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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttattctcttttgttctctctgcctttttcttcttgattttgtatagtcttttccccgtactaatgctagaactgcaatatgatatggtccttgaatttgtctgttgtcttctgtaatacgagaaaacccttatgctatcttttgtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATGGCATTTAAGCTCTTTCATGGGAAGGATGGGGTTGTCCCACTCTCAGGGA

Basic information

species Vitis vinifera
transcript Vv02s0033g01160.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0033g01160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g43060.1 (Oryza sativa), 3'ss of exon 2
gtgagttgttattctcttttgttctctctgcctttttcttcttgattttgtatagtcttttccccgtactaatgctagaactgcaatatgatatggtccttgaatttgtctgttgtcttctgtaatacgagaaaacccttatgctatcttttgtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATGGCATTTAAGCTCTTTCATGGGAAGGATGGGGTTGTCCCACTCTCAGGGA
                                                 ||| || | ||| ||  | | |     | ||      |||   ||| | ||  ||    |  | ||| || ||  || | |     |   |||   || |  ||  |    |||   |||||| ||  ||||||||||| |||||||| ||||||||||| |||||||||    | || |||||  | ||||||||||| ||||| |||    
-------------------------------------------------gta-agccctttacc--ttccatcctcataatct---tatcgcatgtttctgaaaa--attggatgtattgtg-gatgccattgctcaactatatcatttgctgcttgtaaagGCAAGAGGAGACAAGGGTCCAATTTTTGAAGATGGACCCAATTTTGACATGGCATTTCGAGTTTTCCATGGCCAAGATGGGGTTGTTCCACTTTCACATG

upper sequence: Vv02s0033g01160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G394410_T01 (Zea mays), 3'ss of exon 2
gtgagttgttattctcttttgttctctctgcctttttcttcttgattttgtatagtcttttccccgtactaatgctagaactgcaatatgatatggtccttgaatttgtctgttgtcttctgtaatacgagaaaacccttatgctatcttttgtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATGGCATTTAAGCTCTTTCATGGGAAGGATGGGGTTGTCCCACTCTCAGGGA
                                                 ||||   |||| |  | |  |  |  |   | |   | |  ||    | ||| |  |      | || ||||| ||     |   |    |||  | | |  ||  |    |||   |||||||||  || || |||||||||||||| || |||||||| |||||||||    | || ||||| |  ||||||||||| ||||| ||||   
-------------------------------------------------gtatgccctttacttcctgttcctctttacattatcacaccatccatttcttaagatcac---tggtgttctggaacgatcgctgaattctat--tgtttgctgcttgtgaagGCAAGAGGAGCCAAGGGACCGATTTTCGAAGATGGGCCTAATTTTGACATGGCATTTCGAGTTTTCCATGGTAGAGATGGGGTTGTTCCACTTTCAGAAG

upper sequence: Vv02s0033g01160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G34650.2 (Glycine max), 3'ss of exon 2
gtgagttgttattctcttttgttctctctgcctttttcttcttgattttgtatagtcttttccccgtactaatgctagaactgcaatatgatatggtccttgaatttgtctgttgtcttctgtaatacgagaaaacccttatgctatcttttgtc--tcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATGGCATTTAAGCTCTTTCATGGGAAGGATGGGGTTGTCCCACTCTCAGGGA
                                                                             ||  |    |||    |  | | | |  |||| | |       |  |||  | |  ||   ||  ||||  |||  ||  |  | |||| |  ||| |||  ||||| || || |||||||| || | |||||  |||||||||||||| ||||||||||||||||| ||  | || || || | ||
---------------------------------------------------------------------------gtgagttatt-tatccctttctacct-atcttgtatttcagtagttcaaatttgggtcaatattttagctaattttcttcaatatttagGTTCATGGATCCAAGGGTCCTATATTTGAAGATGGTCCTAGTTTTGGCATGGCATTTAAGCTATTTCATGGGAAGGATGGAGTCATTCCCCTATCTGAGA

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|110713215|gb|EE088951.1|EE088951
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|37183440|gb|CF602794.1|CF602794
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCC                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|161718564|gb|FC069317.1|FC069317
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|71868835|gb|DT017890.1|DT017890
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCC                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|352791235|gb|FQ477520.1|FQ477520
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCC                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110726338|gb|EE102030.1|EE102030
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCC                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|352795000|gb|FQ477110.1|FQ477110
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCC                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|352773280|gb|FQ470867.1|FQ470867
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110713285|gb|EE089070.1|EE089070
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|71860480|gb|DT009535.1|DT009535
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCC                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110698939|gb|EE077013.1|EE077013
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110712750|gb|EE088067.1|EE088067
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110727083|gb|EE103459.1|EE103459
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCC                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|352765035|gb|FQ473683.1|FQ473683
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110712841|gb|EE088241.1|EE088241
EST:     TCAACAAA-CCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|161707316|gb|FC056844.1|FC056844
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATTTTTCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110733060|gb|EE108901.1|EE108901
EST:     CTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: CTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110711968|gb|EE089049.1|EE089049
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110711233|gb|EE087512.1|EE087512
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110711111|gb|EE087284.1|EE087284
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|110711472|gb|EE087993.1|EE087993
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
EST: gi|294966579|gb|GW837714.1|GW837714
EST:     TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCT                         GTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG
genomic: TCAACAAACCCACCAGCTTTTCCTTCACTTCATCAAATTTCTCCATTCCTgtgagttgtt ... gtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgttgtcttctgtaatacgagaaaacccttatgctatcttttgtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATGGCATTTAAGCTCTTTCATGGGAAGGATGGGGTTGTCCCACTCTCAGGGA
                                    ctatcttttgtctc  CT-rich tract
                                     tatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttattctcttttgttctctctgcctttttcttcttgattttgtatagtcttttccccgtactaatgctagaactgcaatatgatatggtccttgaatttgtctgttgtcttctgtaatacgagaaaacccttatgctatcttttgtctcatcagGTGCGAGGAGCCAGAGGTCCAATTTTCGAAGATGGCCCCAATTTTGATATGGCATTTAAGCTCTTTCATGGGAAGGATGGGGTTGTCCCACTCTCAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG