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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattatgttgattttatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 18
gtaaattatgttgattttatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
                                                                 | | | || |   | | | |  |      |  | |   | || |||| | | | |||||| |         |  |  |  | ||||||    |||  |||||||| || ||||||||||| || || ||||||||||| || || ||||||||||| | |||||||
-----------------------------------------------------------------gcataattgatttcttttcttctccagattttgaagaaaatattcctttttcaaaattttct---------aataacagttgctttgc----agGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 19
gtaaattatgttgattttatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
                                      || ||  || |  || ||   |  ||  |   |||| | |||  |       | ||  || |||  |   |   | |   |        ||||| | |||       | ||||||    |||| |||||||  || |  || ||||| ||||| |||||||| ||||| ||| | ||||||||||||||||||
--------------------------------------acaagccctataccacttatct--ctcaactgtttagg-acacat-------cgtccaagaaattctccttaagc-gcaccgccgcaccctgaattctagt------tgctttgc----agGAAATTGCTATTGAGGCACATAGTGAATCAAAGTGGAAGCAGTTGGGGGAACTCGCTATGTCCACTGGAAAG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 18
gtaaattatgttgattttatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
                                                                 | | | |  |   | | | |  |      |   ||   | || | || | |    | ||| ||| |    ||| | | | ||||       ||||  |||||||| || |||||||||||||| || ||||||  ||| || || ||||||||||| | |||||||
-----------------------------------------------------------------gcataatcgatttcttttcttctccacattttcgagaaagtatttcttttt--tgaatttttctaa----tagta-gttgttctg------cagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 7
gtaaattatgttgattt-tatgtcagtatagggatataa-actagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
         ||   ||  |||||   |  | |||||||  | | |     ||| | |||  | |||     ||||||       ||| |    |||| |      | ||||    | |||   || |||    | ||    ||| || ||||   || ||||  |||||| | |||||||| |||||||| |||||||||||||||||||||||||| ||||| |||||||||
---------gtaagttcatatgttcctgcaaggatatattatttgactcgtga-aatttcataactctgctatttaa------ttttctgcatttctaatttgc-actagtttgatttga-gtttatattgtgagta----atgctcatcttcttttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 18
gtaaattatgttgattt-tatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
         ||   ||  |||||   |  | |||||||   |  | |||    | |||  | ||      ||||||     |   | | |  ||   | || |  ||  |    || |   || || |  | ||| |    || ||||      || ||||  ||||| || |||||||| |||||||| |||||||||||||||||||||||||| ||||| |||||||||
---------gtaagttcatatgttcctgcaaggatatattattttacttgtgaaatttaataacactgctatttaattttctgcatttctaatttgcacgagt--ttgatt---tgagtttatattgtgagcaatgttcattgttctt------ttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 18
gtaaattatgttgattt--tatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatga-tcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
      |||| | || |  ||||||   |  | |||||    || || | ||| || | ||| |||||   || |||     |||| ||||   |          || |||    | || || |||||| | | | |||  ||   || | ||  | | |||   ||||| | |||| |||| || ||| | |||||||||||||||||||||||||||||||| |||||||||
-----gtatgctcatgtaatatgtctacaaggagatattgtttaatt-tgtgaaagct-gttaacttgggtatctaattt--tcttcatttctcttc--------atcagtttgatttgtca-ttttatatcacaaataatatacctccttttcccatgcagAGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 18
gtaaattatgttgattt--tatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatga-tcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
      |||||| ||    ||| ||   |  | |||||    || ||  |  | |  ||||| |||||   ||  ||    ||  ||  |||||| | |       | |||    | || || |||||| | | | |||  ||   || | |||  || |||   ||||| | |||| | || || ||| | ||||||||||| |||||||||||| ||||||| |||||||||
-----gtatgttcatgcaatatatctacaaggagatattgtttaatttgtgaaaa--ttgttaacttgggtatccaa---tattcttcatttcttttca-------tcagtttgatttgtca-ttttatatcacaaataatatacctcctttttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAATTAACTATGTCTACTGGAAAG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 22
gtaaattatgttgattttatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
                                                 |  ||| ||| |  || | ||||| || |   |||||||| |         |||| |   |    |  |   |||||   ||            |||| |||  |  ||||||||||||  ||| |  |||| ||| || |||||||||||| | ||||||||||||||||| | ||| |||
-------------------------------------------------gttagtctgtagtttttaccatttgagaag--ctttatttcc---------atgacttacc----gatatgtttttactcgat-----------tcttattttttgacagGACATTGCTGTAGAGGCACAAAATGAATCTAAATGGAAGCAACTTGGAGAATTAGCTATGTCAAGTGGGAAG

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|110728301|gb|EE103751.1|EE103751
EST:     ATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGATTAGAGGTTGCAAAG                         GACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAA
genomic: ATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGATTAGAGGTTGCAAAGgtaaattatg ... ttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAA
EST: gi|161716849|gb|FC068107.1|FC068107
EST:     ATTACCGATTTGAGCTAGCGATGCAGCTTGGCAGATTAGAGGTTGCAAAG                         GACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAA
genomic: ATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGATTAGAGGTTGCAAAGgtaaattatg ... ttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
                                       tcttctttgctttc  CT-rich tract
               aattttatctgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattatgttgattttatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA