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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttttgcaaaagacattttgggggggttaggaatgtaattttactcctattttccttttagggctgacctgaacttggtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA

Basic information

species Vitis vinifera
transcript Vv19s0177g00300.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 3
attttttgcaaaagac--attttgggggggttagga-atgtaattttactcctattttccttttagggctgacctgaacttggtaggtgcttgtct--gtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
||| ||| ||   | |   | |||    ||||||   | | |  | | ||||| || || || |     |||  | |||   || | || || ||    || |||| || ||||| |||||||| || ||||| || |||||||| |||||||| || |||||||| |||||||||||||| ||||| ||||| ||||| |||||
attgtttccagtggtctggtcttgctcaggttagctcaggcaggtcttctcctgttctctttctc---ttgatgttaac--agttgttgtttctcctcataccagGATTCATGGGTGCCATGATATCAAACCTTGCATTTGTTTTCCGCAACATCTTCTCAAAGAGGGGCATGAAGGGGAAATCTGTCAGTGGCATGAATTACTA

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
-------attttttgcaaaagacattttgggggggttaggaatgtaattttactcctattttccttttagggctgacctgaacttggtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
       | |||  ||  |||| |             ||  ||| | || |  | | ||| |      ||| || |  ||   |  ||  |  |||      | |||| |||||||| |||||||| || ||||| || |||||||| |||||||| || || ||||| ||||||||||||||||| || ||||| ||||| |||||
tagactaaatttaagcttaagatagagataaaatacgagtcatggacttgt-tttcaattgtttccaaaggtctaa--tgttttccgtttgcccttcc----accagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G431314_T01 (Zea mays), 3'ss of exon 3
------attttttgcaaaagacattttgggggggttaggaat-gtaattttactcctattttccttttagggctgacctgaacttggtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
        |||  ||  |||| |    |       ||||| |  ||    || |   | ||   |   |||  | |  |    ||   |  |||    |  |  |||| |||||||| || ||||| || ||||| || |||||||| |||||||| || || ||||| ||||||||||||||||  || ||||| ||||| |||||
agaatagatttaagcttaagataga--gaaaaaaataggagtcatagacatatttgcaattgtttccaaggtataatgt----ttaccatttgccctcccct-ccagGATTTATGGGTGCTATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTTCGTCAGTGGCATGAATTACTA

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 3
attttttgcaaaagacattttgggggggttaggaatgtaattttactcctattttccttttagggctgacctgaacttg--gtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
|      ||||  |  ||||    |      || ||    | | |    |||  |||| |  |  ||  |||||  ||   ||    |  | | | |  ||||||||||||| |||||||| |||||  |||| ||||| || || || || ||||| || |  ||||||||||| |||||||||||||||||||| |||||
accaagcgcaagtgtgatttacttgcataatggtatcatttctcataattatagtcctct--gcactctcctgactttaatgtcatcgacttttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 2
attttttgcaaaagacattttgggggggttaggaatgtaattttactcctattttccttttagggctgacctgaacttggtaggtgcttgtc--tgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
       | || |    ||    |      | |  ||  ||||| ||| |||||     ||     |   || ||    |      ||||    ||| ||||| || ||||| || ||||| || ||  |||| ||||| || ||||| ||||| ||||||| ||| |||||||| | ||||||||||||||||||||||||
-------gtaagactatttaaatgaaaaacaaggttgagatttt-ctcttatttggtagttcaa--tattctaaatagagagaacacttgatgatgtttcagGCTTCATGGGGGCTATGATATCAAATTTGGCATTTGTCTTCCGCAATATATTCTCAAAGAAAGGGATGAAGGGAATGTCTGTTAGTGGAATGAACTACTA

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 2
-------------------------------------------attttttgcaaaagacattttgg---gggggttaggaatgtaatt---ttactcctattttccttttagggctgacctgaacttggtagg--tgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
                                              |  ||  |||   ||  |||   ||  |||     | |||||   ||| | |     || || |  |  |    ||   |  | |    |  |    ||| ||||| |||||||| || |||||||| ||  |||| |||||  ||||||| ||||| |||||||  || ||||| |||| |||||||||||||||||| |||||
gtaaacctatttaatgatttaagtgattacatggttgaaattcggatgctgacaaattaatagtggataggatgttgaatctctaattagtttagttcatcaatctttgtgagagttcaatgctttaagaaaacctcttcacatgtttcagGGTTTATGGGGGCTATGATTTCCAATTTGGCCTTTGTCCTTCGCAATATATTCTCAAAGAAGGGAATGAAAGGGATGTCTGTTAGTGGAATGAATTACTA

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 2
--------------------------------------------attttttgca--aaagacattttgggggggtta-ggaatgtaat-tttactcctattttccttttagggctga----cctgaacttggtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
                                            |||| |   |    |||||||||      | |   |||| ||   |||     ||| |   |||   || | |     || ||    |      ||||  ||| ||||| |||||||| || ||||| || ||  |||| || || || ||||| ||||| ||||||| ||| |||||||| | ||||||||||||||||||||||||
gtaagactatttgctgaaaaaaaaaaaaacaaggtttagatgagatttctcatactgtagacatttttaatacgatgtagaatttatcatttgtgtatatatatttttggtggttcaatattctaaatagagagaacacttga-tgtttcagGCTTTATGGGGGCTATGATATCAAATTTGGCATTCGTCTTCCGCAATATATTCTCAAAGAAAGGGATGAAGGGAATGTCTGTTAGTGGAATGAACTACTA

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G12080.1 (Glycine max), 3'ss of exon 3
------attttttgcaaaagacattttgggggggttaggaa--tgtaattttactcctattttccttttagggctgacctgaacttggtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
       | |  |  |      ||| ||  ||   ||        ||||| || |||| |   |  |      ||||| | || ||  | |   ||| | | | ||||||||||||||||| ||||| |||||  |||| ||||| || || || || ||||| || |  ||||||||||| |||||||| ||||||||||| |||| 
gtaatggtgtcatttatggttgattgtgctggaactaatttctcataattatagtcctctgcactctc-----ctgactttaatttcattga--cttttttttttcaGGTTTTATGGGAGCTATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCCAAAAAGGGCATGAAGGGAAAGTCTGTCAGTGGAATGAATTACT-

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G38830.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------attttttgcaaaagacattttgggggggttaggaatgtaa----ttttactcctattttccttttagggctgacctgaacttggtaggtgcttgtc-tgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
                                                                        || | |   |    |||    ||  |||   | |||||    |||   || |    ||||| |  |  |    ||   |  | |    |||  | ||| ||||| ||| |||| || |||||||| ||  |||| |||||  |||| || ||||| |||||||  || ||||| |||| |||||||||||||||||| |||||
gtaaacctatttaatgatttaagtgattgcatggttgaaatttagatgctgacaaatagtgactatgttttattctagtggataggattgataggatgttgaaattgtaattagtttagttcatcaaatccttgtgagagttcgatgctttaagaaacctcttcacatgtttcagGGTTTGTGGGGGCTATGATTTCCAATTTGGCCTTTGTCCTTCGGAATATATTCTCAAAGAAGGGAATGAAAGGGATGTCTGTTAGTGGAATGAATTACTA

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------attttttgcaaaagacattttgggggggttaggaatgtaattttactcctattttcct-tttagggctgacctgaacttggtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
                  || ||||  | | |||||  || |   || ||| ||  |||| |      ||| | | |||     || | | || |  |  | | |||   | |  ||||||| |||||||| |||||||||||| ||||||| || || || ||||| || || ||||  || |||||||| |||||||| || || |||||||||||
gtaacatatatcttcatcttatttgttagatacattgaggtgtaattgggattgagatttgaaatggctttgcatgtttgattttggcttcaaatctgctgctccttactttt--cagGTTTCATGGGAGCTATGATTTCGAACTTGGCTTTCGTGTTCCGTAACATCTTCTCGAAGAAGGGAATGAAGGGAAAGTCTGTGAGCGGGATGAACTACTA

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|30300650|gb|CB977444.1|CB977444
EST:     CGGAGGTTGTGCTCTAGCCGCCGTCACCGAGCTGAACTTCAACATGATTG                         GTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
genomic: CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTGgtaataatag ... tctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
EST: gi|110417550|gb|EC983615.1|EC983615
EST:     CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTG                         GTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
genomic: CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTGgtaataatag ... tctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
EST: gi|33405610|gb|CF211237.1|CF211237
EST:     CGGAGGTTGTGCTCTAGCCGCCGTCACCGAGCTGAACTTCAACATGATTG                         GTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
genomic: CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTGgtaataatag ... tctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
EST: gi|110719157|gb|EE096814.1|EE096814
EST:     CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTG                         GTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
genomic: CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTGgtaataatag ... tctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
EST: gi|110357684|gb|EC921351.1|EC921351
EST:     CGGAGGTTGTGCTCTAGCCGCCGTCACCGAGCTGAACTTCAACATGATTG                         GTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
genomic: CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTGgtaataatag ... tctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
EST: gi|110398825|gb|EC965301.1|EC965301
EST:     CGGAGGTTGTGCTCTAGCCGCCGTCACCGAGCTGAACTTCAACATGATTG                         GTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
genomic: CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTGgtaataatag ... tctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
EST: gi|110382211|gb|EC938786.1|EC938786
EST:     CGGAGGTTGTGCTCTAGCCGCCGTCACCGAGCTGAACTTCAACATGATTG                         GTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
genomic: CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTGgtaataatag ... tctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
EST: gi|110380178|gb|EC945423.1|EC945423
EST:     CGGAGGTTGTGCTCTAGCCGCCGTCACCGAGCTGAACTTCAACATGATTG                         GTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT
genomic: CGGAGGTTGTGCTCTGGCCGCCGTCACCGAGCTGAACTTCAACATGATTGgtaataatag ... tctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctattttccttttagggctgacctgaacttggtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA
                  ggctgac  putative branch site (score: 3)
                                         cttgtct  putative PPT
     atttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttttgcaaaagacattttgggggggttaggaatgtaattttactcctattttccttttagggctgacctgaacttggtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - -aaaagac
- - - - - - - - - - -ggggggg
- - - - - - - - - - - - - - - -ggaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcttg