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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgactggagttacatttcttgttctttttctgtccagggctttaaaccatctaaattatacactcaaacatgccatgtatccttttttggaa...

Basic information

species Vitis vinifera
transcript Vv05s0102g01180.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os09g34100.1 (Oryza sativa), 5'ss of exon 5
CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgact-----ggagttacatttcttgttctttttctgtccagggctttaaaccatctaaattatacactcaaacatgccatgtatccttttttggaa
 ||  |  ||| | |||| || ||||| || ||||| |||||||||||||| ||||| ||| | |||||||| || ||||| ||||| |||||  |||||||   |||| | |      |||| |   ||| ||| |  ||| ||   | |   ||||||     |   |||    |     || |||||||    ||  |    
TCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttctttttaatttttacagagtcat-cttcatgtgcactttatgg--aagtaattaaacaccaaatgctatgttttgcttgattccatgtacttgttcattc--

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G150533_T01 (Zea mays), 5'ss of exon 1
CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgactggagt-tacatttcttgttctttttctgtccagggctttaaaccatctaaattatacactcaaacatgccatgtatccttttttggaa
 ||  |  |||  || ||| | || |  || || || |||||||| ||||||||||||| ||||||||| || || ||||| ||||| |||||  | ||||    |||| ||| |  |  |  | | ||  | |   | | |   | ||       |  ||  | | |  |  |||      | | | |  |  |||    
TCATGTGTGCTATTATTTTGCTGGTTTTGGAGCTATGTTTACAGGTGACACTTTGTTCAATCTATCATGCGGAAAGCTTTTTGAAGGGACTCCACAGCAGggttttttttacttgcttgcaagtatgttcatatacatatatgttgtgcgaaggtgctactggactctcgagacaagatactcctctgtagtgcttttat-

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA11G13470.1 (Glycine max), 5'ss of exon 5
CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgactggagttacatttcttgttctttttctgtccagggctttaaaccatctaaattatacactcaaa-catgccatg-tatccttttttggaa
 ||  | ||||||||||||||||| || |||||||||||||| || ||||||||||||||  ||||||||||||| || || |||||||| ||  |||||||  ||||  | || | |||  ||||   || ||||||||        |||  | | |       |   | |     | ||      |||   ||| | |  
TCATGTAAGCTTCTACTTTCCGGGTTCTGGGGCAATTTTTACCGGAGACACTTTGTTCAGCTTATCATGTGGCAAGCTCTTAGAAGGAACCCCCAAACAGgttgatttgaattgcattta-gtttcacattttttttctggttgtacatttctatctttagggacaagtaattgcctcttgttgcaatatttatttcttgt-

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA12G05470.2 (Glycine max), 5'ss of exon 5
CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgactggagttacatttcttgttct-ttttctgtccagggctttaaaccatctaaattatacactcaaac----atgccatgtatccttttttggaa
 ||  | |||||||||||||| || || |||||||||||||| || ||||| ||||||||  ||||||||||||| || || |||||||| || ||||||||  ||||  | ||   |||  |||||  || | |||||||        |||  | | ||      |     |   |      ||| |||| | |||| |||   
TCATGTAAGCTTCTACTTTCCAGGTTCTGGGGCAATTTTTACTGGAGACACCTTGTTCAGCTTATCATGTGGCAAGCTCTTAGAAGGAACCCCCGAACAGgttgatttgaattgctttta-gtttctcattttgttttctggttgtacatttctatcttcagggacaagtgattgcatcttgttgcaatgt-ttctttcttg---

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA15G03320.1 (Glycine max), 5'ss of exon 5
CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgactggagttacatttcttgttctttttctgtccagggctttaaaccatctaaattatacactcaaacatgccatgtatccttttttggaa--------
||| || |||||||| ||||| ||||| |||||||||||||| || ||||||||||||||  ||||||||||||| || || |||||||| ||  | |||||   |||  | || | ||    || ||  |  |||| | ||      |||||    | | |  | |  |  ||   ||    ||| | | | ||||||         
CCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTCAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCAGgttgttttaaattgtacttgtccttttttcttcttttttttct-----tttaag--gtttgagatttctatccagtaataggttgt-tgcatctttggacgtgcctta

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA13G42070.2 (Glycine max), 5'ss of exon 5
CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgactggagttacatttcttgttctttttctgtccagggctttaaaccatcta---aattatacactcaaacat-----gccatgtatccttttttggaa
||| || |||||||| ||||| ||||| |||||||||||||| || ||||||||||| ||  ||||||||||||| || || |||||||| ||  | |||||   |||| | || |  |    | ||| || |||||   |  |  | ||| |    ||||   | | |||   |    |||     |  ||||||  |||||     
CCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCAGgttggttttaattgtacctg---tccttttttttttttcctttaaaggtttgagatttctatccagtgataagttgttgcatcttgggatatgtattattttt-----

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G06130.2 (Arabidopsis thaliana), 5'ss of exon 5
CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgactggagttacatttcttgttctttttctgtccagggctttaaaccatc---taaattatacactcaaacatgccatgtatccttttttggaa
||| ||||| ||||||||||| ||  || | |||||||| || |||||||| ||||| ||  |||||||||| ||||| |||||||| ||||| || ||||||||  |    |    |   || | | ||||| | |           | | ||   ||   |   |||     |     |     || ||| |||  || | 
CCATATTAGTTTCTACTTTCCAGGGGCACGAGCAATTTTCACCGGGGACACCTTGTTTAGCTTATCATGTGGTAAACTCTTCGAAGGTACTCCAGAGCAGgtaaacatcattta---tctaatctttggttctctctgaacttgactttattaagtgtcagttgttttaattggttttcaacaatctgcatcttttgctgcag

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|34319830|gb|CF372584.1|CF372584
EST:     CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAG                         ATGCATTCTTCCCTTAGTAAGATTATGTCTTTGNCAGACGAAACAAATATC
genomic: CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttg ... tgtgttccagATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
EST: gi|77584541|gb|DV221342.1|DV221342
EST:     CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAGCAG                         ATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
genomic: CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttg ... tgtgttccagATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
EST: gi|110404767|gb|EC970289.1|EC970289
EST:     CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAG                         ATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
genomic: CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttg ... tgtgttccagATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
EST: gi|110708395|gb|EE085884.1|EE085884
EST:     CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAG                         ATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
genomic: CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttg ... tgtgttccagATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
EST: gi|110718180|gb|EE094717.1|EE094717
EST:     CTTTGTTCAGTCTATCATGTGGCAAACTTTCCGAAAGAACTCCTGAGCAG                         ATGCATTCTTCCCTTANTAAGATTATGTCTTTGCCAGACGAAA-AAATATC
genomic: CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttg ... tgtgttccagATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
EST: gi|110715392|gb|EE093393.1|EE093393
EST:     CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAG                         ATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
genomic: CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttg ... tgtgttccagATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
EST: gi|34549778|gb|CF518010.1|CF518010
EST:     CTTTGTTCAGTCTATCATGTGGGATCCTTTTCGAAGGAACTCCTGAACAG                         ATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
genomic: CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttg ... tgtgttccagATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
EST: gi|110688962|gb|EE068114.1|EE068114
EST:     CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAGCAG                         ATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC
genomic: CTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttg ... tgtgttccagATGCATTCTTCCCTTAGTAAGATTATGTCTTTGCCAGACGAAACAAATATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgactggagttacatttcttgttctttttctgtccagggctttaaaccatctaaattatacactcaaacatgccatgtatccttttttggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA