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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaaaatttaacagccaaaatatgaaagccacacccagatagacgttttatagttatattatatctttgtttttagttcaaccattttttttttcaattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAGAGCCCAGACAAAGGAGCAAGTAAATGCCCCCGAAGATTTACCACCACAA

Basic information

species Vitis vinifera
transcript Vv11s0016g02270.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AC208327.4_FGT003 (Zea mays), 3'ss of exon 11
gtaaggaaaatttaacagccaaaatatgaaagccacacccagatagacgttttata-gttatattatatctttgtttttagttcaaccattttttttttcaattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAGAGCCCAGACAAAGGAGCAAGTAAATGCCCCCGAAGATTTACCACCACAA
        |  |        |   | |         || | | | |   | | | | |   |      | |||| ||  |  ||   | |   || |||  |||   ||||| |||||||| ||  | |||| ||||| ||| ||||||||||||||||||||  |||  |||||||| | ||| || || |||||||| || ||||||
------gtagctccctctttaccttctccggtttggacgc-gctgggtttctgaaatgccgtgcctagtatttgcttacacctc--tcctgaattgtttggatt--tagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAA

upper sequence: Vv11s0016g02270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G28040.2 (Glycine max), 3'ss of exon 11
gtaaggaaaatttaacagccaaaatatgaaagccacacccagatagacgttttatagttatattatatctttgtttttagttcaaccattttttt--tttcaattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAGAGCCCAGACAAAGGAGCAAGTAAATGCCCCCGAAGATTTACCACCACAA
      | ||  ||   ||      ||||    || | |   |  |    ||| |  || | |||| | | | |||    ||  || | |||| |    |   |   ||| ||||||||||| ||||||||||| |||||||||||||||||||| || | |||  | || || || ||||| |||||||| |||||||| || || |||
-----cagaacctacatgc----gcatgagcttcatagcaccactgctccttttttctt-tgttatttatgtatttgggatttgacaagttttgtaacctttctccacagTATATGGGACCTTTCTTTAGAAAAGGATGAGGAAGAGGAGGCTGAATTTAAAGCTAAAACCAAAGAACAAGTTAATGCCCCTGAAGATTTGCCTCCCCAA

upper sequence: Vv11s0016g02270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G11020.1 (Glycine max), 3'ss of exon 11
-gtaaggaaaatttaacagccaaaatatgaaagccacacccagatagacgttttatagttatattatatctttgtttttagttcaaccattttttttttcaattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAGAGCCCAGACAAAGGAGCAAGTAAATGCCCCCGAAGATTTACCACCACAA
  |  ||            | | ||  |  ||||  |||     |   | |||| |  || | |||||| |  | ||| |    |   || |    |||||     ||||||||||||||| ||||||||||| || ||||||||||||||||| || | |||  | || || || ||||| ||||| || |||||| | || || |||
ctttgggtctgacccttcccaagaacttacaagcaccac-----tgccccttttctctttgttttatatttgggatttaa--caagttatgtaacctttcacca--cagAATATGGGACCTTTCTTTAGAAAAGGACGAGGAAGAGGAGGCTGAATTTAAAGCTAAAACTAAAGAACAAGTTAATGCTCCTGAAGATCTGCCTCCCCAA

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|110369277|gb|EC933431.1|EC933431
EST:     CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGAC                         AATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGACgtaaggaaaa ... caattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
EST: gi|110410877|gb|EC976571.1|EC976571
EST:     CCACATGAAGCCTCCACATTGGCAGTTTTTTCATCCGACAATCAACTGAC                         AATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGACgtaaggaaaa ... caattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
EST: gi|110362753|gb|EC926305.1|EC926305
EST:     CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGAC                         AATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGACgtaaggaaaa ... caattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
EST: gi|110389219|gb|EC954039.1|EC954039
EST:     CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGAC                         AATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGACgtaaggaaaa ... caattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
EST: gi|110714196|gb|EE090829.1|EE090829
EST:     CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGAC                         AATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGACgtaaggaaaa ... caattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
EST: gi|30137851|gb|CB923189.1|CB923189
EST:     CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGAC                         AATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGACgtaaggaaaa ... caattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
EST: gi|30134182|gb|CB919520.1|CB919520
EST:     CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGAC                         AATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCCTCCACATTGGCAGTTTCTTCATCCGACAATCAACTGACgtaaggaaaa ... caattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttatattatatctttgtttttagttcaaccattttttttttcaattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAGAGCCCAGACAAAGGAGCAAGTAAATGCCCCCGAAGATTTACCACCACAA
                                ccattttttttttc  CT-rich tract
     tatattatatctttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaaaatttaacagccaaaatatgaaagccacacccagatagacgttttatagttatattatatctttgtttttagttcaaccattttttttttcaattaccagAATATGGGACCTCTCTTTAGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAGAGCCCAGACAAAGGAGCAAGTAAATGCCCCCGAAGATTTACCACCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA