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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttattatgcatgtcttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG

Basic information

species Vitis vinifera
transcript Vv04s0008g03720.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 3'ss of exon 5
-------------taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttatt---atgcatgtcttgtttttaatttg--------tatattccttcc--tagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG
             | |||| |   | |     |       | || | |     ||     |||    ||   |||   |   |||| |   |   ||||||         || ||  || |   ||  |  |||||||||||||||||||||| || |||||||| ||| | || ||| ||| ||| || |||||  | |||| ||||
gtattgcagtttttgaaattttcttattacaatggatgtgtatactactgaactttagcatttcaaaaaagaattgaaacatatgtttccatacaaatttggtaatgatcatttttatttcaccagCCTAGCAGAAATTCAGAATGCACGAGGCATCATGGATGTTCTTTCCGAGATGTTGAATGCTTTGGATCCTAGTAACAGAGAG

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 5
-------taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttattatgcatgtcttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG
       | ||     |   | |  ||  | ||||| ||   |  ||| |  | | |  | ||| ||| |  ||  |  | || |       | || |||   | |||||||||||||| ||||||||||| ||| | |||||||| ||| |||| ||| ||| |||  | ||||| || |||| ||||
ggccttgtcaagcaactgcatgtaattccc-tctttaatattaaagttgccttttctaaggaaggtataaatcacattatcttgt------atctactccccaccagTTTGACAGAAATCCAGAATGCACGTGGTGTCATGGATGTTCTTTCAGAGATGTTGAATGCTATTGATCCTGGCAACAGAGAG

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G053925_T02 (Zea mays), 3'ss of exon 5
taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttattatgcatgtcttgtttttaatttgtatattc-cttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG------------------
| | || | | ||  || || | || |||     | || | | |   ||  |  |   |||   ||||      ||  ||||   |    |   || | ||  | |||||||||||||| ||||| || || |||||||| ||| |||| ||||||  ||| ||||||||||| |||| ||||                  
ttatatttatttca-tgttttagatgtttgtgaacttgctgttgtcattggtttagcctatccagcatacaagtttggtaatgattgcggtaatttaccagCCTTACAGAAATTCAGAACGCACGTGGCATCATGGATGTTCTTTCAGAGATGCTGGATGCTTTAGATCCAGGTAACAGAGAGGTACTTTCCTGATGCACC

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 5
taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttattatgcatgtcttgtttttaatttgtatattc-cttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG
| | || | | ||  || || | || |||     | || | | |   ||  |  |   |||   ||||      ||  ||||   |    |   || | ||  | |||||||||||||| ||||| || || |||||||| ||| |||| ||||||  ||| ||||||||||| |||| ||||
ttatatttatttca-tgttttagatgtttgtgaacttgctgttgtcattggtttagcctatccagcatacaagtttggtaatgattgcggtaatttaccagCCTTACAGAAATTCAGAACGCACGTGGCATCATGGATGTTCTTTCAGAGATGCTGGATGCTTTAGATCCAGGTAACAGAGAG

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G153138_T02 (Zea mays), 3'ss of exon 5
--taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttatta-tgcatgtcttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG
   |||  |    |  |  ||  | || |    |   |    | |       |||    |||| | ||||| | |  |   | | |    |||   |||  ||  || |||| ||||||||||| || |||||||||||||| ||||| || ||||||| ||| ||||  || ||||||| ||||
agcaaatgcccaatagcacgtgcaaatttcccttgagaataatacatctgagttgttt-ttatgactgcatttataatgaatgaatgccctatattttc--agCATGTCAGAGATTCAGAATGCTCGTGGTATTATGGATGTACTTGCCGAGATGCTGAATGCTTTAGGCCCTGGAAACAGAGAG

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G062953_T01 (Zea mays), 3'ss of exon 5
taaaatctgtctctctggttaacatct-tttattgcatggtttcgatctttttgcaagttattatgcatgt-cttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG
  ||| | |    |   |   | |    |||  |    |  |     | | | |   ||| | |||  ||  ||| |  | |||   |   |   ||   ||  || | || ||||| || ||  | |||||||||||||| ||||| || ||||||| ||| ||||| |||||||||| ||||
--aaagcagcaagtacagcacatacaaatttcctttgagactatatacatctgggttgttttcatgactgcgcttatactgaatgaatgcctatattttcagCATGTCGGAGATTCATAACGCTTGTGGTATTATGGATGTACTTGCTGAGATGCTGAATGCTTTAGACCCAGGAAACAGAGAG

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 5
---taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttattatgcatgtcttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG
   | |      |     ||      |  ||||  | ||   | ||     | | |  |   | |||     |||  | | | |||  | | ||| || |||||||||| ||||||||||||||||| || || |||||||| |||||||||||||| | ||| ||||| ||  | |||||||| 
gtattagggtgatgataatgagagttaagttttggtacagattgtca--tatatagttatgcagtattttcttctaatatctgattgatct-ttcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 5
------taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttattatgcatgtcttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG----
      | |      |       |||||  | |  ||  |  ||   |  ||  || ||||   |||||||    |||  | | |||||  | | ||| ||  ||||||||| ||||||||||||||||| || || |||||||| |||||||||||||| | ||| ||||| ||  | ||||||||     
gtattatgacgatgataatgagagttaagttttggtacagattgccatatatagttatgcag--tattatgt---tctaatatctaattgatct-ttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 5
taaaatctgtctctctggttaacatcttttattgcatggtttcgat-ctttttgcaagttattatgcatgtcttgtttttaatttgtat---attccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG
     | ||  |   | ||| |   | | ||| | |||  || | | ||   |     ||  |   ||    ||  || |  | | | |   |||| ||   |||||| | || ||||| ||||||  |||||| |||||||| ||||| || ||||||||||||||||| || |||||||| |||
---tgtttgcttgctttgtttaggacgtatat-gtatgcctttgttgctcagtatttattgcttctcaaaattttattctgctgtatgtcaaattctttttcagTTTGTCGGAGATTCAAAATGCAAAAGGTATCATGGATGTGCTTGCGGAGATGCTGAGTGCATTAGAGCCCGGAAACAAGGAG

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|352764099|gb|FQ467669.1|FQ467669
EST:     CGGCAAGAAGGAGCTGAGTCTTCTACCGAGTCTGAGTTTCCTACCTTGAG                         TTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAAT
genomic: CGGCAAGAAGGAGCTGAGTCTTCTACCGAGTCTGAGTTTCCTACCTTGAGgtacatctat ... tccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAAT
EST: gi|33406474|gb|CF212101.1|CF212101
EST:     CGGCAAGAAGGAGCTGAGTCTTCTACCGAGTCTGAGTTTCCTACCTTGAG                         TTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAAT
genomic: CGGCAAGAAGGAGCTGAGTCTTCTACCGAGTCTGAGTTTCCTACCTTGAGgtacatctat ... tccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAAT
EST: gi|18459792|gb|BM438070.1|BM438070
EST:     CGGCAAGAAGGAGCTGAGTCTTCTACCGAGTCTGAGTTTCCTACCTTGAG                         TTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAAT
genomic: CGGCAAGAAGGAGCTGAGTCTTCTACCGAGTCTGAGTTTCCTACCTTGAGgtacatctat ... tccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttgcaagttattatgcatgtcttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG
                              ttttaat  putative branch site (score: 3)
                                          tattccttcct  putative PPT
                        tcttgtttttaatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttattatgcatgtcttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - -tctctct
- - - - - - - - - - - - - - - - -gcatggt
- - - - - - - - - - - - - - - - - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcatg