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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA

Basic information

species Vitis vinifera
transcript Vv14s0060g02260.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 2
-------ataggaattggtgagtgaacaggcttaattgaagctgaagttctagta-acttggttctcactacatttttttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
         || ||||| ||  |    |   |||||   | ||   ||| | | | | |||  | |    ||  | |  ||| |  ||||      |      |||||||  ||||||||||||| |||||||| || ||||| |||||||| ||||||||| | ||||| || ||||| ||||||||||||||| |||| || || |
gctattaccagaaattgctgtttcccta---ttaatgtgacctattgttttggaacaattgcgtattgtaaccatatggtttctgcttttctcaactg-----tttagATTCTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAATATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACTTCCA

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 2
ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttt-----tttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
    |  ||   ||||      |  |  |   ||| ||| |  | |||  |    |    | | ||| |         |||     ||||   |     ||| |||| |||||||||||||| |||||||| || || || |||||||| || || ||||| || || || ||||| |||||||| ||||||||||| ||||| |
----gtcttttcgagtccttgagaatg-tcagagcagaattcttcgtagttctaattctgcaagattgtgggggcaaatttacaagttcttacttcctatttcagATATTGGAAATGAACCCCGAGGATGAGGCTGAAGAGGATGGTGCGAACATCGATCTGGATTCACAAAGGAAAGGAAAATGCGTTGTTTTGAAGACATCCA

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
----ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
    |||  | |||||   ||  |||||    |     ||| |  |    ||  ||| ||||   |   |  | |     ||   || |  | ||   ||||||||||||||||||||||| |||||||| || ||||| |||||||| || |||||| | ||||| || ||||| ||||||||||||||| |||| || || |
ttccatattatttggtctttgt-caggcagggt---gtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 2
ataggaattg-gtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
 || || ||   |   | ||     ||||        |||| |  |    |  |||   |  ||     |   ||   | | | |   | ||   |||||||| |||||||||||||| |||||||| || || ||||||||||| || || ||||| ||||| || ||||| ||||||||||||||| |||| ||||| |
-taagattttcatatttcaaagtttttaagatgtaaggaagctgcatacccaaggtggacgatatgggctccattacttatatacatctcaactgttttagATTTTGGAAATGAACCCTGAGGATGAGGCTGAAGAAGATGGTGCTAACATCGATCTGGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACATCCA

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
------------------------------------------------ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgttt----ttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
                                                 | ||  |||     ||||     |  | || |    ||    | ||  |||| || |  || |||| || ||    | |    || | | | |||    |||||| ||||||||||||||||| || || || || ||||||||||| ||||||||||||||||| || ||||||||||| ||||||||  | || || ||||
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttct-cattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgttt----ttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
                                                | |   ||      ||||    ||  | || |    ||    | ||  |||| || | |  ||||||||  ||   | |    || | | | |||    |||||| |||||||||||||| || || || || || ||||||||||| ||||||||||||||||| || ||||||||||| ||||||||  | || || ||||
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaa-acatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
ataggaattggtgagtgaacaggcttaattgaagctgaagttctagta-acttggttct-cactacattttttttt---ttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
     |||||          |   ||    | | ||| |||  |  |  ||||| || | || | | |  | ||     ||||    |    ||  |||||| |||| |||||||| || ||||| ||||| ||||| ||||||||| | || |||||||||||||| || ||||| ||||||||||||||  | || |||||||
-----aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttttcattccctaatgttccaaattctgacatgatatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 2
ataggaattggtgagtgaacaggcttaattgaagctgaagttct--agtaacttggt--tctcactacatttttttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
   | | |     |||   |     | |||   | |    | ||  ||   |||     | | | |  | || |   | |  | || |    | ||| | |||||| ||||| ||||| ||||| ||||| || |||||||||||||||||||||||||||||||| ||  |||| |||||||||||||| |||||||| ||||
---gtattcaactagttttcttatcttatttttggtattttcctacagagtcttacctatttgatttgaattctaactgttgtgttaccatatcatgctattagATTTTGGAGATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTA

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 2
--ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
      ||||   ||    |  ||     |   |   |    |   | |   ||   | | |  |     ||    ||   | |  |        ||| |||||  | || ||||  ||||||||||| |||||||||||||| || ||||| ||||| |||||||||||||||||||| ||||| ||| | |||||||| |
ttccttgaatctttgccacagtagttcagac--attttaccatcaaatttttttttgtgtaatgatggaattaggatttgatctattatccgtgctttctagATTCTTGAGATGAGTCCAGAGGATGATGCAGAGGAAGATGGAGCGAATATCGATCTGGACTCTCAGAGGAAGGGAAAGTGTGTCGTTCTAAAAACATCAA

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|71864441|gb|DT013496.1|DT013496
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|71860997|gb|DT010052.1|DT010052
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|110724320|gb|EE100046.1|EE100046
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|71859210|gb|DT008265.1|DT008265
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|71858458|gb|DT007513.1|DT007513
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|110711112|gb|EE087285.1|EE087285
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|71857850|gb|DT006905.1|DT006905
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|110685213|gb|EE063376.1|EE063376
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|294964455|gb|GW838258.1|GW838258
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|71859776|gb|DT008831.1|DT008831
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|71863186|gb|DT012241.1|DT012241
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAGCCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|110724441|gb|EE100272.1|EE100272
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|110722856|gb|EE099502.1|EE099502
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|71861858|gb|DT010913.1|DT010913
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|110732813|gb|EE108430.1|EE108430
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|34549827|gb|CF518059.1|CF518059
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|34544589|gb|CF512821.1|CF512821
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|37184438|gb|CF603792.1|CF603792
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
EST: gi|71879123|gb|DT028178.1|DT028178
EST:     AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAG                         ATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT
genomic: AGATCAAGCTCAACAAGCAGCTTCCCTACTTGGTCGGCAACATAGTCGAGgttattctct ... atgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacttggttctcactacatttttttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA
                    tttttttttttctttt  CT-rich tract
                   atttttttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataggaattggtgagtgaacaggcttaattgaagctgaagttctagtaacttggttctcactacatttttttttttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
ataggaa
- - - - tggtgag
- - - - - - - - - - - - - aattgaa