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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcacattcccatagattgttaaggcatttattctctgtgtttgtctgtctgtttccttttttgcttctcattttttctctgcatttaactttct...

Basic information

species Vitis vinifera
transcript Vv08s0007g07420.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os03g57940.1 (Oryza sativa), 5'ss of exon 14
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcacattcccatagattgttaaggcatttattctctgtgtttgtctgtctgtttccttttttgcttctcattttttctctgcatttaactttct--
|||||||||||||| |||||||| |||||||| ||||| |   |||||||||| ||  | ||||| || || |||||||| ||||| ||||||||| | | || ||  |    || |     | | ||| |      ||| || | | ||     ||        |    ||  |    ||  ||   |    
GATTGGATTATGGAGCAGTGGGAGAAGAATTATTACATAACGGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttgg-taaaataccttttctctgctggcaaactaattttactaccttggctatttcttagaacttgaaacaacc-ccgttgatgaatatgaaatagttgaa

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 14
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgtt-ggatcacattcccatagattgttaaggcatttattct-ctgtgtttgtctgtctgtttccttttttgcttctcattttttctctgcatttaactttct
|||||||||||||| || ||||| || ||||||||||||||  | ||||| || ||  | ||||| ||||| ||||| |||||||| ||||||| |  |||  |   | |   |||  | | |  | ||  | ||    ||||   |||   |           | |  |||     ||     |   | |||
GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctcagctgttcttttgttgg-aggtctctcatgttactaccattgttattcttcataaaggaccatctat-gtttagaaacttggcctgtttctct

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 14
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcacattcccatagattgttaaggcatttattctctgtgtttgtctgtctgtttccttttttgcttctcattttttctctgcatttaactttct
|||||||||||||| ||||||||||| || |||||||||||  | ||||| || ||    ||||||||||| ||||| |||||||| ||||||  |  |  |||        |  || |||| | |  | | | |   |   |   |   |           |    |  | |||    | |||| |    
GATTGGATTATGGAGCAGTGGGAAAATAACTACTACATCAGTGCCATAGCTGGTGCAATGAATGGGAGTTCCTTGGTGGTCATGTCAAAAGgtctgccctaattgatggctgtatttgaggcctcttatatttattagttattacattcatatgaaaaaaaattgagtggtgtctacatagttaaatgctc

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G164265_T02 (Zea mays), 5'ss of exon 14
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttgga---tcacattcccatagattgttaaggcatttattctctgtgtttgtctgtctgtttccttttttgcttctcattttttctctgcatttaactttct
|| ||||| ||||| |||||||| || | ||||||||| |   |||| || ||  |  | ||||||||||| |||||||||||||| ||||||  ||   | || || |     |||| | |  | |  ||  |     |   | | |||      |||     |     |      ||   || |  || |  
GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattttacttttcttattattgctcacacgtgcatattgaccctccattt-tctcaccattttcccagtagcagtacaaaatcctaatgtttctct--

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcacattcccatagattgttaaggcatttattctctgtgtttgtctgtctgtttccttttt----tgcttct-cattttttctctgc-atttaactttct
|| ||||||||||| |||||||| || |||||||| ||||| |||||||| || || | |||||| ||||| |||||||||||||| ||||||   ||   ||  | |||  ||  | |   | |  | ||     |     ||  |  ||  |||||    ||| | | ||   | ||  ||| |||| ||||   
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgt---atataatatctataattttatgacctactcctccttcacatactattgattaatttatttttgaaatgcctttgcaaaatctccttgctattttactt---

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 5'ss of exon 14
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcacattcccatagattgttaaggcatttattctctgtgtttgtctgtctgtttccttttttgc-ttctcattttttctctg---catttaactttct--------------------------------
|| |||||||||||||| ||||||||||| ||||| ||||| || ||||| ||  | | ||| ||||  || || ||||| ||||| |||||||||     ||     ||   ||  ||    |||||              || || |      | | |   | ||||| |  |  |    |||  |   ||||                                
GACTGGATTATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTTCAGATAACGGGAACTCATTAGTTGTTATGTCAAAAGgttggtgttaatggtagtaatctgcaaa--tttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtag

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 5'ss of exon 14
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttgg--atcacattcccataga---ttgttaaggcatttattctctgtgtttgtctgtctgtttccttttttgcttctcattttttctctgcatttaactttct
|| ||||| |||||||| ||||||||||| ||||| ||||| || ||||| || ||   |||||| || || |||||||| ||| |||||||| ||   |||| |  |   | |   |||  || | | |||||   |      |  ||   |     ||  ||  | | | ||  |    |||  |         
GACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAGgtcggtagtcacgtctcatgataactttgccaatgaacttattgattcataaagcatgaaagccgttttacttattccac-ttcatgtaatgcgatag-------

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 13
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgt-------tggatcacattcccatagattgttaaggcatttattctctgtgtttgtct---gtctgtttcct--tttttgcttctcattttttctctgcatttaactttct----------------------------------------------------------
|| ||||| |||||||||||||||||||||| ||| |||||  |||| || || |||  ||||||||| |||||||| |||||||| ||||||       |||||   ||  || | |||   ||  | || |||| || | |||  |||   |  |||||  |  ||| | ||| | |||| |  | || |      ||| |                                                          
GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAGgtattttattggatagtat--cctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtag

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 13
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcacattcccatagatt---gttaaggcatttattctctgtgtttgtctgtctgtttccttttttgcttctcattttttctctgcatttaactttct
|| ||||| |||||||||||||||||||||| ||| |||||  | || || || ||   ||| || || || ||||| |||||||||||||||    ||||       || |||    ||||  |  | |||   ||  | |||   ||  |||  | ||||  |  |  |  ||  | |   |  |  | |  
GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgt-atttcacccgatgttacatttagattaacactatcatttcatgcatatgtacttcaattttttatttttatcatgctgcttaatttttgtagatttat--

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|110363759|gb|EC927370.1|EC927370
EST:     TCAATAGCAGGGGCTGCTAATGGGAGTTCTTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
genomic: TCAATAGCAGGGGCTGCTAATGGGAGTTC-TTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|34544477|gb|CF512709.1|CF512709
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|110379519|gb|EC944719.1|EC944719
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|37190348|gb|CF609697.1|CF609697
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|22012560|gb|BQ797594.1|BQ797594
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTCA
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|37190390|gb|CF609739.1|CF609739
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGCCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCC
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcacattcccatagattgttaaggcatttattctctgtgtttgtctgtctgtttccttttttgcttctcattttttctctgcatttaactttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT