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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctccagattttttgtttaaaccatggtttttatttatctcttttacaaatcttgcaatttatcaaagagcaggtttaggtggtagttgtaataactgcctataagctttcttagtatctaaattttatagtatgcttgtctacgtgcttcagaattatatgatgcctgcttattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGATGGTCAGTTGAGAAAGTTCTCCAAGTCATAATCATCAACTGCAGATCTT

Basic information

species Vitis vinifera
transcript Vv05s0020g04100.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA10G00550.1 (Glycine max), 3'ss of exon 14
gtgagctccagattttttgtttaaaccatggtttt-tatttatct-cttttacaaatcttgcaatttatcaaagagcaggtttaggtggtagttgtaataactgcctataagctttcttagtatctaaattttatagtatgcttgtctacgtgcttcagaattatatgatgcctgcttattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGATGGTCAGTTGAGAAAGTTCTCCAAGTCATAATCATCAACTGCAGATCTT
||  | | ||  | |||  ||  || |||  |    |||  || | |  ||  ||||||||||| ||   ||| ||||  |||   ||||   | | |||    | | | | | || |   |||  |||    | | |||| ||      ||| |  || | | |    |   || | |||||  |||| ||||||||||| ||||||||||||||||||||| ||||||||||||  ||||| ||  |   ||| |||||||| ||||| || |||||  | ||||
gtatgtttcatgtatttcattctaatcatattacaatatacatttgccctttaaaatcttgcaactt--taaatagcacatttca-tggtgtctatgata--cacttgtgaaccttgtctttatagaaa----acattatgttt-cgagtgtgttcaagcaatgtggtctatttggt-attttgcagGTGTTAGATTTTTTTAATAGTCGCATGGATGCCCAAAGAATGAATGGTGATTGGTCTGTCAATTTAGTGCTCCAAGTGATAATTATGAACTGTCGGTCTT

upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA15G24080.1 (Glycine max), 3'ss of exon 16
gtgagctccagattttttgtttaaac-catggtttttatttatctcttttacaaatcttgcaatttatcaaagagcaggtttaggtggtagttgtaataactgcctataagctttcttagtatctaaattttatagtatgcttgtctacgtgcttcagaattatatgatgcctgcttattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGATGGTCAGTTGAGAAAGTTCTCCAAGTCATAATCATCAACTGCAGATCTT
||  | | ||  | |||  | ||| |  ||     |      | ||  ||  ||||||||||| ||   ||||||||  |||   ||||   | ||||         | |   || |   |||  ||    || | |||| || |    ||| | ||  | | |    |   || |   |||  |||| ||||||||||| |||||||| |||||||||||| ||||||||||||  ||||||||  |  |||| |||||||| |||||  | |||||  | ||||
gtatgtttcatgtatttcatctaatcatattacaatacaaactttccctttaaaatcttgcaactt--taaagagcacatttca-tggtg--tctaatg--------tgaatcttgtctttataaaa----tacattatgttt-tgagtgtgttccatcaatgtggtctatttggta--tttgcagGTGTTAGATTTTTTTAATAGTCGTATGGATGCCCAAAGAATGAATGGTGATTGGTCAGTCAATGAAGTGCTCCAAGTGATAATTGTGAACTGTCGGTCTT

upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA20G28880.1 (Glycine max), 3'ss of exon 13
--gtgagctccagattttttgtttaaaccatggtttttatttatct---cttttacaaatcttgcaatttatcaaagagcaggtttaggtggtagttgtaataactgcctataagctttcttagtatctaaattttatagtatgcttgtctacgtgcttcagaattatatgatgcctgcttattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGATGGTCAGTTGAGAAAGTTCTCCAAGTCATAATCATCAACTGCAGATCTT
   || |    | || |||| ||||||  |  ||    |  |||     |  ||   ||||||| || || | || ||||| |||| | || ||  | || | ||       ||||||     || | |  ||  || |  ||| || || | |||  |   || | |||      |   |||||   ||||||||||||||||||||||||| |||||||| ||| ||  | ||||||  ||||||||  |  |||| ||||||||||||||  |||| ||  | ||||
gtatgtgtcatatatgttttatttaaatgaaagtaccaaaatatgctgaccctttgcaatcttgtaacttttaaaggagcaagttttg-tgctatctttagtcacattaatgaagctt-----gtctttgtataataaatcatgtttctcaa-gtgtgtgcaaaatgtat--ctattaaatatttac-agGTATTAGATTTTTTCAATAGTCGAATGGATGCTCAAAGAGAGGATGGTGACTGGTCAGTCCATGAAGTGCTCCAAGTCATAATTGTCAATTGTCGTTCTT

upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA10G38920.2 (Glycine max), 3'ss of exon 14
gtgagctccagattttttgtttaaaccatggtttttatttatctcttttacaaatcttgcaatttatcaaagagcaggtttaggtggtagttgtaataactgcctataagctt-tcttagtatctaaattttatagtatgcttgtctacgtgcttcagaattatatgatgcctgcttattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGATGGTCAGTTGAGAAAGTTCTCCAAGTCATAATCATCAACTGCAGATCTT
                                                                          ||| |||  ||| ||  | || | ||       |||||| |||| ||||  ||||  | |    | ||    |  ||||   | |  ||| |  |   |  |||      ||||||||||||||||||||||||| |||||||| ||| ||  | ||||||  ||||||||  |  |||| || |||||||||||  |||| ||  | ||||
-------------------------------------------------------------------------tcagtttt--gtgctatctttagtcacattaatgaagcttgtctttgtataaaaatcatgt----ttctcaagtgtgtgca--aaatgtatctattaaatatttac-----agGTATTAGATTTTTTCAATAGTCGTATGGATGCTCAAAGAGAGGATGGTGACTGGTCAGTCCACGAAGTGCTACAAGTCATAATTGTCAATTGTCGTTCTT

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|352769602|gb|FQ468530.1|FQ468530
EST:     CTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACT                         GTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGA
genomic: CTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACTgtgagctcca ... tattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGA
EST: gi|351024882|gb|FQ433299.1|FQ433299
EST:     CTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACT                         GTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGA
genomic: CTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACTgtgagctcca ... tattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGA
EST: gi|352780976|gb|FQ466289.1|FQ466289
EST:     CTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACT                         GTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGA
genomic: CTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACTgtgagctcca ... tattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGA
EST: gi|110362374|gb|EC925903.1|EC925903
EST:     CTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACT                         GTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGA
genomic: CTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACTgtgagctcca ... tattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtatgcttgtctacgtgcttcagaattatatgatgcctgcttattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGATGGTCAGTTGAGAAAGTTCTCCAAGTCATAATCATCAACTGCAGATCTT
                                       cctgcttatttttt  CT-rich tract
                                            ttatttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctccagattttttgtttaaaccatggtttttatttatctcttttacaaatcttgcaatttatcaaagagcaggtttaggtggtagttgtaataactgcctataagctttcttagtatctaaattttatagtatgcttgtctacgtgcttcagaattatatgatgcctgcttattttttagGTATTAGATTTTTTCAATAGTCGCATGGATGCCCAAGGAATGAATGGTGGATGGTCAGTTGAGAAAGTTCTCCAAGTCATAATCATCAACTGCAGATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT