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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTAAAGGGAGGGAAGTTGAGGATGATGACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttattatatatttggtcaagagtctgacaagtatcaaaaacataattttaaatgattttgtaatttttatgtacttgatttttctttttttaac...

Basic information

species Vitis vinifera
transcript Vv10s0003g03710.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA15G10030.2 (Glycine max), 5'ss of exon 14
TTGCCTAAAGGGAGGGAAGTTGAGGATGATGACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttattatatatttgg-----tcaagagtctgac-aagta---tcaaaaacataattttaaatgattttgtaatttttatgtacttgatttttctttttttaac----------------------------------------------
||||| || || || || || |||||||||||||||||| | || |||||||||||||| |||||||| || |||||||| ||    | |    ||  || |     | | |  || ||  ||||       |||| || ||||    |    ||| | ||   ||    ||     | || |   |||                                               
TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAAGGGTTTACAGCTCCTCTTTATCGTATAAAGgtacaat-acccgatgcttaggagcattagggatcagattaagtgaatcttaaaatatcatttgcgttttagttgcagttaccata-gtttagccctcctctaaataatgattatgcgattctttttccaactaatttgatgttggggagtgtag

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA13G29010.1 (Glycine max), 5'ss of exon 15
TTGCCTAAAGGGAGGGAAGTTGAGGATGATGACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttattatatattt-ggtcaagagtctgacaagtatcaaa--aacataattttaaatgattttgtaatttttatgtacttgatttttctttttttaac--------------------------------------------
||||| || || || || || |||||||||||||||||| | || |||||||||||||| |||||||| || |||||||| || | | ||    ||  || || |  | |      | | |||| |  ||   ||| |||||   |  | |   ||||||    ||   | | || |   |||                                             
TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAAGGGTTTACAGCTCCTCTTTATCGTATAAAGgt-actatacctgatgcttaggacttgggagcattagggatcagattaagtgaatcttaaaatttcatttgcgttttata-gtttagctctcctctaaataatgattgaggttctttttccaactaatttggtgttggggattgcag

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA08G10180.1 (Glycine max), 5'ss of exon 14
TTGCCTAAAGGGAGGGAAGTTGAGGATGATGACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtga-gtttattat------atatttggtcaagagtctgacaagtatcaaaaacataattttaaatgattttgtaatttttatgtacttgatttttctttttttaac----------------------------------------
 |||| ||||| || || || ||||| |||||||||||| | || ||||| |||||||| |||||||| ||||||||||| ||     | |||        | | ||||||     | |   | | |||  ||   |  |||||| | |   |  || ||  |    |   ||   | ||| |||||                                         
ATGCCCAAAGGAAGAGATGTGGAGGACGATGACTCATTTGTTTTTAATGATGGGTTTACAGCTCCTCTTTACCGTATAAAGgtattactcattgcttttgaacacttggtctcatatattggatgaatctgaactgtg-ttttaattcaacctcaaaattaaaaactcagtataaatttttctttaatcaggttgttttcatactaattttgaagttatgaaatgcag

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA05G27240.1 (Glycine max), 5'ss of exon 14
TTGCCTAAAGGGAGGGAAGTTGAGGATGATGACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagttta-------ttatatatttggtcaagagtctgacaagtatcaaaaacataattttaaatgattttgtaatttttatgtacttgatttttctttttttaac----------------------------------------
 |||| ||||| || || || ||||| ||||||| |||| | || ||||| |||||||| |||||||| ||||||||||| |||  | |        ||  | | ||||||     |  ||  | | | ||        |||||| | |   |  || ||  | |      ||   | | | |||||                                         
ATGCCCAAAGGAAGAGATGTGGAGGACGATGACTTATTTGTTTTTAATGATGGGTTTACAGCTCCTCTTTACCGTATAAAGgtgtttctcattgcttttgaacacttggtctcatattggaggaatctgaactttgcg-ttttaattcaacctcaaagttaaaagcttggcataaatttgtctttaatcaggtttttttcatactaatttttaagttatgaagtgcag

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|110358187|gb|EC922223.1|EC922223
EST:     ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAA                         GTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
genomic: ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttat ... ttaaatacagGTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
EST: gi|71878599|gb|DT027654.1|DT027654
EST:     ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAA                         GTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
genomic: ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttat ... ttaaatacagGTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
EST: gi|110357401|gb|EC920914.1|EC920914
EST:     ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAA                         GTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
genomic: ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttat ... ttaaatacagGTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
EST: gi|110417958|gb|EC984063.1|EC984063
EST:     ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAA                         GTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
genomic: ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttat ... ttaaatacagGTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
EST: gi|71879873|gb|DT028928.1|DT028928
EST:     ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAA                         GTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
genomic: ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttat ... ttaaatacagGTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
EST: gi|30133901|gb|CB919240.1|CB919240
EST:     ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAA                         GTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT
genomic: ACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttat ... ttaaatacagGTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCTAAAGGGAGGGAAGTTGAGGATGATGACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAAgtgagtttattatatatttggtcaagagtctgacaagtatcaaaaacataattttaaatgattttgtaatttttatgtacttgatttttctttttttaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaca