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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttacaattcctaaatttcttttaccatagatgtcaatatagtgtttgaagatggttaatgtcttcgccttatgcatcccacaacatatatgtgttgctcttgcagGACTGATCCCCATTTACCTGAGATGCCAATCGTTTATGCAAGTGATGCCTTCTTAAAATTGACAG

Basic information

species Vitis vinifera
transcript Vv01s0026g01590.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g01590.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G04920.1 (Glycine max), 3'ss of exon 2
gtgagtttttacaa-ttcctaaatttcttttaccatagatgtcaa--tatagtgtttgaagatggttaatgtcttcgccttatgcatcccacaacatatatgtgttgctcttgcagGACTGATCCCCATTTACCTGAGATGCCAATCGTTTATGCAAGTGATGCCTTCTTAAAATTGACAG
||||||| ||  || |  |||  ||| || |  | |       |   |||  | |  | |||   ||||| | ||     ||||  |             || ||| | ||||||| ||| |||| | |||| | || ||||| || |||||||| |||||||||||||| ||||||||||
gtgagttgttggaaatgtctagttttgttattacttttccacaagcttatgctttccgcagacccttaatttgttgcttgtatgattt------------tgagtttc-cttgcagAACTAATCCGCGTTTATCAGACATGCCTATTGTTTATGCTAGTGATGCCTTCTTGAAATTGACAG
















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|161720305|gb|FC071158.1|FC071158
EST:     GGTGCTTCCTTAATTATATCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGATCCCCATTTACCTGAGATGCCAATCGCTTATGCAAGTGATGCCTT
genomic: GGTGCTTCCTTAATTATATCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttttt ... gctcttgcagGACTGATCCCCATTTACCTGAGATGCCAATCGTTTATGCAAGTGATGCCTT
EST: gi|110427355|gb|EC993791.1|EC993791
EST:     GGTGCTTCCTTAATTATATCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGATCCCCATTTACCTGAGATGCCAATCGTTTATGCAAGTGATGCCTT
genomic: GGTGCTTCCTTAATTATATCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttttt ... gctcttgcagGACTGATCCCCATTTACCTGAGATGCCAATCGTTTATGCAAGTGATGCCTT
EST: gi|110379815|gb|EC945035.1|EC945035
EST:     GGTGCTTCCTTAATTATATCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGATCCCCATTTACCTGAGATGCCAATCGCTTATGCAAGTGATGCCTT
genomic: GGTGCTTCCTTAATTATATCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttttt ... gctcttgcagGACTGATCCCCATTTACCTGAGATGCCAATCGTTTATGCAAGTGATGCCTT
EST: gi|71859761|gb|DT008816.1|DT008816
EST:     GGTGCTTCCTTAATTATATCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGATCCCCATTTACCTGAGATGCCAATCGCTTATGCAAGTGATGCCTT
genomic: GGTGCTTCCTTAATTATATCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttttt ... gctcttgcagGACTGATCCCCATTTACCTGAGATGCCAATCGTTTATGCAAGTGATGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttaatgtcttcgccttatgcatcccacaacatatatgtgttgctcttgcagGACTGATCCCCATTTACCTGAGATGCCAATCGTTTATGCAAGTGATGCCTTCTTAAAATTGACAG
  ggttaat  putative branch site (score: 4)
                                           ttgctctt  putative PPT
                               aacatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttttacaattcctaaatttcttttaccatagatgtcaatatagtgtttgaagatggttaatgtcttcgccttatgcatcccacaacatatatgtgttgctcttgcagGACTGATCCCCATTTACCTGAGATGCCAATCGTTTATGCAAGTGATGCCTTCTTAAAATTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG