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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggattcctaatttatattaaatatttgttgtaatttgagtgaaacattttggtggatctttcttttgattgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG

Basic information

species Vitis vinifera
transcript Vv14s0030g01350.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os12g06810.3 (Oryza sativa), 3'ss of exon 3
gtatggattcctaatttatattaaatatttgttgtaatttgagtgaaacattttggtggatctttcttttgattgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG-----
             |||  |  ||||    || | |   |  ||| |||   |   |   |    | | |   |||  |  |    |  |||| ||||| ||||| ||||||||  | ||| |  |  ||||| || ||||||||||  ||||||| || |||||||||||||||||||| ||  | | ||     
-----------gtattactgataaactcatgatctctgtgtagtaaaaatctgctgcttactagtatgtaatttgtgtctttacttttaggttagCATACCTGCCTGGTTTACCATGGATGCTCGATTGGGATGCCTGTCTGTCCACCTGGATACACCTCAATGCTTTTCTGCAGAAATATATGCAGTTGACTTA

upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 13
gtatggattcctaatttatattaaatatttgttgtaatttgagtgaaacattttggtggatctttcttttgattgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG
             |||  |  ||||    || | |   |  ||| |||   |   |   |    | | |   |||  |  |    |  |||| ||||| ||||| ||||||||  | ||| |  |  ||||| || ||||||||||  ||||||| || |||||||||||||||||||| ||  | | ||
-----------gtattactgataaactcatgatctctgtgtagtaaaaatctgctgcttactagtatgtaatttgtgtctttacttttagGTTAGCATACCTGCCTGGTTTACCATGGATGCTCGATTGGGATGCCTGTCTGTCCACCTGGATACACCTCAATGCTTTTCTGCAGAAATATATGCAGTTG

upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G167999_T01 (Zea mays), 3'ss of exon 13
gtatggattcctaatttatattaaatatttgttgtaatttgagtgaaacattttggtggatctttcttttgattgcattatcttgt--ccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG
    | ||| || |  ||| | |  |  ||  | |  |||   | ||| | ||||||   |  | || |  | |   |||  |  |    |||| ||||| ||||| ||||| ||  | ||| |  |  | ||  |||||||||||||  ||||||| ||||||||||||||||||||||| ||  | | ||
----gtattactgaaatatgtca--tgatttctatgtttta--ttaaaaagtttggtacctactactgtgtaatttgttaattgattattagGTAAGCATACCTGCTTGGTTCACCATGGATGCTCGATTAGGGTGCTTGTCTGTCCACCTGGATACTCCACAATGCTTTTCTGCAGAAATATATGCGGTTG

upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA19G43070.1 (Glycine max), 3'ss of exon 13
----------------------------------gtatggattcctaatttatattaaatatttgttgtaatttgagtgaaacattttggtggatctttcttttgattgcatt---atcttg-tccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG
                                    |   |||  |  ||      ||  |    |    ||||     |     |||| |  |  |  ||||| |||   ||   ||  || |  |||| ||||||||||||||||| || || ||||| ||||| ||||||||||| ||||||||||| || || ||||| ||||| ||||| ||||| || ||||
gtatgattactgatttaaaccattgatttcattttaaaatatttttttttctaggcaagaaaacatgacgatttccagtagtttatttgttcaagttggcttttaattttcttccaatgctgctttagGTTAGCATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCCCAATGTTTTTCAGCAGAGATGTATTCAGCTG

upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 13
----------------------------------------gtatggattcctaatttatattaaat----atttgttgtaatttgagtgaaacattttggtgg-atctttcttttgat--tgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG
                                         |||   || ||    || |  | ||    ||||    || |||   ||    | || | |   |  |||| |   ||  ||||||  ||  |  |||| || |||||||||||||| || || ||||| ||||| ||||||||||| ||||||||||| || || ||||| || |||||||| ||||| || || |
gtatgattactgatttacctcattgatttcattttaaaatatatttttttcttggctagaaaacatgacgatttccaatagtttatttgttcaagttggcttttaattttcctccaatgctgcattg-ctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCTCAATGTTTCTCTGCAGAGATGTATTCAGCAG

upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA03G40440.3 (Glycine max), 3'ss of exon 13
-----------------------------------------------------------gtatggattcctaatttatattaaatatttgttgtaatttgagtgaaacattttggtggatctttcttttgattgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG
                                                            ||     |   ||   ||  | | |    |||||   ||   | || |    |  |   | | |      |  |||||  ||  |  |||| |||||| |||||||||| || || ||||| ||||| ||||||||||| ||||||||||| || || ||||| ||||| ||||| ||||| || ||||
gtatgataactgatttacgtcatggattccatttttaataattatgctttaattattttttacttggtaagaaaacatgatgatttacagttgtttatttgttcaagctggcttttaattttcttccaataccgcattg-ctgctttagGTTAGCATTTCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCCCAATGTTTTTCAGCAGAGATGTATTCAGCTG

upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA03G40360.1 (Glycine max), 3'ss of exon 13
----------------------------------------------gtatggattcctaatttatattaaatatttgttgtaatttgagtgaaacattttggtgg-atctttcttttgat--tgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG
                                               | |   ||   ||   |   | |  ||||   ||| |||   ||    |  | | |   |  ||||||   ||  ||||||  ||  |  |||| ||||||||||||||||| || || ||||| ||||| ||||||||||| ||||||||||| || || ||||| || ||||| || ||||| || || |
gtatgattactgatttacatcattgatttcattttaaaatatttttttttttctttgcaaggaaacatgatgatttccagtagtttatttgttcaagctggcttttaattttcttccaatgctgcattg-ctgctttagGTTAGCATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCCCAATGTTTCTCTGCGGAGATGTATTCGGCAG

upper sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT3G05090.2 (Arabidopsis thaliana), 3'ss of exon 13
gtatggattcctaatttatattaaa------tatttgttgtaatttgagtgaaacattttggtggatctttcttttgattgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG
|||  |  || | ||  || || ||      || ||  | ||   | |||||  |     |||   | |   | ||| |   ||||  || |  |||| ||||||||  | ||||||||||| |||||  | || ||| |||| ||||| |||||||| || ||||||||||| ||||| |||||||| || || |
gta-agtctcttgatcgattttcaaaggttataatttatttatcgttagtgaggctagcaggtttgtttacttattgctcatattactttctt-agGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCTGTACATTTGGAGACTCCACAATGCTTCTCTGCTGAAATGTATTCAGCAG

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|71881516|gb|DT030571.1|DT030571
EST:     GTCTCATTTGAGGAGAAGAAAGAAGAATTGTTCGAGATG                         GTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCT
genomic: GTCTCATTTGAGGAGAAGAAAGAAGAATTGTTCGAGATGgtatggattc ... tcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgagtgaaacattttggtggatctttcttttgattgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG
                               ttttgat  putative branch site (score: 4)
                                             tcttgtcc  putative PPT
          aaacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggattcctaatttatattaaatatttgttgtaatttgagtgaaacattttggtggatctttcttttgattgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG