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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatattgatggaaaaattcaacatgacgaaatcggagagaaaaatgttgcaattttcatagttgtgtgctgattttccgttgcccttttcttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAGGATCTTTCTACAATGCTTATTTTGAG

Basic information

species Vitis vinifera
transcript Vv15s0048g01810.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g01810.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G01960.1 (Glycine max), 3'ss of exon 7
aaatattgatggaaaaat-tcaacatgacgaaatcggagagaaaaatgttgcaattttcatagttgtgtgctgattttc-cgttgcccttttcttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAGGATCTTTCTACAATGCTTATTTTGAG
     ||   | ||| || | ||  |||         |   | | | | |   |     | | |||  ||   ||| |  |  ||   |||| ||   | ||||||||| | ||| |||||||| || ||||| ||||||||||||||||||||||| ||||| ||| |||||||||||
-ggagttagcgcaaatatgtgaatgtgagactgcaataatcatacaagctttgaagaaaaaatttggctgacaattgtggcactgttgttttattctgt-agATGGACACAGTGAAGCAGAATTTGGTATGTCTTGGTGTGCTGGCTTTGGAGGATCATTCTATAATTCTTATTTTGAG

upper sequence: Vv15s0048g01810.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G08570.1 (Glycine max), 3'ss of exon 12
--aaatattgatggaaaaattcaacat---gacgaaatcggagagaaaaatgttgcaattttcatagttgtgtgctgattttccgttgcccttttcttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAGGATCTTTCTACAATGCTTATTTTGAG
  | || |  |||  | | | ||| ||    || || |  ||   |||||  | ||     | | |||||||   ||| |    ||||   | ||||     | |||||||| | ||| |||||||| || ||||| ||||||||||||||||||||||| ||||| ||| |||| ||||||
aaatatgtgaatgtgagactgcaatattcatacaaactttgaagaaaaaaattggc-----tgacagttgtgg--tgact----gttgttttattctg----tcgatggacacagTGAAGCAGAATTTGGTATGTCTTGGTGTGCTGGCTTTGGAGGATCATTCTATAATTCTTACTTTGAG

upper sequence: Vv15s0048g01810.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G61080.1 (Arabidopsis thaliana), 3'ss of exon 7
aaatattgatggaaaaattcaacatgacgaaatcggagagaaaaatgttgcaattttcatagttgtgtgctgattttccgttgcccttttcttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAGGATCTTTCTACAATGCTTATTTTGAG
           | | ||     |||    ||||    || | |  | || | ||||||| ||    ||  |||| |  | || | | |          |||||| ||||| ||||| || || |||||||| ||||| || || ||||||| ||||||||||||||| |||||  ||
-----------gtataagctttcattctcaaattcttgatata--ttttaccattttca-agcaccgttttgatct--cattcctcctccac------agATGGGCATAACGAGGCGGATTTTGGAATGTCGTGGTGCGCAGGATTTGGAGAATCTTTCTACAATGCCTATTTCAAG

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|28966833|gb|CB345866.1|CB345866
EST:     CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACT                         ATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
genomic: CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACTgtaagtccaa ... cttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
EST: gi|351033360|gb|FQ446592.1|FQ446592
EST:     CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACT                         ATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
genomic: CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACTgtaagtccaa ... cttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
EST: gi|30320371|gb|CD003633.1|CD003633
EST:     CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACT                         ATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
genomic: CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACTgtaagtccaa ... cttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
EST: gi|351044742|gb|FQ448996.1|FQ448996
EST:     CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACT                         ATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTTGAG
genomic: CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACTgtaagtccaa ... cttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
EST: gi|32245151|gb|CD710970.1|CD710970
EST:     CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACT                         ATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGTTGGCTTTGGAG
genomic: CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACTgtaagtccaa ... cttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
EST: gi|18458320|gb|BM436598.1|BM436598
EST:     CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACT                         ATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
genomic: CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACTgtaagtccaa ... cttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
EST: gi|71881177|gb|DT030232.1|DT030232
EST:     CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACT                         ATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
genomic: CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACTgtaagtccaa ... cttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
EST: gi|28966778|gb|CB345811.1|CB345811
EST:     CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACT                         ATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG
genomic: CAGCTCTGACAAGAATGGAGAGCCTGTTATACTTGACCCAGCATGTTACTgtaagtccaa ... cttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcaattttcatagttgtgtgctgattttccgttgcccttttcttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAGGATCTTTCTACAATGCTTATTTTGAG
                      tgctgat  putative branch site (score: 3)
                            ttttccgttgcccttt  CT-rich tract
      aattttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatattgatggaaaaattcaacatgacgaaatcggagagaaaaatgttgcaattttcatagttgtgtgctgattttccgttgcccttttcttgaattagATGGACATAATGAGGCAGAATTCGGAATGTCATGGTGTGCTGGCTTTGGAGGATCTTTCTACAATGCTTATTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - ggaaaaa
- - - - - - - - - - -acatgac
- - - - - - - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgc