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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTTTGGGTTGCTTTTAGTCTTTATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcatttcactatcttcttttcaatacagtctcctactttggctttcttttcttaattcttagggttcatcatgtggctttccag

Basic information

species Vitis vinifera
transcript Vv04s0044g01940.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA16G21960.4 (Glycine max), 5'ss of exon 2
GGTTTTTGGGTTGCTTTTAGTCTTTATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcatt-tcactatcttcttttcaatacagtctcctactttggctttcttttcttaattcttagggttcatcatgtggctttccag----------------------------------
  |||| || |||||||| ||  | |||||||||||  ||||||||| ||||||||  || |||||| |||||||||||| ||| | | |||  | || | | ||   |        ||    || || |  |  || | | | | ||   | ||  | ||  |                                  
ACTTTTCGGTTTGCTTTTCGTGCTGATGGTGATTCCTGTTGATGAAAAGAGCAAATTCGGTAGAAAATTATCCAGgtacttattattattat--tattattattattattattattattattattattattatgcttttcatgatacacagtttgagtatcttgtttttgtgtttgaataaaaaaatgtcttctccag

upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA16G21960.2 (Glycine max), 5'ss of exon 2
GGTTTTTGGGTTGCTTTTAGTCTTTATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcatt-tcactatcttcttttcaatacagtctcctactttggctttcttttcttaattcttagggttcatcatgtggctttccag----------------------------------------------------------------
  |||| || |||||||| ||  | |||||||||||  ||||||||| ||||||||  || |||||| |||||||||||| ||| | | |||  | || | | ||   |        ||    || || |  |  || | | | | ||   | ||  | ||  |                                                                
ACTTTTCGGTTTGCTTTTCGTGCTGATGGTGATTCCTGTTGATGAAAAGAGCAAATTCGGTAGAAAATTATCCAGgtacttattattattat--tattattattattattattattattattattattattatgcttttcatgatacacagtttgagtatcttgtttttgtgtttgaataaaaaaatgtcttctccagaagaaaaaaaaaaatttgggtgtgtttcag
















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|110719781|gb|EE095207.1|EE095207
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|351031411|gb|FQ445436.1|FQ445436
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|351042865|gb|FQ451159.1|FQ451159
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|349830416|gb|FQ420676.1|FQ420676
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|110366687|gb|EC930603.1|EC930603
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|110718650|gb|EE095723.1|EE095723
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|110405821|gb|EC971375.1|EC971375
EST:     AAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: AAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|349810065|gb|FQ401511.1|FQ401511
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|349810606|gb|FQ402849.1|FQ402849
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|77585642|gb|DV221915.1|DV221915
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGAC
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGAC
EST: gi|156739053|gb|EV243166.1|EV243166
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
EST: gi|110719222|gb|EE096951.1|EE096951
EST:     ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAG                         GTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA
genomic: ATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcattt ... ggctttccagGTATATCTGTAAGCATGCTTGCGGTTATTTTCCGGTGACTCTATATGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTTTGGGTTGCTTTTAGTCTTTATGGTGATTCCAATTGATGAAAGGAGCAAATATGGGAGAAAACTATCCAGgtactcatttcactatcttcttttcaatacagtctcctactttggctttcttttcttaattcttagggttcatcatgtggctttccag

- - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA