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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccatttaataccagtttttaacaacatcaaatgaacagctttatgctctccacattggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT

Basic information

species Vitis vinifera
transcript Vv13s0101g00100.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G24340.1 (Glycine max), 3'ss of exon 1
cccatttaataccagtttttaacaacatcaaatgaacagctttatgctctccacat----tggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT
        | | |  |||   |  | || |||  |  |   ||  |    | | ||    |   ||| | || || ||| |  ||| ||  |||   |||| || ||  ||||||| || ||||||||||| ||||||||||| || |||||  | || ||||||||||||||||| ||||| ||  |||||||||||||  | 
--agggggaaatccttttagcagtaaataaaaaaactatacttgagtcgacaatatgatataatatggtgtccttgtttcaagcaactatgtttt--gttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGCCTTCGGGGATGTATTGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC

upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G18290.1 (Glycine max), 3'ss of exon 1
cccatttaataccagtttttaacaacatcaaatgaacagctttatgctctccacat----tggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT
   |      |     ||||| |   |  | | |   |   ||  |    | | ||    |   ||| |||| || |||||  |||   || || || ||| || ||  ||||||| || ||||||||||| ||||||||||| || |||||| | || || || || |||||||| ||||| ||  |||||||||||||  | 
--taagggggaaatccttttagcggaaaaataagtctatacttgagtcgacaatatgatataatatggtatccttgtttgaagcaa-cgatgttttg-ttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCTTCGGGGTTGCATCGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC

upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G38710.2 (Arabidopsis thaliana), 3'ss of exon 1
cccatttaataccagtttttaacaacatcaaatgaacagctttatgctctccacattggcatgttatcattatt--tgacacaaataattttctggtttc--agCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT
   ||||  |      | || |    ||       | |   | | || |      || |  |   ||  ||| |  ||   ||     ||| ||  ||    || ||  ||||||| |||||||||||| ||||||||||||| || ||||| ||||||||||||||||| || || ||||| ||  ||||||||| |||||| 
--tattttgtgttgaatgtttatgg-atgggtgatataatctgaagcgcatactttttgtgt-ccattcttactgatggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC

upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S47_221V6.1 (Physcomitrella patens), 3'ss of exon 1
--cccattta----ataccagtttttaacaacatcaaatgaacagc--tttatgctctccacattggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT
  |   ||||    ||    || || |   |   | |||   | |     |||| | ||    || |  ||||  |  |  ||           || | ||    ||||||| | ||||| || |||||||||||| |||||||||||||||| || ||||| || || ||||| || |||||||| || |   | ||||  || || 
ggcttgtttaccgcatgtatgtcttcagagagtcccaattcgccggagcgtatgttttcagagtttgggtgttgactgtgatttgtg-----ggttctgtga---cagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTC

upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ07623 (Selaginella moellendorffii), 3'ss of exon 1
cccatttaataccagtttttaacaacatcaaatgaacagctttatgctctccacattggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT
                                        |   || |||   |||||   ||  ||  |   ||  |||     ||||||    | |||||| ||||| ||||| ||||||||||| ||||||||||| || ||||| ||||| ||||| || || || || |||||||| |||||||||| |||||| 
---------------------------------------gtaagtgttcttggcattg-tttgccattctctcttt-cacgttccattttccccatgcagCCCACTGTTCGTGACTTGGAAGAAAGTTGTGAATGGTGGAGAGCCTCGCTTGCGAGGATGCATCGGGACGCTGGAAGCTCGCTGCTTGATCACTGGCTTC

upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ11024 (Selaginella moellendorffii), 3'ss of exon 1
cccatttaataccagtttttaacaacatcaaatgaacagctttatgctctccacattggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT
                                        |   || ||    |||||   ||  ||  |   ||  |||     |||||||   | |||||| ||||| ||||| ||||||||||| ||||||||||| || ||||| ||||| ||||| || || || || |||||||| |||||||||| |||||| 
---------------------------------------gtaagtgttcatggcattg-tttgccattctctcttt-cacgttccattttctccatgcagCCCACTGTTCGTGACTTGGAAGAAAGTTGTGAATGGTGGAGAGCCTCGCTTGCGAGGATGCATCGGGACGCTGGAAGCTCGCTGCTTGATCACTGGCTTC

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|110410525|gb|EC976208.1|EC976208
EST:     CCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|349827778|gb|FQ422646.1|FQ422646
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|110401758|gb|EC968377.1|EC968377
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|110384273|gb|EC948699.1|EC948699
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCTTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGAAAGAAAGGAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|161711919|gb|FC060012.1|FC060012
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGACAGTAGTGAATGGTGGGGAACC
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACC
EST: gi|26258672|gb|CA809735.1|CA809735
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|71863642|gb|DT012697.1|DT012697
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|26267150|gb|CA818213.1|CA818213
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|110373876|gb|EC938294.1|EC938294
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|26258698|gb|CA809761.1|CA809761
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|161713972|gb|FC063157.1|FC063157
EST:     CACTACAACAGCCAACATCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGGAGTGAATGGTGGGGAACCGCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|26265515|gb|CA816578.1|CA816578
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGGAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|33408857|gb|CF214484.1|CF214484
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|33410301|gb|CF215928.1|CF215928
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGGAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|294966108|gb|GW837475.1|GW837475
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
EST: gi|161707628|gb|FC056896.1|FC056896
EST:     CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACA                         CCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT
genomic: CACTACAACAGCCAACAGCCCCCTCCTCCTGCCTTCGACGAGGCTCAACAgtattctccc ... ctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctccacattggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT
                          atttgac  putative branch site (score: 4)
                                         ttttct  putative PPT
                  ttatcattatttgaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccatttaataccagtttttaacaacatcaaatgaacagctttatgctctccacattggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
cccattt
- - - -aatacca
- - - - - - - - - - - caacatc
- - - - - - - - - - - - - - -aaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaaat