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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacaattactcactgttaccgtcccttgaacctccacgtggctccaattttgagtctgttaccgtgagccaactaattatttttctgtcatgatccgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCGATCCTCGACGGTACCTCCACGTGGCACTTCATGACCTCGTGGGCCGAGA

Basic information

species Vitis vinifera
transcript Vv16s0050g00830.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00830.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g44840.1 (Oryza sativa), 3'ss of exon 1
gacaattactcactgttaccgtcccttgaacctccacgtggctccaattttgagt-ctgttaccgtgagccaactaatt--atttttctgtcatgatcc--gcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCGATCCTCGACGGTACCTCCACGTGGCACTTCATGACCTCGTGGGCCGAGA
 || |  |  ||||||     |   ||    ||  |||  |  | | | |  | | |    |   | |   |  || |   ||     || |  | | |  |||||| ||    ||  | || ||  | ||| |||| ||||| |||||||||||  |||||||||| |||||||| |||||||||||||| || ||||| ||| 
-accaccaa-cactgtccaaatttatta---ctatacggagtactagtatatattacaaacaaatttaattaggtactctgatggaattgacgcggtgcatgcagTTGACACGTCTGCGGGACGGGGTGGCAGTGGGGTGCGCCTTCAACCACGCCGTCCTCGACGGCACCTCCACCTGGCACTTCATGACGTCATGGGCGGAGC

upper sequence: Vv16s0050g00830.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G179703_T02 (Zea mays), 3'ss of exon 1
gacaattactcactgttaccgtcccttgaacc-tccacgtggctccaattttgagtctgttaccgtgagccaactaattatttttctgtcatgatc-------cgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCGATCCTCGACGGTACCTCCACGTGGCACTTCATGACCTCGTGGGCCGAGA
  ||| ||| | |     | |   | || ||  | ||| |      ||   |  | | |  | | | || || ||  || ||     |    | |         ||||||||| ||||| |  || || || ||  |||| ||||| |||||||||||| | || ||||| ||||||||||||||||||||| |||| ||||||||| 
--caagtaccc-caacagcggctgcctgtacagtgcacata-----aaccattggccaggcaacataagtcatcttgtttttacagcgatgcgtttgcatgcatgcagTTCACAAAGCTCAAGGACGGTCTGGCGGTGGGGTGCGCCTTCAACCACGCGGTGCTGGACGGCACCTCCACGTGGCACTTCATGTCCTCCTGGGCCGAGC

upper sequence: Vv16s0050g00830.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G24900.1 (Glycine max), 3'ss of exon 1
gacaattactcactgttaccgtcccttgaacctccacgtggctccaattttgagtctgttaccgtgagccaactaattatttttctgtcatgatc-cgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCGATCCTCGACGGTACCTCCACGTGGCACTTCATGACCTCGTGGGCCGAGA
 |      | ||||| |  | |  |     |   | |     |   |||||  || | | | | |    |   | |||   ||||| |     || | ||||| || ||||| | |||||| |||||| ||||    || |||||||| ||  || | ||||| ||  |||||||||| ||||||||||| ||||||||||
tagtgcaccccactgatcacctatcacattcactctctcttttattattttctgtttttcatcttctaact-ttcattgcctttctatttctttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCTGTCTTGGACGGGACTGCCACGTGGCAGTTCATGACCTCATGGGCCGAGA

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|71873624|gb|DT022679.1|DT022679
EST:     CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAG                         TTCACCAAGCTAAGAGATGGACTCCCACTGGGATGCGCTTTCAACCACGCG
genomic: CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAGgtaacaattt ... tgatccgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
EST: gi|351029795|gb|FQ427635.1|FQ427635
EST:     CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAG                         TTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
genomic: CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAGgtaacaattt ... tgatccgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
EST: gi|351013235|gb|FQ424940.1|FQ424940
EST:     CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAG                         TTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
genomic: CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAGgtaacaattt ... tgatccgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
EST: gi|352786278|gb|FQ478889.1|FQ478889
EST:     CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAG                         TTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
genomic: CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAGgtaacaattt ... tgatccgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
EST: gi|351028124|gb|FQ426025.1|FQ426025
EST:     CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAG                         TTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
genomic: CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAGgtaacaattt ... tgatccgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
EST: gi|351048406|gb|FQ448680.1|FQ448680
EST:     CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAG                         TTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG
genomic: CCCAAGTCTTGAACTTTGAGGGTCTTCATAAACCCCTCCTGGTCCTACAGgtaacaattt ... tgatccgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttgagtctgttaccgtgagccaactaattatttttctgtcatgatccgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCGATCCTCGACGGTACCTCCACGTGGCACTTCATGACCTCGTGGGCCGAGA
                         aactaat  putative branch site (score: 2)
                         aactaattatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacaattactcactgttaccgtcccttgaacctccacgtggctccaattttgagtctgttaccgtgagccaactaattatttttctgtcatgatccgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCGATCCTCGACGGTACCTCCACGTGGCACTTCATGACCTCGTGGGCCGAGA

- - - - ctcactg
- - - - - - -tgttacc
- - - - - - - - - ccgtccc
- - - - - - - - - - - - - - -acctcca
- - - - - - - - - - - - - - - - - - - - gctccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacta