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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttttgtacgcattcaagcacagtagtgtttccagttagaataattcgaggattgagaaccatttttctcaatggacatgtttggtttgacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA

Basic information

species Vitis vinifera
transcript Vv12s0057g01270.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 8
agtttttgtacgcattcaagcacagtagtgtttccagttagaataattcgaggattgagaaccatttttctcaatggacatgtttggtttgac------attgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA
    ||| |  |||  ||       |  ||||   || ||      |||    ||   |    || | | ||  |     | |||  | |||       | | ||||| ||||| |||||||||||||| ||||| |  |||||    |||||||||||||||||||||||||| || || || || |||||    || || || |
----tttattagcaagca--tttcattctgttgtgagatatttctgttctcttatcatgttgtatatgtatctctaattctcttttttctgatcaaatgaattcagCTCGTTTCATGGGAAGAAGGTGGCTATAAAATTTCTGATTCTCCAATGCCCCGAGGAGAGGTTGTAGTTGGTGGATACAGCATAACAAAAGGTTATTTCA

upper sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G07060.1 (Glycine max), 3'ss of exon 7
agtttttgtacgcattcaagcacagtagtgt---ttccagttagaataattcgaggattgagaaccatttttctcaa----tggacatgtt---tggtttgacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA
         |    || |   | |||| | |   || ||||| |    | |  |   || ||| || |   |   |     | ||  | ||   |  | ||    |  |||||||||||||||||||||| ||||||  |||||| |||||||||||||| || |||||| ||||||| ||||| | |||| | ||||| || |||||||
-------acatatcttgagttatagtactataagttgcagttggtgccacttaa---ttaagagccttaaatgggaggagtttgatttctttattaatgtggttatatagCTTGTTTCTTGGGAAGAAGGAGGGTATCTGACATCAGACAAACCAATGCCACGCGGAGAGATTGTAGTTGGGGGATTTAGTGTGACTGCCGGTTACTTTA

upper sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 8
----------agtttttgtacgcattcaagcacagtagtgtttccagttagaataattcgaggattgagaaccatttttctcaatggacatgtttggtttgacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA
          |  | ||   |    |  | |     | || | | | ||||||    |  | | | | |||||   |||||  |   |  || |||         |  |||||||||||||||||||||| ||||||  |||||| || |||||||||||  | |||||| ||||||| || || | |||| | || ||||| |||||||
acaaattcatatctcttaatctgtatagaacttgcaattgatgctacttagaaggcctatatggt-gggaacctgatttctttactaatgtgcttg---------tatagCTTGTTTCTTGGGAAGAAGGAGGGTATCTGACATCAGATAAACCAATGCCAAGGGGAGAGATTGTAGTTGGAGGATTTAGTGTGACAGCTGGTTACTTTA

upper sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G07280.1 (Glycine max), 3'ss of exon 7
agtttttgtacgcattcaagcacagtagtgtttccagttag-aataattcgaggattgagaaccatttttctcaatggacatgtttggtttgacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA
    || ||     || |     | |||   || ||||| |  ||| || || |  | | |         |   ||     ||||   ||||    |  |||||||||||||||||||||| ||||||  |||||| || |||||||||||  | |||||| ||||||| || || | |||| | || ||||| |||||||
caaattcgtgtctcttaatctgtattagaacttgcagttggtgatacttagaaggctcatatggtgggaacctgatttctttgtt-aatttggttgtatagCTTGTTTCTTGGGAAGAAGGAGGGTATCTGACATCAGATAAACCAATGCCAAGGGGAGAGATTGTAGTTGGAGGATTTAGTGTGACAGCTGGTTACTTTA

upper sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT2G04350.2 (Arabidopsis thaliana), 3'ss of exon 8
agtttttgtacgcattcaagcacagtagtgtttccagttagaataattcgaggattgagaaccatttttctcaatggacatgtttggtttgacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA
       ||  |||  ||| |    ||      |  |||   | |||  |    || |     ||  |    ||   |         ||| |  |||||||| |||||||||||||||||||| || |  |  || || |||||||||||  |||| ||| |||| || || ||  | ||| |||| || || ||||| |
-------gtttgcagacaatctt--taacacaccatgttg--acaatgtgcaagtttattgtaatcatgagtaacaaa---------tttcatcttgcagCTCGTTTCTTGGGAAGAAGGTGGCTACAGAATTTCAGATAAACCAATGCCTAGAGGGGAGATTGTGGTAGGTGGTAACAGTGTAACAGCAGGTTACTTCA

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|110688644|gb|EE067428.1|EE067428
EST:     ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAG                         CTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
genomic: ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAGgtatgccatg ... gacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
EST: gi|110696839|gb|EE073301.1|EE073301
EST:     ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAG                         CTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
genomic: ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAGgtatgccatg ... gacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
EST: gi|352786143|gb|FQ478754.1|FQ478754
EST:     ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAG                         CTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
genomic: ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAGgtatgccatg ... gacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
EST: gi|351023858|gb|FQ423281.1|FQ423281
EST:     ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAG                         CTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
genomic: ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAGgtatgccatg ... gacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
EST: gi|351031287|gb|FQ445312.1|FQ445312
EST:     ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAG                         CTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
genomic: ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAGgtatgccatg ... gacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
EST: gi|349830561|gb|FQ416859.1|FQ416859
EST:     ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAG                         CTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
genomic: ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAGgtatgccatg ... gacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
EST: gi|351023101|gb|FQ430976.1|FQ430976
EST:     ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAG                         CTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
genomic: ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAGgtatgccatg ... gacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
EST: gi|351040054|gb|FQ425140.1|FQ425140
EST:     ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAG                         CTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC
genomic: ACCCAAATGTGGGGCATGTTGGACCGCCCCTTCCTTGTGCCTATATCAAGgtatgccatg ... gacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgaggattgagaaccatttttctcaatggacatgtttggtttgacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA
                                         gtttgac  putative branch site (score: 4)
                  atttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttttgtacgcattcaagcacagtagtgtttccagttagaataattcgaggattgagaaccatttttctcaatggacatgtttggtttgacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - -gtacgca
- - - - - - - -tcaagca
- - - - - - - - - - - - - - tgtttcc
- - - - - - - - - - - - - - - - - - - -agaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgg