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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG

Basic information

species Vitis vinifera
transcript Vv12s0035g01980.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 3'ss of exon 1
---ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttc-ttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
    | |||  |    ||  ||||  |     |||||  |   |||     | ||||      ||   | ||  | ||  | |   | | | | | | ||  |||||| ||||| |||||| | ||||| ||||| ||||||||||||||||| ||| |||||| ||||||||| ||||| |||||||||||||||||  | ||
ccaatgtttcttggctacgatttatttcgattatataacttccatga----aaaaatttccagaaaacgattgatatgcttctgaattattgtttacattgcagAGAAAGAGAATTTGTGTTTATATGGTCTTCCCAATGAGACATGGGAAGTGAACTTGCCTGCTGAGGAGGTTCCTCCAGAGCTTCCAGAACCAGCTCTGGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g35600.1 (Oryza sativa), 3'ss of exon 2
ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttg----gatgt--ttgtaaatt--tgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
       ||  | | |  | ||||||     | |  |  | |||||    || | |      |||| |||| |       |||   | || |  |  | || ||  |||||| |||||| |||| || |||||| | || |||||||| ||||| || | ||| || | |||||| ||||||||||| ||||||||||||||| | ||
------aatgatgaatggt-acattacat-cacaagtagtctgttgaatgaagttatcttcccttgtttatgtcatagtaatgacatagtgatctcctattttttcagAGAAAGAGAACCTGTGCCTTTATGGATTGCCCAATGAGACCTGGGACGTGACCCTTCCAGCTGAGGAAGTACCTCCTGAACTTCCAGAACCAGCACTGGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g34640.1 (Oryza sativa), 3'ss of exon 2
ttattttatattcactttttacattatccatatatatcttatgttg-gcataaatgagtgcaacttgcttat----tttggatgtttgtaaa-----tttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
          |||  | |||   ||    | ||    |||   ||  ||||||   |||||  |  |   ||     ||   ||| |   ||     ||  |||  | ||| |||||||||||||| || |||||    || ||||| ||||||||||||| | |||||| |||||| || ||||| ||| | || |||||||| |||||
---------tttctttctttgtcttgcgtagattctgcttgccttttgcataa-caagtgctgcccggacataactcttatgtgtctactaattcctttcattcgaacagAAAAGGAGAACTTGTGCCTTTATGGGTACCCTAATGAAACATGGGAAGTTACCTTGCCTGCTGAGGAAGTTCCTCCGGAGATCCCTGAACCAGCTTTAGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G153087_T01 (Zea mays), 3'ss of exon 2
ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtt-tgtaaatttgttct-tatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
|  |  |  |||    ||| |  | | | || |     |||   |  |  |||  | ||||| |  ||||||   ||| || | |   |||||| |  | ||||||||||||||| ||| | ||||||||||| ||||||||||||||| | ||| |||||| ||| ||||| |||||||| || ||||| |||||  | ||
tcttgattcatttttgtttgaagtgagctattttaggtttagagt--ctgaaacaactgcaaataccttattcgagatattattttcttttgttttgcacagAGAAGGAGAACTTATGTTTATATGGACTTCCTAATGAGACATGGGAAATAAACTTGCCTGCTGAAGAGGTCCCTCCTGAACTGCCAGAGCCAGCTCTTGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
--ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtt-tgtaaatttgttct-tatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
  ||  || || |||| ||    ||  | |||| |     |||    | |  |||  |  |||| |  ||||||    || || | |   |||||| |    ||||||||| || || ||| | ||||||||||| ||||||||||||||||| ||| |||||| ||||||||| |||||||| || ||||| |||||  | ||
tcttggttcattttcaattaaagca--agccattttagatttaga--gcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 2
ttattttatattcactttttacattat-ccatatatatcttatgttggcataaatgagtgcaacttgcttattttgga-tgtttgtaaattt-----gttcttat---agAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
         | | |  ||    |  ||  ||||  ||  | | ||   ||||   || | ||  |   || |||||   ||||   | ||||      || ||||   |||||| ||||||||||| || |||||  | ||||||||||| ||||| ||||  || || | |||||| ||||||||||||||||||||||||||| | ||
---------actgatgttcagtaacatgtcataactag-tgacgtgaacatatcagattccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G008259_T02 (Zea mays), 3'ss of exon 2
ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttg--cttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
      | |  |     |  |   | |  || || ||   |||   | |   ||     |||   |  ||    |   | | || | |  || |  ||  |||||| |||||  ||||| ||||||| ||||| ||||| ||||||||||| ||| ||||||  |||||||| |||||||| |||||||| |||||  | ||
-cgaactttcctggtcctggattcttttaat-tagatagcatggaagaaaggatcttgacaaaaagacctagaatcttaaggttttgacgttttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGAACTTGCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCAGCTCTGGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G063864_T01 (Zea mays), 3'ss of exon 2
-ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
  |  | |  | | |  |   | ||| |  | ||  | |  ||        | ||   |     |||     ||   ||  |  |   ||| || |   |||||| ||||||||||| || |||||  | ||||||||||| ||||| || |  || || | |||||| ||||||||||||||||||||||||||| | ||
actgatgttcagtaatatgccatattgttgacatgaa-cacatcagattccatatttttttgttttgtcccgttgacatagtgctttctttcttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTCACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G00630.1 (Glycine max), 3'ss of exon 2
-ttattttatattcactt---tttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
  |  || ||| || |     |    |  | ||| |   ||  | | |||   |   |   |||||  || ||  ||   || | ||| |  || |  || ||||||||||||| |||||||| |||||  |||||||||| ||||||||||| ||  ||||||||||||| || |||||||| ||||| || |||||||||||
tgtccttcataatctcccaaataggaagaacccaaaagaatgattttttgaagtgt-tatttgcaatgtgttttgttaacat-tatgtta--ttctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
-ttattttatattcactt---tttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
  |  || ||| || |     |    |  | |||     ||  | | |||   |   |   |||||  || ||  ||   || | ||| |  || |  || ||||||||||||| |||||||| |||||  |||||||||| ||||||||||| ||  ||||||||||||| || |||||||| ||||| || |||||||||||
tgtccttcataatctcccaaataggaagaacccaagagaatgattttttgaagtgt-tatttgcaatgtgttttattaacat-tatgtta--ttctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
-----ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
     | | | | | |    ||| ||| | |     |  ||  |    |||   |   |       ||||  |  |     | ||||     |||| |  |  ||||||||| ||||||||||| |||||||||||||||||||||||||| ||||| || || ||||||||||| |||||||||||||| |||||||| |||||
ctttttaagtgtttgtgagatttgtacctaagatgaagttagttctctttgtggtttctcttcttgacttcttagtgaattacgttt-----tttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG

upper sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------------------------ttatttta--tattcactttttacattatccatatatatc---ttatgttggcataaatgagtgcaactt------gcttattttggatgt-ttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
                                                                     || ||  |  | || |  || ||  || |  |  | | |    | | | | |  | | | ||| |  ||       | || | ||  | || ||  |   |||||  | ||||||||||||| |||||||| |||||||||||||||||||||||||| ||||| || || |||||||| || |||||||||||||| |||||||| |||||
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG

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|30296137|gb|CB972931.1|CB972931
EST:     AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTG                         AGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACA
genomic: AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTGgtaagttatt ... gttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACA
EST: gi|110712767|gb|EE088111.1|EE088111
EST:     AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTG                         AGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTA
genomic: AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTGgtaagttatt ... gttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTA
EST: gi|161715590|gb|FC068346.1|FC068346
EST:     AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTG                         AGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTA
genomic: AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTGgtaagttatt ... gttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTA
EST: gi|110368641|gb|EC932630.1|EC932630
EST:     AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTG                         AGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTA
genomic: AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTGgtaagttatt ... gttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTA
EST: gi|110702763|gb|EE079018.1|EE079018
EST:     AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTG                         AGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTA
genomic: AAGTTGAAAAGTTCTACCAGCAGTGCGATCCTGgtaagttatt ... gttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG
                                          tttgttctt  CT-rich tract
                                      taaatttgttcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - tattcac
- - - - - - - - - - - - - -ccatata
- - - - - - - - - - - - - - - - - - - - -tgttggc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgagtgc