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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttgctaggcaccttctaagattatcttgctcatctatttgcctatatataagttttatcctcttgataagttgacaggttttttttttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCATGTCTTTGCTTTCTCACTTGCTGATGATCATATATGGTTCCGGAACTACC

Basic information

species Vitis vinifera
transcript Vv07s0005g04550.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 4
tattttgctaggcacctt--ctaagattatcttgctcatctatttgcctatatataagttttatcctcttgataa-gttgacaggttttttttttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCATGTCTTTGCTTTCTCACTTGCTGATGATCATATATGGTTCCGGAACTACC
     |||  |    | |  |||  ||| |||   |     ||   | | |  |     | |||    ||  ||  | |      ||| ||| ||||  | ||||||||| ||| || ||||| ||||| || ||||| ||||  |||||||| || |||| ||||||| | | |||||| ||||||||||||||||| ||||
---catgcatgttttcctgtctacaattttctctatttctgatgctcttgtccaagtactgtatttgattattactgatatactatttctttcttttattcagATATTTGAAACACCAAAGGACCACAGAAAGGCTAAGCCTTTCCATGATCACGTTTTTGTTTTCTCAATAGTTGATGACCATATATGGTTCCGGAATTACC

upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G28320.2 (Glycine max), 3'ss of exon 5
tattttgctaggcaccttctaag-attatcttgctcatctatttgcctatatataagttttatcctcttgataagttgacaggttttttttttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCATGTCTTTGCTTTCTCACTTGCTGATGATCATATATGGTTCCGGAACTACC
  ||        |   | ||    |  || ||    || | | |||   |     |||  | |  |        | ||| |  ||| ||| | ||  | ||||||||| ||| || ||||| ||||| || || || ||||  |||||||| || |||| ||||||| | | |||||| ||||||||||||||||| || |
-gttccatgcatcttttcctgtctacaattttctgtatttctatgctcttggccgagtactgtatttgattattgctgatatatttctttctcttcttcagATATTTGAAACACCAAAGGACCACAGAAAGGCCAAGCCTTTCCATGATCACGTTTTTGTTTTCTCAATAGTTGATGACCATATATGGTTCCGGAATTATC

upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 4
tattttgctagg--caccttctaagattatcttgctcatctatttgcctatatataagttttatcctcttgataagttgacaggttttttttttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCATGTCTTTGCTTTCTCACTTGCTGATGATCATATATGGTTCCGGAACTACC
  | |||| ||   ||  | ||  ||| || ||  |  || ||| |     |   |   |||  | || | || ||||    | ||| ||| | |   | || | || |||| ||| ||||| ||||||||| |||| ||||| ||||| ||||| ||||  || ||| ||| |||||| |||||||||||||| || ||||
gttgttgccagattcatatccttggataatgtttttggtccattagttctca---agactttcacatcctaattagtt--ttgttttgtttatctc--tcagGTCTTCGGAATTCCTAAGGAACACAGGAAATCTAAGCCTTACCATGACCATGTATTTGTCTTTTCAATTGTTGATGAGCATATATGGTTCCGAAATTACC

upper sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G15460.1 (Arabidopsis thaliana), 3'ss of exon 4
tattttgctaggcaccttctaagattatcttgctcatctatttgcctatata-taagttttatcctcttgataagttgacaggttttttttttttggtta--gATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCATGTCTTTGCTTTCTCACTTGCTGATGATCATATATGGTTCCGGAACTACC
     |   |  | |  | |   ||| |   |   |||  ||||         | |||||  |     |  | |  |   | ||||| |||||||| |||  ||| ||||||| |||  |||  || |||||  |||||||||| ||||| ||||| |||| ||||||  ||| |||||| |||||||||||||| || ||||
----gtctcattctcacttttgaattgtg--gacgatccttttgtagtcgcggttagtttggtttatatcttcaacttttaagttttgtttttttgcttacagATTTTTGGAATTCCCGAGGGACATAGGAAGTCTAAACCTTACCATGACCATGTGTTTGTTTTCTCCATTGTTGATGACCATATATGGTTCCGTAATTACC

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|161716827|gb|FC068099.1|FC068099
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|34544827|gb|CF513059.1|CF513059
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGGGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110417096|gb|EC983122.1|EC983122
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110723555|gb|EE101001.1|EE101001
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|34549744|gb|CF517976.1|CF517976
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGGGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110731138|gb|EE109014.1|EE109014
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|30252907|gb|CB970458.1|CB970458
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110702082|gb|EE080390.1|EE080390
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110720764|gb|EE096972.1|EE096972
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGANAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|30329834|gb|CD013096.1|CD013096
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110719294|gb|EE097103.1|EE097103
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110685809|gb|EE062855.1|EE062855
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110732371|gb|EE107597.1|EE107597
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110373531|gb|EC937775.1|EC937775
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|27585576|gb|CB008271.1|CB008271
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110718547|gb|EE095508.1|EE095508
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|30330375|gb|CD013637.1|CD013637
EST:     CAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: CAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|30252991|gb|CB970542.1|CB970542
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
EST: gi|110685111|gb|EE063162.1|EE063162
EST:     ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAG                         ATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT
genomic: ATTTTGATAAGGACCCCCACTGGAAACTTCTCAAGGAGATGATCACACAGgtatatctat ... ttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatatataagttttatcctcttgataagttgacaggttttttttttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCATGTCTTTGCTTTCTCACTTGCTGATGATCATATATGGTTCCGGAACTACC
                           agttgac  putative branch site (score: 4)
                                     ttttttttttttggtt  putative PPT
                                     ttttttttttttggtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttgctaggcaccttctaagattatcttgctcatctatttgcctatatataagttttatcctcttgataagttgacaggttttttttttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCATGTCTTTGCTTTCTCACTTGCTGATGATCATATATGGTTCCGGAACTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - ttgctag
- - - - - - caccttc
- - - - - - - - - - - - - - cttgctc
- - - - - - - - - - - - - - - - - - - - - tgcctat