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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagtaaggttgcaagaatccgtatgaaaaattgcattcttcaaaatataatcatttaccatcttaatctgtgagaccctgattgatagatcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG

Basic information

species Vitis vinifera
transcript Vv14s0108g01110.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 8
-gcagtaaggttgcaagaatccgtatg----aaaaattgcattcttcaaaatataatcatttaccatcttaatctgtgagaccctgattgatagatcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG
    | ||  |    |   | | | ||    | ||  |       |   | ||      |||    | ||  | | |  ||  ||   | ||     ||    || |   | | ||||| ||||| ||  ||||||||||||| |||||||| ||||||||| | |||||||| || |||||||| ||  | |||||||||
gtttgcaaactctgcacttttcatttgttgtacaagctatgaagctacgagtagttctttttgttgtgttgttttttctgagtct--cttatttcctatccttagATTGCACGTGTCTACTATCCTGGTCTGCCAAGTCACCCAGAACATCACATTGCCAAGAGTCAGATGACCGGCTTTGGTGGTGTCATTAGTTTTGAG

upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G075153_T02 (Zea mays), 3'ss of exon 8
gcagtaaggttgcaagaatccgtatgaaaaattgcattcttcaaaatataatcatttaccatcttaatc-tgtgagaccctgat-tgatagatcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG
                     || ||||    |   ||  | ||    |   ||||     | | |||  | | ||    |||| | ||   |  ||  ||| |     | ||||| ||||| |||||||||||||||||||||||||| ||||||||| | || |||||||| ||||| || || || |||||||||
---------------------gtgtgaa---ctatgtttcttaattagtgg-cattccatgtttcaattgttttagctaatgatgttatctcttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATTGCCAAGAGTCAAATGACTGGCTTTGGCGGTGTTGTTAGTTTTGAG

upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G113873_T02 (Zea mays), 3'ss of exon 8
gcagtaaggttgcaagaatccgtatgaaaaattgcattcttcaaaatataatcatttaccatc-ttaatctgtgagaccctgattgatagatcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG
   ||  |              |||  | |  || || |     | |   ||    |    || ||  | | |   |   || |  ||   |  ||  ||| |     | ||||| ||||| |||||||| || |||||||||||||| ||||||||| | || |||||||| |||||||| || || |||||||||
---gtgtgaactatgtttcttttattgatatatgtatgcaaactagtggtattccatgttttcattgttttatttaatgttgtt--atctcttgttcccagATTGCCCGTGTCTACTATCCTGGCTTGCCTAGCCACCCTGAACATCACATTGCCAAGAGTCAAATGACTGGCTTTGGTGGTGTGGTTAGTTTTGAG

upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G37020.3 (Glycine max), 3'ss of exon 8
-----gcagtaaggttgca-agaatccgtatgaaaaattgcattcttcaaaatataatcatttaccatcttaatctgtgagaccctgattg-atag-atcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG----
         ||   ||  | ||| ||  |||| |||     ||| ||||  ||  | || | ||   ||| |        | |  | |||  |||  |  |||||||||||||  | ||||| |||||||||||||| ||||||||||||||| |  |||||||| | |||||||||||||| ||||| || ||||||||||||    
ataccattttatcattttacagattcaatatgtaaa----tatt-ttcatgattgagtcctgta---tctgatgtgacttggctttaattacatactactattggcagGTGAAGCGGGTCTACTATCCAGGCTTGCCGAGTCACCCTGAACATGAGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGGTGG

upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G37020.1 (Glycine max), 3'ss of exon 8
-----gcagtaaggttgca-agaatccgtatgaaaaattgcattcttcaaaatataatcatttaccatcttaatctgtgagaccctgattg-atag-atcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG
         ||   ||  | ||| ||  |||| |||     ||| ||||  ||  | || | ||   ||| |        | |  | |||  |||  |  |||||||||||||  | ||||| |||||||||||||| ||||||||||||||| |  |||||||| | |||||||||||||| ||||| || ||||||||||||
ataccattttatcattttacagattcaatatgtaaa----tatt-ttcatgattgagtcctgta---tctgatgtgacttggctttaattacatactactattggcagGTGAAGCGGGTCTACTATCCAGGCTTGCCGAGTCACCCTGAACATGAGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG

upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G49660.1 (Glycine max), 3'ss of exon 8
gcagtaaggttgcaagaatccgtatgaaaaattgcattcttcaa-aatataatcatttaccatcttaatctgtgagaccctgattg-atag-atcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG
    |    |  ||      | | | | | |||   |   | || | | | || ||| |      ||     || | |  | |||  |||  || |||||||||||||  | ||||| |||||||||||||| ||||| ||||||||| |  |||||||| | |||||||||||||| ||||| || ||||||||||||
---ttcttataccattttatcattttacagattcagtatgtaaacattttcatgattgagtcctgtatctgatgtggctttaattacatactattattggcagGTGAAGCGGGTCTACTATCCAGGCTTGCCGAGTCATCCTGAACATGAGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG

upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G01120.1 (Arabidopsis thaliana), 3'ss of exon 8
gcagtaaggttgcaagaatccgtatgaaaaattgcattcttcaaaatataatcatttaccatc----ttaatc-tgtgag---accctgattgatagatcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG
                     ||||| || ||  | || || |  | |||  |    || |||    | | || ||||||   |    |||  |    | ||| ||||||||     || || ||||||||| | |||||||| || |||||| |  | ||||||||||| |||||||||||||| || || |||||||| |||
---------------------gtatgcaatatctcttttttgagtaaatatcctgacactatccagGTGAGTCATGTGAGTAAATATCGATGCAATTTTGATTTGCAGGTGAGTCATGTGTACTATCCAGGCCTTCCAAGTCATCCCGAACATGAACTCGCCAAGCGACAAATGACTGGTTTTGGAGGTGTGGTCAGTTTCGAG

upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S49_246V6.1 (Physcomitrella patens), 3'ss of exon 8
----gcagtaaggttgcaagaatcc----gtatgaaaaattgcattct-tcaaaatataatcat-ttaccatcttaatctgtgagaccctg--attgatag-atcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG
    |||||  | |     | |||      | ||    | ||| |    || |  | || |||  ||     ||| | || |  |  | |   ||| ||    |   | |||||||  | | ||  ||||||| || ||   |||||| || |||||||| ||||| ||||||||||||||||| ||||| || ||  | |||||||||
gtttgcagtgtgttgaactggatcttgaaatgtgttttactgcgtggagtctatttctagtcaggttgattacttgacctatagggtcttataattcatgatgttgcttgcagGTGGCACGTGTACATTATCCTGGATTAGAAAGTCATCCAGAACATCAGATTGCGAAGCGACAGATGACTGGCTTTGGCGGTGTCATTAGTTTTGAG

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|30131657|gb|CB916996.1|CB916996
EST:     AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAG                         GTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCAT
genomic: AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAGgtgcatttca ... tcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCAT
EST: gi|28969813|gb|CB348846.1|CB348846
EST:     AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAG                         GTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT
genomic: AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAGgtgcatttca ... tcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT
EST: gi|110731786|gb|EE106500.1|EE106500
EST:     AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAG                         GTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT
genomic: AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAGgtgcatttca ... tcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT
EST: gi|30128490|gb|CB913829.1|CB913829
EST:     AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAG                         GTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT
genomic: AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAGgtgcatttca ... tcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT
EST: gi|110702814|gb|EE079112.1|EE079112
EST:     AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAG                         GTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT
genomic: AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAGgtgcatttca ... tcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT
EST: gi|30133528|gb|CB918867.1|CB918867
EST:     AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAG                         GTGANATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT
genomic: AAAATTCAACAGCATTGAGGATGGCCAAGATTTTAGAGGCCCATCCTAAGgtgcatttca ... tcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataatcatttaccatcttaatctgtgagaccctgattgatagatcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG
     atcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagtaaggttgcaagaatccgtatgaaaaattgcattcttcaaaatataatcatttaccatcttaatctgtgagaccctgattgatagatcattggcagGTGAAATGCGTCTATTATCCAGGCTTGCCAAGTCACCCTGAACATCATATTGCCAAGCGACAGATGACTGGTTTTGGTGGAGTAGTCAGTTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - -gcaagaa
- - - - - - - - - - - - tgaaaaa
- - - - - - - - - - - - - - - - -gcattct
- - - - - - - - - - - - - - - - - - - - -caaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accctga