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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accctttattttatcacatgaaatgtgtatttccatagtttgccaattttgggtcattttattgttgaaccaacttcactaactggttgatgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG

Basic information

species Vitis vinifera
transcript Vv01s0026g02470.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
accctttattttatcacatgaaatgtgtatttccatagtttgccaattttgggtcattttattgttgaaccaacttcactaactggttgatgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG
                  ||| ||||    || |||   |       | |  |   |     | |||  |   | | |||        ||  || ||||||||||  ||||||| |||||||||||| | ||||| |||||||| ||||| |||    | ||||| ||||| || ||  |||| || |||
-------------gtgagtgagatgtagcctttcatttgtacttggatgttagcggtccagatattgctctgtcctgact-------cgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 6
-----accctttattttatcacatgaaatgtgtatttcca-tagtttgccaattttgggtcattttattgttgaaccaacttcactaactggtt--gatgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG
         || | ||| ||   | |      |  ||||| |  |||    ||||      | |  | | | || ||||| | |    | | |    ||  | ||||||||||||||||||| |||||||| ||| || | || |||||||| ||||| ||||| || |||||  ||||||||||  |||| || || 
gtgagtgatttgagtttttctttttagtcaaattcttccaatgttttattgatttcaa---aatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G11960.1 (Glycine max), 3'ss of exon 6
-------------accctttattttatcacatgaaatgtgtatttcca-tagtttgccaattttgggtcattttattgttgaaccaacttcactaactggttgatgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG
                 ||| ||||    || |   |    || |||| |  |||    ||||      | |  | ||  || || || | |    ||   | ||  | ||||||||||||||||||| || ||||| ||| || | || |||||||| ||||| ||||| || |||||  ||||||||||  |||| || || 
gtaagtgatttgagttttttctttttagtcaagttcttcccatgtccaatgttttattgatttcaa---aatgcaatgcagagcccacctaatctgctcact-attttctgcagCTTTTCTTGCTTCGTGCCGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA

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|30327724|gb|CD010986.1|CD010986
EST:     TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCT                         CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
genomic: TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
EST: gi|351030409|gb|FQ432347.1|FQ432347
EST:     TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCT                         CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGGC
genomic: TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
EST: gi|110685836|gb|EE062903.1|EE062903
EST:     TACAGATGCAGATACTGATGGAGATGATGACACATTCA-CTTTTTTCTCT                         CTTTTCTTGCCTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
genomic: TACAGATGCAGATACTGATGGAGATGATGACACAT-CAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
EST: gi|110689841|gb|EE066416.1|EE066416
EST:     TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCT                         CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
genomic: TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
EST: gi|110713173|gb|EE088860.1|EE088860
EST:     TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCT                         CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
genomic: TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
EST: gi|32248365|gb|CD714184.1|CD714184
EST:     TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCT                         CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
genomic: TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
EST: gi|32249399|gb|CD715218.1|CD715218
EST:     TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCT                         CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
genomic: TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
EST: gi|30298557|gb|CB975351.1|CB975351
EST:     TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCT                         CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGGTACATTATGGCC
genomic: TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
EST: gi|30327239|gb|CD010501.1|CD010501
EST:     TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCT                         CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
genomic: TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
EST: gi|110715491|gb|EE093604.1|EE093604
EST:     TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCT                         CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC
genomic: TTACAGATGCAGATACTGATGGAGATGATGACACATCAACTTTTTTCTCTgtgagatttg ... tgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgggtcattttattgttgaaccaacttcactaactggttgatgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG
          attttattgttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accctttattttatcacatgaaatgtgtatttccatagtttgccaattttgggtcattttattgttgaaccaacttcactaactggttgatgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
-cccttta
- - - - - - -tcacatg
- - - - - - - - - - - - - - - - - - -gtttgcc
- - - - - - - - - - - - - - - - - - - - - - - ttttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttga