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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcaccaacccccttccacaattaaattttcactttgacttgttttgcttgatttttcaaagatttaaaagataattgccccttgttgtgggtgatccagGTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTCGGAATTAGAGAAATTGCTAGAACTGGAAAG

Basic information

species Vitis vinifera
transcript Vv05s0094g01110.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g01110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g14950.1 (Oryza sativa), 3'ss of exon 4
--agcaccaacccccttccacaattaaattttcactttgacttgttttgcttgatttttcaaagatttaaaagataattgccccttgttgtgggtgatccagGTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTCGGAATTAGAGAAATTGCTAGAACTGGAAAG
  |   | |      |   ||  |  |  |  ||| | |||   |  | ||||   |||  | ||   |||| | |  | |   || || |   || |  |||||||||||||||| || || || |||||||| ||||| ||  ||||||| || ||||| | ||||||||| |||||||| |||
gtaatcctatgtttatcttaccttgcagat--cacatcgacc-ataattcttgtggtttttatgaaagaaaaaaaatcttctttttttttttcatgttgaagGTAACTGGAGATCCTGGAAAAATTGTTGCTGTACAGAGGAACCTAAGCAAATTTGGAATCAAAGAAATTGCCAGAACTGGCAAG
















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|29782147|gb|CB347237.2|CB347237
EST:     TTTCAGAGTGAAAGA-TGTGGATATCTCAGAGCATTCAGTAACCATTGAG                         GTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TTTCAGAGCGAAA-ATTGTGGATATCTCAGAGCATTCAGTAACCATTGAGgtgatagcca ... ggtgatccagGTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|32247510|gb|CD713329.1|CD713329
EST:     TTTTCAGAGCGAAA-TTGTGGATATCTCAGAGCATTCAGTAACCATTGAG                         GTAACTGGAGATCCAGGGA
genomic: TTTTCAGAGCGAAAATTGTGGATATCTCAGAGCATTCAGTAACCATTGAGgtgatagcca ... ggtgatccagGTAACTGGAGATCCAGGGA
EST: gi|352772784|gb|FQ473822.1|FQ473822
EST:     TTTTCAGAGCGAAAATTGTGGATATCTCAGAGCATTCAGTAACCATTGAG                         GTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TTTTCAGAGCGAAAATTGTGGATATCTCAGAGCATTCAGTAACCATTGAGgtgatagcca ... ggtgatccagGTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|110708435|gb|EE085972.1|EE085972
EST:     TTTTCAGAGCGAAAATTGTGGATATCTCAGAGCATTCAGTAACCATTGAG                         GTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TTTTCAGAGCGAAAATTGTGGATATCTCAGAGCATTCAGTAACCATTGAGgtgatagcca ... ggtgatccagGTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|110690986|gb|EE068568.1|EE068568
EST:     CTCAGAGCATTCAGTAACCATTGAG                         GTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: CTCAGAGCATTCAGTAACCATTGAGgtgatagcca ... ggtgatccagGTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG
EST: gi|110723613|gb|EE101123.1|EE101123
EST:     TTTTCAGAGCGAAAATTGTGGATATCTCAGAGCATTCAGTAACCATTGAG                         GTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG
genomic: TTTTCAGAGCGAAAATTGTGGATATCTCAGAGCATTCAGTAACCATTGAGgtgatagcca ... ggtgatccagGTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttgatttttcaaagatttaaaagataattgccccttgttgtgggtgatccagGTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTCGGAATTAGAGAAATTGCTAGAACTGGAAAG
 gcttgat  putative branch site (score: 5)
      atttttcaaagattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcaccaacccccttccacaattaaattttcactttgacttgttttgcttgatttttcaaagatttaaaagataattgccccttgttgtgggtgatccagGTAACTGGAGATCCAGGGAAGATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTCGGAATTAGAGAAATTGCTAGAACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- -accaacc
- - - - - cccttcc
- - - - - - - - - -aattaaa
- - - - - - - - - - - - - - - - - -tgacttg
- - - - - - - - - - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagat