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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttattgatctctctgttagggttctttcaatttttagcttcttttgtttttttttttgaaaggttattgacttgtttatcttggttgaggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAGTTCATGCAATGGATGAAGAGATACTGTGACTCGGTTAATGGAGGCCTTT

Basic information

species Vitis vinifera
transcript Vv07s0129g01080.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0129g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g35580.1 (Oryza sativa), 3'ss of exon 2
--------ggttattgatctctctgttagggttctttcaatttttagcttcttttgtttttttttttgaaaggttattgacttgttta-tcttggttgaggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAGTTCATGCAATGGATGAAGAGATACTGTGACTCGGTTAATGGAGGCCTTT
         |  |||| |   | | |||   |  || | | |  | |  |  |  |  | | || ||  ||  || |||  |  |||  || |  ||      |  ||||| || || || | |||||||   || ||||| || ||||| |||||||| |||||||||||||||||| |||||||||| ||||| ||||||||| |  
aaaaaacctgggattgttgcttatattaa--tcattgctagtactgg--tactgcgactgtgttcttacaattttcttgtttgctttgctccttatta-----tcgcagCACATCGAAGTGAACAAGCTTACCAAGGGAAGGCCCCTTGACAATCTGGAATTCATGCAATGGATGAAGCGATACTGTGATTCGGTCAATGGAGGCTTCA

upper sequence: Vv07s0129g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G163409_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------ggttattgatctctctgttagggttctttcaatttttagcttcttttgtttttttttttgaaaggttattgacttgtttatcttggttgaggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAGTTCATGCAATGGATGAAGAGATACTGTGACTCGGTTAATGGAGGCCTTT
                                                     || || || |   | |  |   ||  |  |  |    | || | | || ||  |  |   |  |||||    |  || |||  ||| |   |   |||||||| ||||| | ||||||| | |||||||| || ||||| ||||||||||||||||| ||||||||  |||| ||||| || || ||||| ||| |  
gtgaatcacggctttggtttctcgcccttctcttgtgccgcccgcatgggattttttttattttattttctgaaatcgattgaactgccccatcgtgttttgttgctaatatgatcttatttttgttgttttctctgttaatttggcgcagCATATAGAGGTGAACAAGCTTATCAAAGGAAGGCCCCTTGACAATCTGGAGTTCATGCAGTGGATGAAACGATATTGTGATTCTGTCAATGGTGGCTTCA

upper sequence: Vv07s0129g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G05560.1 (Glycine max), 3'ss of exon 2
ggttattgatctctctgttagggttctttcaatttttagcttcttttgtttttttttttgaaaggttattgactt-gtttatc------ttggttgaggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAGTTCATGCAATGGATGAAGAGATACTGTGACTCGGTTAATGGAGGCCTTT
   |||   ||    | |      ||||| |||||       || || || |||  |||   | | | |||| ||   ||| |      || ||||     |||||||| || ||||| |||||||| ||||||||||| || || ||||| || ||||||||||||||||||||  ||||||| || || ||  ||   |||||| 
--gtatcactcaacttctctctcgtcttttaatttc--atccctgttattctttaattttggacgatcttgatttcagttaccgaattgttcgttgtatattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTC

upper sequence: Vv07s0129g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G39720.1 (Glycine max), 3'ss of exon 2
ggttattgatctctctgttagggttctttcaatttttagcttcttttgtttttttttttgaaaggttattgacttgtttatcttggttgaggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAGTTCATGCAATGGATGAAGAGATACTGTGACTCGGTTAATGGAGGCCTTT
               |   |   | | |     |||||  ||     | | ||   ||  |    ||| ||| ||| |  |  || ||        |||||| || ||||| |||||||| ||||||||||| || || ||||| || ||||||||||||||||||||  ||||||| || || || |||   |||||| 
--------------gtaacactctccctctgtattttaattttggacgatcttgaattcaa----ttactgaattgctcgttgtgttt-------ctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTC

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|110732455|gb|EE107757.1|EE107757
EST:     AGAATTACAAGGTTCTTCAAGACGTCTTCAACAAACTCAGGATCACCAAG                         CATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAG
genomic: AGAATTACAAGGTTCTTCAAGACGTCTTCAACAAACTCAGGATCACCAAGgtatatctct ... ggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAG
EST: gi|34544613|gb|CF512845.1|CF512845
EST:     AAAATTACAAGGTTCTTCAAGACGTCTTCAACAAACTCAAGATCACCAAG                         CATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAG
genomic: AGAATTACAAGGTTCTTCAAGACGTCTTCAACAAACTCAGGATCACCAAGgtatatctct ... ggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAG
EST: gi|110702076|gb|EE080376.1|EE080376
EST:     AGAATTACAAGGTTCTTCAAGACGTCTTCAACAAACTCAAGATCACCAAG                         CATATTGAAGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAG
genomic: AGAATTACAAGGTTCTTCAAGACGTCTTCAACAAACTCAGGATCACCAAGgtatatctct ... ggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAG
EST: gi|33406833|gb|CF212460.1|CF212460
EST:     AGAATTACAAGGTTCTTCAAGACGTCTTCAACAAACTCAAGATCACCAAG                         CATATTGAGGTAAGCAAGCTTGGGAAAGGAAGACCTCTTGATAATCTGGAG
genomic: AGAATTACAAGGTTCTTCAAGACGTCTTCAACAAACTCAGGATCACCAAGgtatatctct ... ggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttttttttttgaaaggttattgacttgtttatcttggttgaggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAGTTCATGCAATGGATGAAGAGATACTGTGACTCGGTTAATGGAGGCCTTT
                     tattgac  putative branch site (score: 2)
     tttttttttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttattgatctctctgttagggttctttcaatttttagcttcttttgtttttttttttgaaaggttattgacttgtttatcttggttgaggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAGTTCATGCAATGGATGAAGAGATACTGTGACTCGGTTAATGGAGGCCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - -tctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttga