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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctgggacaagcttcaactcgaaccagattgcattttcgtctagctaaactatattaggtaataaatttctcgttgctctccttgccatgacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGCTGCTGGGCTCACAGTTGACCATCCTATTATGACAACAACTGAGTTCTGG

Basic information

species Vitis vinifera
transcript Vv18s0001g06250.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G35370.1 (Glycine max), 3'ss of exon 2
gtctgggacaagcttcaactcgaaccagattgcattttcgtctagctaaact-atattaggtaataaatttctcgttgctct-ccttgccatgacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGCTGCTGGGCTCACAGTTGACCATCCTATTATGACAACAACTGAGTTCTGG
       ||    ||  ||  |  | | | ||  ||||  |   | ||   | |  ||||||||    |   |      |    | ||   ||  ||   ||||| || || || ||  |||| |||||||| || ||||| |||||||||||||||||||||||||| |||||||| || |||| ||||||||| ||||||
--tgcttacttttttttacaaggtctataatgtttttttttaatggtagtgtgactttaggtaaattgtaattaaacatttaatcatgttttggtatggtagGTACCGAGAGCTTGCTAACCGAGTTGATGAGGCTCTTGGATTCATGGCTGCTGCTGGGCTCACAGTGGACCATCCCATAATGAGAACAACTGAATTCTGG

upper sequence: Vv18s0001g06250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G37080.1 (Glycine max), 3'ss of exon 2
gtctgggacaagcttcaactcgaaccagattgcattttcgtctagctaaactata---ttaggtaataaatttctcgttgctct--ccttgccatgacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGCTGCTGGGCTCACAGTTGACCATCCTATTATGACAACAACTGAGTTCTGG
       ||    ||     | |     |||   || |  | ||     | | |    | ||||||   ||   |      |    |||     ||  ||   ||||| || || || ||  |||| |||||||| |||||||| ||||||||||||||||||||||| || |||||||| || |||| ||||||||| ||||||
-----ttacttttttttttacaaggtctattatgttgttctttaatggtagtgtgacttaaggtaaattataattaaacatttaaacctgtttttggtatggtagGTACCGAGAGCTTGCTAACCGAGTTGATGAGGCCCTTGGATTCATGGCTGCTGCTGGGCTCACGGTGGACCATCCCATAATGAGAACAACTGAATTCTGG
















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|34544767|gb|CF512999.1|CF512999
EST:     GTGACCCAGTGGAATTTGGATTTCACAGAGCACAGTGAGCAGGGAGATAG                         GTATCGGGAAC
genomic: GTGACCCAGTGGAATTTGGATTTCACAGAGCACAGTGAGCAGGGAGATAGgtatatttca ... gacataccagGTATCGGGAAC
EST: gi|110699818|gb|EE077162.1|EE077162
EST:     GTGACCCAGTGGAATTTGGATTTCACAGAGCACAGTGAGCAGGGAGATAG                         GTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC
genomic: GTGACCCAGTGGAATTTGGATTTCACAGAGCACAGTGAGCAGGGAGATAGgtatatttca ... gacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC
EST: gi|110701596|gb|EE079344.1|EE079344
EST:     CACAGAGCACAGTGAGCAGGGAGATAG                         GTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC
genomic: CACAGAGCACAGTGAGCAGGGAGATAGgtatatttca ... gacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC
EST: gi|110685780|gb|EE062798.1|EE062798
EST:     GTGACCCAGTGGAATTTGGATTTCACAGAGCACAGTGAGCAGGGAGATAG                         GTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC
genomic: GTGACCCAGTGGAATTTGGATTTCACAGAGCACAGTGAGCAGGGAGATAGgtatatttca ... gacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC
EST: gi|110423681|gb|EC990032.1|EC990032
EST:     TGGATTTCACAGAGCACAGTGAGCAGGGAGATAG                         GTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC
genomic: TGGATTTCACAGAGCACAGTGAGCAGGGAGATAGgtatatttca ... gacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC
EST: gi|110689789|gb|EE066321.1|EE066321
EST:     GTGACCCAGTGGAATTTGGATTTCACAGAGCACAGTGAGCAGGGAGATAG                         GTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC
genomic: GTGACCCAGTGGAATTTGGATTTCACAGAGCACAGTGAGCAGGGAGATAGgtatatttca ... gacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaactatattaggtaataaatttctcgttgctctccttgccatgacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGCTGCTGGGCTCACAGTTGACCATCCTATTATGACAACAACTGAGTTCTGG
 agctaaa  putative branch site (score: 3)
      tatattaggtaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgggacaagcttcaactcgaaccagattgcattttcgtctagctaaactatattaggtaataaatttctcgttgctctccttgccatgacataccagGTATCGGGAACTAGCACACCGTGTTGATGAAGCCCTTGGTTTCATGGCTGCTGCTGGGCTCACAGTTGACCATCCTATTATGACAACAACTGAGTTCTGG

- - - -acaagct
- - - - - - - - - - - aaccaga