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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatccctgtgtgtttattatctgtggttatgtgattttttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA

Basic information

species Vitis vinifera
transcript Vv02s0025g00480.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
acatccctgtgtgtttattatctgtggtta--tgtgattttttttggttga-gactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
   |  ||  |||  | |   |||| || |  | | ||| || ||  |    || |    ||| ||   |||      ||||  || ||   |    |  ||||||||||| ||||| ||||| || ||||| ||| | ||||| || ||||||||||| ||||| || || ||||||||||| |||||||| || || ||||
---tttctcagtgaatctctgctgtagtgaactattattgttattattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
--acatccctgtgtgtttattatctgtggttatgtgat-tttttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
  |||||   | ||| | ||    ||  | | ||  ||  | ||||||||| |  |    || |||   | |    | | |     ||    |   ||  ||||| || || ||||| ||||| ||||| |||||  | ||||| || || |||||||| ||||| || |||||||| ||||||||||||||||||||  |||
aaacatcta-gagtgctcatctgttg-agctgtgaaatactattttggttgtgcattgccttgattaccattgacttctcttcaactgaatctac-ttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G041822_T02 (Zea mays), 3'ss of exon 2
acatccctgtgtgtttattatctgtggttatgtgattt---tttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
| |   ||  | ||    ||||||| |   ||||| ||    ||||||||| |       || |||   | |    ||||| |   ||    |   ||  ||||| || || ||||| ||||||||||| |||||  | ||||| || || |||||||| ||||| || |||||||| ||||| ||||||||||||||  |||
aaacatcta-gagtgctatatctgttgagctgtgaattacaattttggttgtgcactgctttcattaccattgacttttttaac--tgaatctaacttcacagGTCGTAGAGGATGGCTATGAGTTTTTCGCAAATCGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTTGACAATGCTGGTGCACTGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G37370.1 (Glycine max), 3'ss of exon 2
acatccctgtgtgtttattatctg--tggttatgtgattttttttggttga-gactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
  || |   ||| ||    || ||  ||| |      | ||  |   |||   | ||   || | |||   ||   |||   || |||||| |    || |||||||| || ||||| |||||||||||||| ||| | ||||| ||||| |||||||| |||||||||||||| || || || || ||||||||||| ||||
-tatgctgatgtattgggcatttgcttggctcatcagtcttaatccattggtaaatctggtttaatgt--tttccttttaaaattttgggctttgtgtttcagGTTGTAGAGGATGGATATGAGTTTTTTGCCAAGCGTCAGCTGGTGACGATATTCTCCGCACCAAATTACTGCGGTGAATTTGATAATGCTGGTGCTATGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G02180.1 (Glycine max), 3'ss of exon 2
-----acatccctgtgtgtttattatctgtggttatgtgattttttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
          | | ||  |   | ||| ||  | ||    |||  |    | | || ||   ||  || ||  ||   | |   || |||||| |   | |  ||||||| || ||||| || ||||||||||| ||| | ||||||||||| |||||||| |||||||| |||||||| || || || ||||||||||| ||||
atgtattgggcatttgcttggctcatcagtcttaatccattttaatgaattggtgaatctggtt--ttatgttttccttctaaaattttgggctt---tgtatagGTTGTAGAGGATGGATACGAGTTTTTTGCCAAGCGTCAGCTAGTGACTATATTCTCCGCACCAAACTACTGTGGTGAATTTGATAATGCTGGTGCTATGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------acatccctgtgtgtttattatctgt--------ggttatgtgattttt-tttggttgagactcaaattaattgtgacttgt------------gtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
                                                             || ||||  | || ||||         ||||| |  ||  |   |  ||||  | |  ||  |  |||   || |            |||||   |        |||   | |||||||| |||||||| || ||||| ||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||| ||||||||||||||  |||
gtaaagctaaaatttattccttgagttctctcttttgatttctctggattggtttgttcttctctgtgactgttctctgaattcagagggttaagaaatcataactcagttgttaatgcaaggatctgtagttttttcaccaagccaagttttacttaactatactgttcctgcagGTTGTAGAAGATGGATACGAGTTCTTTGCAAAGAGACAACTAGTGACAATATTCTCTGCACCCAATTACTGTGGCGAGTTTGACAATGCTGGTGCATTGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G64040.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------acatccctgtgtgtttattatctgtggttatgtgattt-----tttttggttgagactca-aattaattgtgacttgtgtttttgatcttgggcatgt--atttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
                               | | | | | ||  |||  |||  | ||  ||  |     |  | |    | ||| |  ||| ||      |    |  ||||  |||    | |     |  ||||||||||||| |||||||| || |||||||| || |||||||| || ||||||||||| ||||| ||||| || ||||| || || || || || ||||
gtaatattttgctttagacatgtatctgtggtacgtctcttttgtttacttgtcatcataggacctacaaataatggacgaatacttatgatttatctcttttaacctcattgaagttgattgttttgccctttagGTTGTGGAAGACGGGTATGAATTCTTTGCAAATAGACAGCTAGTAACGATATTCTCGGCCCCAAACTACTGCGGAGAGTTTGATAACGCAGGAGCAATGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EDO97337 (Chlamydomonas reinhardtii), 3'ss of exon 4
-----------------------------------------------------------------acatccctgtgtgtttattatctgtggt--tatgtgattt--tttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
                                                                     |   | ||         | | |||  | |||| |    | | ||   ||    || |     | |||  | || ||    |||||    ||   ||  |||| ||||| || ||||| ||||| || |||||| | ||||| ||||||||||||||||| || || ||||| ||||||||||| ||||| || || ||||
gtgcgggtcgtcgcctaggtgttccgcgggtttatggggttggcggaacacgcatcgcatgtcaagggacggggggtacccgactccgggggtcttgtgtggtcccgtatctgcccgaagtgcagagctcctctgaactttgctt---gtcttgcatgtggtattgtagGTGGTGGAGGAGGGGTACGAGTTCTTCGCAAAGCGCCAGCTTGTGACCATATTCTCGGCGCCGAACTACTGCGGCGAGTTCGAGAATGCGGGAGCGATGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S22_185V6.1 (Physcomitrella patens), 3'ss of exon 3
acatccctgtgtgtttattatctgtggttatgtgattttttttggttgagactcaaattaa-ttgtgacttgtgt-ttttgatcttgggcatgtatt---------tccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
          |  ||||  |  |||    ||||||||   | |  |   |  |  |||||  || |  || |||| |||  |     | ||||| |          | ||||| ||||| ||||| |||||||||||||| ||  | ||||| || || || ||||| ||||||||||||||||| || || || ||||| ||||| ||||
----------gattttacaaattgta-caatgtgattcagtctcctaatgggtagaattaccttattcctggtgtgtttcaagtactgacatgtgtgaatgtcacatgcagGTAGTGGAGGATGGTTATGAGTTTTTTGCTAAACGCCAGCTGGTCACTATTTTCTCTGCACCAAATTACTGTGGTGAATTTGATAATGCGGGTGCGATGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ20637 (Selaginella moellendorffii), 3'ss of exon 2
acatccctgtgtgtttattatctgtggttatgtgattttttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
                              | ||||  |  |  |||    ||    ||     ||  ||| |       |||     |   | |  ||||| |||||||| || || |||||||| || || || || || ||||| ||||| |||||||| || || ||||| |||||||||||| | || || ||||
-----------------------------gtatgatgctcgtgagtt----ctttctttctcgttgctttgagccccatgtctgcaata-acaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA

upper sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
acatccctgtgtgtttattatctgtggttatgtgattttttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
                              | ||||  |  |  |||    ||    ||| |  ||  ||| |       |||     |   | |  ||||| |||||||| || || |||||||| || || || || || ||||| ||||| |||||||| || || ||||| |||||||||||| | || || ||||
-----------------------------gtatgatgctcgtgagtt----ctttctttattgttgctttgagccccatgtctgcaata-acaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA

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|110701638|gb|EE079434.1|EE079434
EST:     CTGAATTCCTTCAGAAACATGACCTTGATCTCATTTGCCGAGCTCATCAG                         GTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATA
genomic: CTGAATTCCTTCAGAAACATGACCTTGATCTCATTTGCCGAGCTCATCAGgtaattgtaa ... gtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA
                                              tatttcc  CT-rich tract
       tcaaattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatccctgtgtgtttattatctgtggttatgtgattttttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
-catccct
- - - - - - - - - - - - - - - - - - - - - tggttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacttg