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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaaatatctacggtctacctccactctccctacaaagtttccttttctattaattttatgttccacaatttaaggtcactccttatgcttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT

Basic information

species Vitis vinifera
transcript Vv08s0007g02300.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g01250.1 (Oryza sativa), 3'ss of exon 2
taaaaatatctacggtctacctccactctccctacaaagtttccttttctatta--attttatgttccacaatttaaggtcactccttatgcttttgct-cagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT
|  | || |    |  || | |   ||   ||| | || || | |  |||||||   |  | || ||  |  | ||  |||  |   ||||||||     |||||| ||||| |||||||||||||| |||||||||||||  ||||||||||||||| | |||||  | || ||| ||||||||||||||||||| 
tgtatatcttgttgagct-cttttgcttctccttcgaa-ttacttactctattacggtactgtgctcatctgtatactgtc-ttatatatgctttcctgacagGTACGAAGGGCAGCGTGACATGCTGTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G092468_T02 (Zea mays), 3'ss of exon 2
-taaaaatatctacggtctacctccactct---ccctacaaagtttccttt--tctattaattttatgttccacaatttaaggtcactccttatgcttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT
  |  |       |   |     | | |      ||| ||     ||| ||  || |    |  || | |||  ||| |    |||| |  | |  ||||   |||||| ||||| |||||||||||||| |||||||||||||  ||||||||||||||| | |||||||| || ||| ||||||||||||||||||||
acaggagctctcccaaacgggacctaatagagaaccttcagtccgtccgttcgtcaacggttactaagctcc-taatct----tcaccctctgttttttt-tacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCGGCAGAGGGACTTAAAGATGCTCAGCAAACT

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 2
taaaaatatctacggtctacctccactctccctacaaagtttccttttctattaattttatgttccacaatt--taaggtcactccttatgcttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT
| |   | || |  |   |   |   |   | || ||   | |   |   || ||| |||| |  |   |||  ||     |  |  || || |||| ||||||||||||| |||||||||||||| ||||| || |||||||| || || ||||||  |||||| |||||||| |||||||||||||| ||||||
ttattctgtcaaatgataataact--ttgtcatataataatacacatgaaatgaatattatatagcggtattcatataacaatgcactacgcctttggtcagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACATTCAATCTCGATCAAGTTCAATTTGCAGCTGAAGGCATTAAAGATGCTCAACAAACT

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 2
taaaaatatctacggtctacctccactctccctacaaagtttccttttctattaattttatgttccacaatt--taaggtcactccttatgcttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT
  |||  || ||     | | | ||   | | |  ||   | |   |   || ||| |||| |  |   |||  ||  |  |  |  ||||| |||| | ||||||||||| |||||||||||||| ||||| || || ||||| || || ||||||  |||||| ||||| || |||||||||||||| ||||||
-gaaataatttataactt-cattcatatttcatgtaatagtacacatgaaatgaatattatatagctgtattcatatagcaatgcactatgcctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G04850.2 (Arabidopsis thaliana), 3'ss of exon 2
taaaaatatctacggtctacctccactctccctacaaagtttccttttctattaat-tttatgttccacaatttaaggtca-ctccttatgcttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT
                     ||     |  ||      ||    | || ||  |  || ||| |    | |||||   || ||  ||    |||| || |||||||||||||| ||||||||||| || || || || || |||||||| |||||||||||||| ||||||||  ||||||||||||| ||||||
--------------------gtcagtgttttctttctgcttcttctctcaatggacattgatgatatggattttaataccaactgtttccatttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT

upper sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G10640.1 (Arabidopsis thaliana), 3'ss of exon 2
------taaaaatatctacggtctacctccactctccctacaaagtttccttttctattaattttatgttccacaatttaaggtcactccttatgcttttg--ctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT
       |  |     |    | ||  |  |  |  |   | ||| | |  | | ||||   |||  | |  | |||  ||   |       ||  || ||   | |||||||||||||| || |||||||| || || || |||||||| || || ||||||||||| || ||||||||| | ||||||||||| ||||||
gtcagtcactagacattgttatttaaattgatccagcaagctaagctactctgtttattggattt--gcttgataataaaacacctaagtacatttttatgaatttagGTATGAAGGACAACGCGACATGCTCTATAATCAGACATTCAATCTCGATCAAGTTTCATTCGCCGCTGAAGGACTCAAAGATGCTCAACAAACT

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|110688527|gb|EE067183.1|EE067183
EST:     CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGAT                         GTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
genomic: CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGATgtatgtgctc ... ttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
EST: gi|33404120|gb|CF209747.1|CF209747
EST:     CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGAT                         GTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
genomic: CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGATgtatgtgctc ... ttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
EST: gi|110686349|gb|EE063885.1|EE063885
EST:     CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGAT                         GTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
genomic: CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGATgtatgtgctc ... ttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
EST: gi|110690195|gb|EE067084.1|EE067084
EST:     CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGAT                         GTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
genomic: CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGATgtatgtgctc ... ttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
EST: gi|71859039|gb|DT008094.1|DT008094
EST:     CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGAT                         GTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
genomic: CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGATgtatgtgctc ... ttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
EST: gi|71868774|gb|DT017829.1|DT017829
EST:     CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGAT                         GTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA
genomic: CAAGAAGCTGTTAAAGCTAGGGCCATGAGGGTTCTCAAGCAAAAAAGGATgtatgtgctc ... ttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctattaattttatgttccacaatttaaggtcactccttatgcttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT
    tattaat  putative branch site (score: 2)
                                   ctccttatgctttt  putative PPT
     attaattttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaaatatctacggtctacctccactctccctacaaagtttccttttctattaattttatgttccacaatttaaggtcactccttatgcttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
-aaaaata
- - - - - - - - ctacctc
- - - - - - - - - - - - -ctctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactcct