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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagattgcattttattaatctaccattttttttcctttttgcatagttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA

Basic information

species Vitis vinifera
transcript Vv19s0014g01390.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
cagattgcattttattaatctaccattttttttcctttttgcatagt-tcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA
              |  ||   | |   |         |||| || | |  | |  |||| | | |      | ||| |||    || | || ||||| |||||||||| |||||||| ||||||||||| || |||||||| ||||||||     | ||||| ||||| || ||||| || |||||  | ||||||||||
-------------gtacataggctaagatacaaaaaacttgcttactatgctatacgttttggttgtcc---ttctggttgaaggtt-tcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA

upper sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 7
cagattgcattttattaatctaccattttttttcctttttgcatagttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA
           ||   |||  |||| |  | |||        ||| |  || | |||||  |   |   ||| ||||| |     |    | |||||||| | ||||| ||  | ||||| ||||||||||||||||||||||||||||||     |||||||||||||| |||||| |||||  || | ||||||||||
----------gttgagaattaaccagtaatattcagaaaataatattgatt-tttgtttttcctcagcgggttctgataga----tgccatcttttgtagCTGTTGGAGCCCTTGGAACTATGTTACAGATCACTCTGTGCTTGTGGTGACTCTGTAATTGCTGATGGAACCCTTCTGGATTTCTTGCGTCAAGTGTCCA

upper sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
cagattgca-ttttattaatctaccattttttttcctttttgcatagttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA
||| ||| |   | |  ||  ||     | |||       |     | | |  | |||||    |  |   ||   || || |  || | || | ||| |||||||||| |||||||| |||||||||||||| || ||||| |||||||| ||  |  |||| |||||||||||||| || ||  | || |||||||| |
caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtctttt-ttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA

upper sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 7
----cagattgcattttattaatctaccattttttttcctttttgcatagttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA
    || |    || ||  ||| |||  | |  | |    | |    |  |    |  | | | | |     |   ||| ||    | ||| | | || |  ||||||||||||| ||||| ||||||||||||||||||||||||||||| || ||| |||||||||||||||||||||| |||||  |||||||||| || |
gagacaaaaaagatatt--taaactagtaatgatgtgaaatatcattttctgagaga-tatcttgatcttccaaacactaatcat-agttaaaatgttgtccagTTCTTGGAACCCCTTGAGCTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGAGCAATTGCTGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA

upper sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 8
---------cagattgcattttattaatctaccattttttttcctttttgcatagttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA
          | | ||  |      |  ||    |  | | || ||||   | |  |||||     |||        || |||  | |   | | | ||| || | |||||||||||||| ||||||||||||||||||||||||||||||||||| || ||  ||||||| |||||||||||||| |||||  |||||||||| || |
agaaaagaaaaaaatgtttaaaccgagactgatgtaatatatcattttgagagatatcttgatc--tta-------cagatacctaatcaaagtaaaattgttgtctagTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA

upper sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------------------------------------------cagattgcattttattaatctaccattttttt------tcctttttgca--tagttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA
                                                                                      |  ||  | ||  ||||  ||  | |||||       || |   || |  ||  | ||   ||  || ||  ||| |  |   | |    |   |   ||| |||||||| ||||| |||||||||| |||||||||||||| ||||||||||||||  || |||||||||||||||||||||| |||||  |||||||||| ||||
gtacatccattgcttttgctttcgtgtacttttccattaacacagttggggttttattatactgttgctagctatgtttttttgttaacttttagttatttaacatattagtttttggatggatcatggatgaatttatgttttccttggatatctttatttgacagacactaactaaagttaatttgtgtagTTCCTGGAATCTCTTGAACTATGTTACAGATCACTATGTGCTTGTGGTGATAGAGCAATTGCTGATGGAAGCCTTCTTGATTTCATGAGACAAGTCTCCA

upper sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------------cagattgcattttattaatctaccattttttttcctttttgcatagttcttg----tctgtttagctgga------ttaggtactgattgggaattatattt---ttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA
                                                                                  | || | ||||| | || || ||| ||  ||  |  ||| || ||   ||    | |||||  || |       |||  |       |  || || | ||   || |||||||| | ||| |||||||||| ||||| |||||||| ||||||||||||||  || |||||||||||||||||||||| |||||  |||||||||| || |
gtacatccattatttttgctttcctgtacttttccattaacacagttgggattttaatatactgttactagctatgttttttgtttac-ttttagttatttaacatgttagtttttggttggatcgtggatgaatttatgttttccttggatatctttatttgacagacgctaactaaagttaatttgtgtagTTCCTAGAATCTCTTGAACTATGTTATAGATCACTATGTGCTTGTGGTGATAGAGCAATTGCTGATGGAAGCCTTCTTGATTTCATGAGACAAGTCTCTA

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|351038307|gb|FQ460999.1|FQ460999
EST:     ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAG                         TTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC
genomic: ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAGgtatcttcat ... ttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC
EST: gi|351018719|gb|FQ425621.1|FQ425621
EST:     ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAG                         TTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTACTTGTGGTGAC
genomic: ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAGgtatcttcat ... ttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC
EST: gi|110691746|gb|EE070200.1|EE070200
EST:     CTTACACCAATCTTGAGCAG                         TTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC
genomic: CTTACACCAATCTTGAGCAGgtatcttcat ... ttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC
EST: gi|351032488|gb|FQ458853.1|FQ458853
EST:     ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAG                         TTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC
genomic: ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAGgtatcttcat ... ttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC
EST: gi|110699775|gb|EE077068.1|EE077068
EST:     ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAG                         TTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC
genomic: ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAGgtatcttcat ... ttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC
EST: gi|349832680|gb|FQ422038.1|FQ422038
EST:     ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAG                         TTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTACTTGTGGTGAC
genomic: ATGGGATCTCTGACATTCCAGGGGAGGCAACTTACACCAATCTTGAGCAGgtatcttcat ... ttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA
                          tactgat  putative branch site (score: 2)
                                          tattttttt  putative PPT
                                     aattatatttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagattgcattttattaatctaccattttttttcctttttgcatagttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - tctacca
- - - - - - - - - - - - - - - - - - - -tgcatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tagctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgg