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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttttcatctactctaattgcaacttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttccataattctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG

Basic information

species Vitis vinifera
transcript Vv14s0171g00330.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 7
gtgggttttcatctactctaattgcaacttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttccataattctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG
||  ||||  |  | |  |  | |   |||      || | |  |||  | |  |    || | ||  | || |   |   |||| |||     |||    |||||||| || ||||| || || || ||| |||||||||| ||||| ||||||||||| |||||||||
gtaagtttctaa-tgcgttgttgggctctta--cagttgtgacatgt--tgggttagcattaagggcctaagcatgattgttgtcatcc-----tctaccacagATGGGCAAGGATGTCGTTTCGTTCTTGTCATGGGCAGCTGAACCTGAGATGGAAGAGAGGAAACTG

upper sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 5
gtgggttttcatctactctaattgcaacttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttccataattctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG
          | || || |  |||     |  |  ||    | |  | | |  | || |          |  |  |||       || ||||  |    || ||||||| ||||||||||| || || ||| ||||||| ||||| || ||||||||||| || ||||||
--------gtagctcctgtttttgagttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG

upper sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G22530.2 (Glycine max), 3'ss of exon 6
gtgggttttcatctactctaattgcaacttgggtgcttct--taactgtaattgcatct---ttttcaaggtgtta-gaaaattgagtgtcttccataattctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG
  |    || || |  |  |   |    ||  ||   |||  | ||  | |||   | |    ||   |    ||| | ||| |   | | |       || || | |||||||| |||||| ||||||||||  |||| ||||| |||||||| ||||||||||| || ||||||
--gtacctttatttgttg-aggagtggtttcagtaaatctcatgacattgattatctatgaacttcggaaaaattatgcaaaatatatttttggttactttttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG

upper sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 6
gtgggttttcatctactctaattgcaacttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttc-cataat-tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG
   |  ||  || | ||      | ||  |||    ||  ||| | |  ||  |  |      |  || |||||  | |    | ||| | |||| | || ||||||||||||| |||||||| ||||| || || ||||| || ||||| ||||||||||| || ||||||
---gtattaaatttgcttctggaggaatatgg---tttagtaaatcttcttaaaaatgg---gatttgatagaatctagctcattttctcttaatgtttgttgcagATGGGGAAGGATGTTGTGTCATTCTTAACTTGGGCCGCCGAACCCGAGATGGAAGAGAGAAAACTG

upper sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 6
gtgggttttcatctactctaattgcaacttgggtgcttctta--actgtaattgcatct---ttttcaaggtgttagaaaattgagtgtcttccata-attctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG
  |   |||  | |  |  |        ||  ||   ||| |  ||    |||   | |    |||  | |  ||| |  |   | | | ||   || ||| || | |||||||| |||||  ||||||||||  |||| ||||| |||||||| ||||||||||| || ||||||
--gtacttttgtttgttg-aggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttatattttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG

upper sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 6
gtgggttttcatctactctaattgcaacttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttcca---taat-tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG
             || | || |||   || | |   |  || | |  |  | | |     |  |  |   | |||||  ||    ||  |   |||| | || ||||||||||||| |||||||| ||||| || |  ||||| || ||||| ||||||||||| || ||||||
------------gtattatatttgtttctggaggaatggtttagtaaatcttcttacaaatagaaattggaaaaaatgtagctcattttattttaatgtttgttgcagATGGGGAAGGATGTTGTGTCATTCTTAAGTTGGGCCGCCGAACCTGAGATGGAAGAGAGAAAACTG

upper sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgggttttcatctactctaattgcaa---cttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttccataattctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG
||   ||||| || |||  || |  ||   | |   |  || |    | |  |    || |||   || ||| |  | ||  | | |  |  |       |||||||||||| |||||| |||||||||| ||| | |||||||| |||||||| |||||||| |||||||||
gttatttttcctccacttaaaatataagaacataaatctttatgccttatggtactgtcctttctcag-tgtcatgatataaactttactttac------ggtgcagATGGGTAAAGATATTGTATCATTCTTGGCCTGGGCAGCTGAACCAGAAATGGAAGAGAGGAAACTG

upper sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgggttttcatctactcta-attgcaacttgggtgcttc-----ttaactgtaattgcatctttttcaaggt--gttagaaaat--------tgagtgtcttccataattctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG
||  |||||| ||| ||  | |    || |||    |        || |    | |||    ||  ||   ||   ||| | |||        |   | | ||  | ||   || |||||||||| |||||||||||||| || ||| | |||||||| ||||||||||||||||| |||||| ||
gttagttttcctctgcttaagaaaataatttgcagaccataaagttttatcagatttgacctttcctctgagtcaattatataatctttaatttttctttttttaaaaaacatgatgcagATGGGTAAAGATGTTGTATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTG

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|110360731|gb|EC924064.1|EC924064
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|77587867|gb|DV223133.1|DV223133
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|110696692|gb|EE073029.1|EE073029
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|161720747|gb|FC069966.1|FC069966
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGA
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGA
EST: gi|110381663|gb|EC935060.1|EC935060
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|110379810|gb|EC945030.1|EC945030
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|349807741|gb|FQ402132.1|FQ402132
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|110426281|gb|EC992684.1|EC992684
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCAGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|71873090|gb|DT022145.1|DT022145
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|349807532|gb|FQ401947.1|FQ401947
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|110374848|gb|EC939786.1|EC939786
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|110690901|gb|EE068387.1|EE068387
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|110379451|gb|EC944646.1|EC944646
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG
EST: gi|110708536|gb|EE086193.1|EE086193
EST:     TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAG                         ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCAGAACCAGAGATG
genomic: TTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttc ... tctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatctttttcaaggtgttagaaaattgagtgtcttccataattctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG
                   ttagaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttttcatctactctaattgcaacttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttccataattctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA