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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagctatggactgtcaagacatggacaatactcagtattaacttcttttataaatatatctatccaagttctaggccccagcaaaaattttccat...

Basic information

species Vitis vinifera
transcript Vv17s0000g02140.t01
intron # 34
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g02140.t01 (Vitis vinifera), 5'ss of exon 34
lower sequence: GLYMA07G11610.1 (Glycine max), 5'ss of exon 32
GGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagctatggactgtcaagacatggacaatactcagtattaacttcttttataaatatatctatccaagttctaggccccagcaaaaattttccat-------
|||||||||||||||||||||||| ||||| |||||| |||||||||||||||| |||||  |||||||||||||||||||||||||||| || |||||||| || | |  |     ||||| | || ||   |  |  ||||    ||  |||||    ||| |    |||   | |||    |  |    || |           
GGGTGGATATGCTGTTGGAGCATTTAATGTATATAATTTGGAAGGAGTTGAGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAGgtcaggaacagtcag--gtcaaaatattgat--ttgtatgtatcccttttctttattgtgatagca---caaaaacgaggggagaaaagtggttgttggaaagccgc

upper sequence: Vv17s0000g02140.t01 (Vitis vinifera), 5'ss of exon 34
lower sequence: AT1G18270.1 (Arabidopsis thaliana), 5'ss of exon 36
GGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagctatggactgtcaagacatggacaatactcagtattaacttcttttataaatatatctatccaagttct------aggcccca-gcaaaaattttccat------------------------------
 ||||||||||| ||||||||||| || || ||||| ||||||||| | || || ||||| || || |||||||||||| | |||||||| || || ||||||||    |   |||    |    ||     |||  || ||  |||  |    || || ||     ||  |||| |      | | || |  |||| |  ||  ||                              
AGGTGGATATGCAGTTGGAGCATTTAACGTGTATAACCTGGAAGGAATAGAAGCTGTTGTAGCGGCCGCAGAGGAAGAAAATAGTCCTGCTATATTGCAGgttagtg--ttctgaccaaaagtggatttctgatatacaatagcaac--caaagattaacattctgttctgagttgttcaaagatgtccgacacaaagagatttgataactgaactttttttggctaccttttttag
















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|349820359|gb|FQ403975.1|FQ403975
EST:     AGGCAGTTGCTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|349819138|gb|FQ412032.1|FQ412032
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|349824597|gb|FQ413264.1|FQ413264
EST:     AGGCAGTTGTTGCTGCTGCAGAGGGAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGCATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|71870716|gb|DT019771.1|DT019771
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|71887135|gb|DT036190.1|DT036190
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|30253243|gb|CB970794.1|CB970794
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         CTCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|71890098|gb|DT039153.1|DT039153
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|349817092|gb|FQ399839.1|FQ399839
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|349808649|gb|FQ405793.1|FQ405793
EST:     AGGCAGTTGTTGCTGCTGCGGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|30323090|gb|CD006352.1|CD006352
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|32247669|gb|CD713488.1|CD713488
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|349826605|gb|FQ418696.1|FQ418696
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|349824745|gb|FQ414603.1|FQ414603
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|30326313|gb|CD009575.1|CD009575
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|30130704|gb|CB916043.1|CB916043
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|30324336|gb|CD007598.1|CD007598
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|32268416|gb|CD717575.1|CD717575
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|349820676|gb|FQ408505.1|FQ408505
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
EST: gi|349808888|gb|FQ406738.1|FQ406738
EST:     AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAG                         ATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT
genomic: AGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagct ... gtttttccagATCCATCCTAGTGCTTTAAAACAAGGAGGAATTCCCTTGGTCGCATGTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagctatggactgtcaagacatggacaatactcagtattaacttcttttataaatatatctatccaagttctaggccccagcaaaaattttccat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaaa