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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgtttaatctttgagtgcatgatacacatgttcttcatctgatcatcttcagttttgagaattttattgaagttagtggcatgtgtctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTACGGGCTTACCACCACACTGCCCAAACGAAGGCAGATAAGAAGCATCTCT

Basic information

species Vitis vinifera
transcript Vv15s0021g02230.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 14
gttctgtttaatctttgagtgcatgatacacatgttcttcatctgatcatcttcagttttgagaattttattgaagttagtggcatgtg--tctgctg-cagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTACGGGCTTACCACCACACTGCCCAAACGAAGGCAGATAAGAAGCATCTCT
                  ||||    |||| |  |  ||||||     |  |     |||     || | ||  | |     |  | |    ||| |  ||||||||||| || || ||||| || || || || ||||| || || |||||| | || |||||||||||||| ||||| ||||| |||||||||||    |
------------------gtgcgacctacaaacctatttcatcaataaaaatctgtcttttgttcttatcttataatccaacgtttatcatcctgttatcagGTGCTTGCAGTAAACGCTGCTAAGGATGCAACCGAATTGGTAGCTAAACTAAGAGCGTACCACCACACTGCACAAACCAAGGCTGATAAGAAGCACTATT

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S39_248V6.1 (Physcomitrella patens), 3'ss of exon 14
-------gttctgtttaa--tctttgagtgcatga-tacacatgttcttcatctgatcatcttcagttttgagaattttattgaagttagtggcatgtgtctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTACGGGCTTACCACCACACTGCCCAAACGAAGGCAGATAAGAAGCATCTCT
       ||   |  | |  |  || |  |  | | || |    ||| ||  ||   | |   || | |    || ||| |  |  |  | ||             ||||| |||||||||||||| || || ||||| || || || ||||| ||||| || || |||||||||| | | ||||||||||| || ||| |||| ||  
agttgatgtagggcctgaagttgttaatcgtgtcagtatatggattcatctgctatccctgcacaatct----aagtttttgaacatgggcggggaacaa-----acagGTTCTTGCTGTGAATGCAGCGAAGGACGCAACAGAGTTGGTTGCTAAACTTCGTGCATACCACCACAGTTCTCAAACGAAGGCTGACAAGCAGCACCTTG
















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|110699451|gb|EE076471.1|EE076471
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|110702474|gb|EE081230.1|EE081230
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|26264285|gb|CA815348.1|CA815348
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GCGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|351037610|gb|FQ462593.1|FQ462593
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCAAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|110701345|gb|EE078813.1|EE078813
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|351017726|gb|FQ436079.1|FQ436079
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGGATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|34545337|gb|CF513569.1|CF513569
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|34545258|gb|CF513490.1|CF513490
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|32272417|gb|CD721576.1|CD721576
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|110688105|gb|EE066273.1|EE066273
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCAAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|351048864|gb|FQ431529.1|FQ431529
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|351026359|gb|FQ428371.1|FQ428371
EST:     CAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: CAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|30138039|gb|CB923377.1|CB923377
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|110371042|gb|EC934755.1|EC934755
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|161712591|gb|FC062193.1|FC062193
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|26266195|gb|CA817258.1|CA817258
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
EST: gi|110362101|gb|EC925611.1|EC925611
EST:     AGCAGTTGGCAATCGCAGAATTTGCTGAATCTTTACTAATAATACCGAAG                         GTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA
genomic: AGCAGTTGGCAATTGCAGAATTTGCTGAATCTTTACTAATAATACCGAAGgttctgttta ... tctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcatcttcagttttgagaattttattgaagttagtggcatgtgtctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTACGGGCTTACCACCACACTGCCCAAACGAAGGCAGATAAGAAGCATCTCT
 atctgat  putative branch site (score: 4)
            ttttgagaattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctgtttaatctttgagtgcatgatacacatgttcttcatctgatcatcttcagttttgagaattttattgaagttagtggcatgtgtctgctgcagGTGCTTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTACGGGCTTACCACCACACTGCCCAAACGAAGGCAGATAAGAAGCATCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC