA