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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttttatttttttatttttttatttttttatttttttattttttatatatatgtttggaggatgaatatctaacagttacattttgttcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAG

Basic information

species Vitis vinifera
transcript Vv01s0244g00010.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0244g00010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G882527_T03 (Zea mays), 3'ss of exon 3
---------atttttttatttttttat-ttttttatttttttatttttttattttttata-tatat-gtttggaggatgaatatctaacagttacat-tttgttcaatttt----agATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAG
          ||  ||   ||   ||| |||  |||  |  ||| |  ||||   ||||| ||    ||||      | ||  |  |  ||  |||  | || |   ||||    || | | ||| ||| | ||  | ||||||||||| |||||||||||  ||||||||||||| ||||| |||
gtcagattagttacttggattaactatatttgatatactgatatctgcttataagttatagtaggccgtttaagtagtaaactttgagaaggaacaaatgtgcttttttttggacagGTTACTGGAAAGGCCCTGATTCTGGATGAGATTATCAACTATGTGCAGTCCCTGCAGAACCAAGTTGAG
















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|110697604|gb|EE074737.1|EE074737
EST:     TCAGTGAGAGAATGAAGTTTTTGCAATCACTTGTTCCTGGTTGTGACAAG                         ATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
genomic: TCAGTGAGAGAATGAAGTTTTTGCAATCACTTGTTCCTGGTTGTGACAAGgtaagaatct ... tcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
EST: gi|110714473|gb|EE091418.1|EE091418
EST:     TCAGTGAGAGAATGAAGTTTTTGCAATCACTTGTTCCTGGTTGTGACAAG                         ATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
genomic: TCAGTGAGAGAATGAAGTTTTTGCAATCACTTGTTCCTGGTTGTGACAAGgtaagaatct ... tcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
EST: gi|32245670|gb|CD711489.1|CD711489
EST:     TCAGTGAGAGAATGAAGCTTTTGCAATCACTTGTTCCTGGTTGTGACAAG                         ATCATTGGCAAGACTCTGGTACTGGATGAGATAATCAATTATGTCAAGTCC
genomic: TCAGTGAGAGAATGAAGTTTTTGCAATCACTTGTTCCTGGTTGTGACAAGgtaagaatct ... tcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
EST: gi|34416539|gb|CF415293.1|CF415293
EST:     TCAGTGAAAGAATGAAGCTTTTGCAATCACTTGTTCCTGGTTGTGACAAG                         CTCATTGGCAAGACTCTCGTACTGGATGAGATAATCAATTATGTCAAGTCC
genomic: TCAGTGAGAGAATGAAGTTTTTGCAATCACTTGTTCCTGGTTGTGACAAGgtaagaatct ... tcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
EST: gi|110424499|gb|EC990862.1|EC990862
EST:     TCAGTGAGAGAATGAAGTTTTTGCAATCACTTGTTCCTGGTTGTGACAAG                         ATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
genomic: TCAGTGAGAGAATGAAGTTTTTGCAATCACTTGTTCCTGGTTGTGACAAGgtaagaatct ... tcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
EST: gi|30135269|gb|CB920607.1|CB920607
EST:     GGTTGTGACAAG                         ATCATTGGCAAGACTCTGGTACTGGATGAGATAATCAATTATGTCAAGTCC
genomic: GGTTGTGACAAGgtaagaatct ... tcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
EST: gi|110695430|gb|EE073439.1|EE073439
EST:     TCAGTGAGAGAATGAAGCTTTTGCAATCACTTGTTCCTGGTTGTGACAAG                         ATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC
genomic: TCAGTGAGAGAATGAAGTTTTTGCAATCACTTGTTCCTGGTTGTGACAAGgtaagaatct ... tcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatatatgtttggaggatgaatatctaacagttacattttgttcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAG
                         atctaac  putative branch site (score: 2)
                                       ttttgttc  putative PPT
                                      attttgttcaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttttatttttttatttttttatttttttatttttttattttttatatatatgtttggaggatgaatatctaacagttacattttgttcaattttagATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgg