Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatagatcatatgaagtatatcaagcaaaagaaactagctttgtctgtctgtatgcacatatttgctgtttttttcctcacttgtttttatttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCACATGTGGAAGAACAGGCAGGAACTTAAGGTCGAGGATGCTGGTATTGCT

Basic information

species Vitis vinifera
transcript Vv19s0014g04860.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g04860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G042078_T01 (Zea mays), 3'ss of exon 1
-tatagatcatatgaagtatatcaagcaaaagaaac---tagctt-tgtctgtctgtatgcacatatttgctgtttttttcctcacttgtttttatttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCACATGTGGAAGAACAGGCAGGAACTTAAGGTCGAGGATGCTGGTATTGCT
 ||   ||   || | | | | ||   | | | ||    || ||| || |  || | ||     | ||    |||| |  |||   |||| ||| ||     |||  | || ||||| ||||| || ||||||||||||||||||| |||||||||  | |||||||||||| |||| || | |||||||||   ||| ||||| 
ttaataatagcattaggaacagcagttagacgcaatatgtaacttgtgccattcaggattttacttttcatggtttctaacctttgttgtgtttgtt-----cagCCTACCAGGTCGCTATGAGTCATTCTGGAAGGAGCTTGATTGTGTCAAGCAGGTATGGAAGAACAGGAAGGACCTCACGGTCGAGGACCTTGGCATTGCG

upper sequence: Vv19s0014g04860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AC194341.4_FGT002 (Zea mays), 3'ss of exon 1
tatagatcat-atgaagtatatcaagcaaaagaaactagctttgtctgtctgtatgcacatatttgctgtttttttcctcacttgtttttat-ttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCACATGTGGAAGAACAGGCAGGAACTTAAGGTCGAGGATGCTGGTATTGCT
  |   |||| ||         |       |||  | |  | |  || | || |   |   | || || ||  |    | |    ||  | | ||  | |||  | || ||||| ||||| || ||||||||||||||||||  |||||||||  | |||||||||||| |||| || ||||| |||||   ||| ||||| 
-gtccgtcattatttgcccctgctcttggtagacgcaatatgtaact-tgtgcaattagggagttacttttcatggttttaaccattgctgtgtttgttcagCCTACCAGGTCGGTATGAGTCATTCTGGAAGGAGCTTGATGGTGTCAAGCAGGTATGGAAGAACAGGAAGGACCTCAAGGTTGAGGACCTTGGGATTGCG

upper sequence: Vv19s0014g04860.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G03410.1 (Glycine max), 3'ss of exon 2
tatagatcatatgaagtatatcaagcaaaagaaactagcttt--gtctgtctgtatgcacatatttgctgtttttttcctcacttgtttttatttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCACATGTGGAAGAACAGGCAGGAACTTAAGGTCGAGGATGCTGGTATTGCT
  ||  |        || | || |      |||    | | |  ||   | |   || |  | |||  || |  |      |  |  |   || |  | |||||| || |||||| |||| || || |||||||| ||||||||||||||| |  | |||||||||||| | || || ||||| || ||||| || ||||||
-gtatctgcctgtctgtctctctacatggcgaagtctgttctatgttaatttaattgtaggtgtttcttgctgctacatataact-ctagaatcttttgcagTATTCCGGGTCGTAATGAGTCCTTTTGGAAGGAACTTGATTATGTCAAGAATTTATGGAAGAACAGGAAAGAGCTAAAGGTTGAAGATGCAGGCATTGCT

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|30304287|gb|CB981081.1|CB981081
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTACGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110429353|gb|EC995844.1|EC995844
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|34362394|gb|CF403979.1|CF403979
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110709551|gb|EE085109.1|EE085109
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|161710877|gb|FC058575.1|FC058575
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110722766|gb|EE099308.1|EE099308
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|71867287|gb|DT016342.1|DT016342
EST:     GAGAAATGCAATTTTTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|71874607|gb|DT023662.1|DT023662
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110361937|gb|EC925443.1|EC925443
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110717104|gb|EE092668.1|EE092668
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAAGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|34415924|gb|CF414678.1|CF414678
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110707803|gb|EE084620.1|EE084620
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110376288|gb|EC941340.1|EC941340
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|71867013|gb|DT016068.1|DT016068
EST:     GAGAAATGCAATTTTTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|30304081|gb|CB980875.1|CB980875
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110699573|gb|EE076691.1|EE076691
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110391148|gb|EC956105.1|EC956105
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110696780|gb|EE073194.1|EE073194
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110361076|gb|EC924529.1|EC924529
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|71868902|gb|DT017957.1|DT017957
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110717754|gb|EE093885.1|EE093885
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
EST: gi|110399726|gb|EC966248.1|EC966248
EST:     GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAG                         TATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA
genomic: GAGAAATGCAATTTGTTGGCAAAGCAACTATTCTACACTCGCCTTGCTAGgtaattctct ... tttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctgtatgcacatatttgctgtttttttcctcacttgtttttatttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCACATGTGGAAGAACAGGCAGGAACTTAAGGTCGAGGATGCTGGTATTGCT
                             tcctcac  putative branch site (score: 2)
                tttgctgtttttttcc  CT-rich tract
                                  acttgtttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatagatcatatgaagtatatcaagcaaaagaaactagctttgtctgtctgtatgcacatatttgctgtttttttcctcacttgtttttatttcctacagTATCCCTGGTCGTTATGAATCTTTCTGGAAGGAGCTTGATTATGTCAAGCACATGTGGAAGAACAGGCAGGAACTTAAGGTCGAGGATGCTGGTATTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - tcaagca
- - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - -tgtctgt
- - - - - - - - - - - - - - - - - - - - - - - - - gtatgca