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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatttccaacagtagagattttcttgaagaggccatgcaagtccttgaacttcaaagaatttaatttctaatcattttagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG

Basic information

species Vitis vinifera
transcript Vv04s0008g04890.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA06G07580.1 (Glycine max), 3'ss of exon 17
---tatatttc-caacagtagagattttcttgaagaggccatgcaagtccttgaacttcaaagaattt-aatttctaatcattttagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG
   | |||||      ||| ||     |  |||  ||  |||||||  | |  | | |     |||||  |  ||| ||  ||     ||| | || |  |  ||||  | ||| | ||||||||||||||||||||||| |||||||| || ||||||||||| || ||  || |||||||||| ||||||||   ||| ||||
ggttgtattttgtcctagttgaa----tggtgagtagtacatgcaatccatacatcctgttgtaattttgacatcttatgcttggtaaatt-taatgttgtgtagTCATTGGAGTTGTGGAACATGAGCGAGAACAAGACGATGACTCTGTCTGCTCATGATGGTCTCATTACTTCCTTGGCTGTTTCAACTGTAAATGGTTTGG

upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA04G07460.1 (Glycine max), 3'ss of exon 17
--tatatttccaac-agtagagattttcttgaagaggccatgcaagtccttgaacttcaaagaatttaatttctaatcattttagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG
  | | |        | | | || |         |  |||| ||     ||| | ||   | |  |||   | |  | | |||| | ||||   |  ||  ||||  | ||||| ||||| |||||||||||||||||||||||||| || ||||||||||| || ||  || ||||||| || ||||||||   ||| ||||
attttgtccttgttgaatggtgagtaataaatgcaatccatacacaatgttgtaattttgacatcttacgct-tgttaaatttaatgttgtg--taactgtagTCATTGGAGCTGTGGAATATGAGCGAGAACAAGACAATGACTCTGTCTGCTCATGATGGTCTCATTACTTCCTTGGCGGTTTCAACTGTAAATGGTTTGG

upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA14G16040.1 (Glycine max), 3'ss of exon 17
tatatttccaacagtagagattttcttgaagaggccatgcaagtccttgaacttcaa--agaatt-taatttctaatcattttagt-attgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG
     |    | | |  |  || ||   || |     |     |     |  |  ||  ||| || ||||||     | || || |   |   ||   || |||||  | ||||| ||||||||||  ||||||||||| |||||||| || |||||||| || || || || || ||||| || || |||||   ||| ||||
----ctgattatattttactttctccctaacaaatagtaattatatccaatttataattagatttgtaattttggcccgttataattggtaccatgatctgcagTCATTGGAGCTCTGGAACATGACTGAGAACAAGACGATGACTCTATCTGCTCATGAAGGTCTTATTGCGGCATTGGCGGTTTCTACTGTAAATGGTTTGG

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|110389658|gb|EC954515.1|EC954515
EST:     GTGTTTTTCACCCAACATATTCATCATTGCTGGTCATCGGTTGTTACCAG                         TCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
genomic: GTGTTTTTCACCCAACATATTCATCATTGCTGGTCATCGGTTGTTACCAGgcaagtcatt ... tttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
EST: gi|22011770|gb|BQ796804.1|BQ796804
EST:     GTGTTTTTCACCCAACATATTCATCATTGCTGGTCATCGGTTGTTACCAG                         TCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
genomic: GTGTTTTTCACCCAACATATTCATCATTGCTGGTCATCGGTTGTTACCAGgcaagtcatt ... tttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
EST: gi|110389080|gb|EC953893.1|EC953893
EST:     GTGTTTTTCACCCAACATATTCATCATTGCTGGTCATCGGTTGTTACCAG                         TCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
genomic: GTGTTTTTCACCCAACATATTCATCATTGCTGGTCATCGGTTGTTACCAGgcaagtcatt ... tttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
EST: gi|110418997|gb|EC985186.1|EC985186
EST:     GTGTTTTTCACCCAACATATTCATCATTGCTGGTCATCGGTTGTTACCAG                         TCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
genomic: GTGTTTTTCACCCAACATATTCATCATTGCTGGTCATCGGTTGTTACCAGgcaagtcatt ... tttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaacttcaaagaatttaatttctaatcattttagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG
                      ttctaat  putative branch site (score: 2)
          aaagaatttaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatttccaacagtagagattttcttgaagaggccatgcaagtccttgaacttcaaagaatttaatttctaatcattttagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - tccaaca
- - - - - - - - - - - - - - - - - ccatgca
- - - - - - - - - - - - - - - - - - - - - - ccttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - caaagaa