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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactacttgcccgtctctttgttgcattttgtttataaacataattctggtcttacttatagcatgtaataatggctacag

Basic information

species Vitis vinifera
transcript Vv13s0019g00840.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactactt---gcccgtctctttgttgcattttgtttataaacataattctggtcttacttatagcatgtaataatg-gctacag
|| || |||||||| || || || ||| |||||||| | || |||||||||||||||||||| |||||||    |  ||   ||   |    ||||   ||     |||| |  |  ||     |  |      ||  | | ||  ||  || |||
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactat----ataatgaagggaggtttttatgttgtactgcag

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 6
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactacttgcccgtctctttgttgcattttgtttataaacataattctggtcttacttatagcatgtaataatggctacag
|| || ||||||||||| ||||| ||| |||||||| |||| ||||| |||||||||||||| ||||  |        ||  | ||    | |||  | ||         |||  |      || | ||| || || || |      | |||
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcag--------tgttcatcatgctattgattcttccaccgcctcatg-tgaaaaactcagttacagaatttattttgaattgcag

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G382038_T01 (Zea mays), 5'ss of exon 7
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactacttgcccgtc--tctttgttgcattttgt-ttataaacataatt-ctggtcttacttatagcatgtaataatggctacag
|| || ||||||||||| ||||| ||| |||||||| | || ||||| |||||||||||||| ||||  |     |     || |   |  ||    |   |  | | | ||||  | || |||   ||| || |    || |             
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcagtgttcatcatgccattgattcttccaacgcctcatgtgaaaaactcagttactgaatttatttttgaattgcag------------

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 5
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactacttgcccgtc--tctttgttgcattttgt-ttataaacataatt-ctggtcttacttatagcatgtaataatggctacag
|| || ||||||||||| ||||| ||| |||||||| | || ||||| |||||||||||||| ||||        |     || |   |  ||   ||   |  | | | ||||  |||| | |   ||| || |    || |             
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcag------------

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 12
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactacttgcccgtc--tctttgttgcattttgt-ttataaacataatt-ctggtcttacttatagcatgtaataatggctacag
|| || ||||||||||| ||||| ||| |||||||| | || ||||| |||||||||||||| ||||  |     |     || |   |  ||   ||   |  | | | ||||  | || |||   ||| || |    || |             
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcagtgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcagttactgaatttatttttgaattgcag------------

upper sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G157772_T02 (Zea mays), 5'ss of exon 3
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactacttgcccgtc--tctttgttgcattttgt-ttataaacataatt-ctggtcttacttatagcatgtaataatggctacag
|| || ||||||||||| ||||| ||| |||||||| | || ||||| ||||||||| |||| ||||  |     |     || |   |  || | ||   |  | | | ||||  | || | |   ||| || |    || |             
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTAGAGCTAGgtcagtgttcatcatgccattgattcttctagcgcctcatgtgaaaaactcagttacagaatttatttttgaattgcag------------

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|110700937|gb|EE078028.1|EE078028
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|71860037|gb|DT009092.1|DT009092
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATG
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATG
EST: gi|30132964|gb|CB918303.1|CB918303
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|33410540|gb|CF216167.1|CF216167
EST:     GTTGGGGCTTGCC-AGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|71882833|gb|DT031888.1|DT031888
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110703601|gb|EE080591.1|EE080591
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110690502|gb|EE067657.1|EE067657
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110702160|gb|EE080556.1|EE080556
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|156736486|gb|EV240607.1|EV240607
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|71859225|gb|DT008280.1|DT008280
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110369469|gb|EC933629.1|EC933629
EST:     CACCTTGAACATGTGGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: CACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110357315|gb|EC920771.1|EC920771
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110723901|gb|EE099257.1|EE099257
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|30132893|gb|CB918232.1|CB918232
EST:     GAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110720753|gb|EE096961.1|EE096961
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110721290|gb|EE098120.1|EE098120
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGGTGATCCTCTTGTGCATC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGG-TGATCCTCTTGTGCATC
EST: gi|110727671|gb|EE104694.1|EE104694
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAAGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110714087|gb|EE090592.1|EE090592
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110719051|gb|EE096588.1|EE096588
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110687991|gb|EE066031.1|EE066031
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110373757|gb|EC938084.1|EC938084
EST:     AACATGTTGGGGCTTGCCAAGAGAGTTGGAG-CAA                         GATTTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATC
genomic: AACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGA-TTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATC
EST: gi|33407947|gb|CF213574.1|CF213574
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|71862913|gb|DT011968.1|DT011968
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110692310|gb|EE071412.1|EE071412
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|110356627|gb|EC919593.1|EC919593
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
EST: gi|30299440|gb|CB976234.1|CB976234
EST:     GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCAAG                         GATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC
genomic: GTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaact ... atggctacagGATTTTGCTCACATCAACTTCAGAGGTGTATGGTGATCCTCTTGTGCATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactacttgcccgtctctttgttgcattttgtttataaacataattctggtcttacttatagcatgtaataatggctacag

- - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG