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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatctctggcttaatcttgtaactggaattctatttgtagcaccaactaaatattcatattaattacttgtacctaattaatatttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT

Basic information

species Vitis vinifera
transcript Vv14s0066g02540.t01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 25
---------------------acaatctctggcttaatcttgtaactgga-attctatttgtagcaccaactaaatattcatattaattacttgtacctaattaatatttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT
                     ||  | | |  | |   |   | | |  |   ||| |   |  ||| |||| | || |||| || | | |||     | |||  | ||        |  |||| |||||||| ||  | || |||||||||||||||||  ||||||||||||||||||| || |||||| | ||   |||   ||   ||||  ||| | 
gtttgttttaagaaagacgttactgtttgttccatccacagatgattatatgctctttgcatgccacaaactgattaatcattttgaatgctt-----tgattggtttt--------cctagATAGCACGTCGGTTACTTGGAAAAATTTTAATTGATCTACGGAACACTCGTGAAGAAGCAATAAGTGTTTCAGATCCAAAATTTACAGAAGATGAAGCTA

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM2G022997_T01 (Zea mays), 3'ss of exon 5
------acaatctctggcttaatcttgtaactggaattctatttgtagcaccaactaaatattcatattaattacttgtacctaattaatatttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT
       |||| |      |  |||  ||  |    || ||| | ||      |     ||  |||  | ||  | | |   ||  ||  || | | ||     |||| || || ||||| ||||| |||||  |||| |||||  | ||||||||||||||||||||||||||||| |||  |||   || | ||||| ||| | 
tgggaggcaatttgaaaagttttctcatagttcctgtt-tatct-taatgtgtatatcttaaccatgctcatatccttt-tttatatataatatatcga---ctagATAGCGCGCCGTTTATTGGGAAAAATCCTAATCGATCTACGCAACACTCGTGAAGAAGCTATCAGTGTTGCCGAACCAAAATTTATTGAAGACGAAGCTC

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 23
acaatctctggcttaatcttgtaactggaattctat-ttgtagcaccaactaaatattcatattaattacttgtacctaattaat--atttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT
  | |   ||  ||  |  || |  || | || ||  ||||| |   | | |  |  | | |   |||  ||  |  | |||  |   ||| ||   | ||||||||||||||| || ||||| |||||||||||||||||||||||||||||||| ||||| || ||||||||||| ||||||||||| |||||||| ||||
tgattagatgcattgtttctgcatatgtacttgtaagttgtatctatagccacctgattaca---attttttaaattttattgtttgttttattttgattcagATTGCACGTCGATTATTGGGAAAAATTTTAATTGATCTGAGGAACACTCGTGAGGAAGCCATTAGTGTTGCTGAGTTAAAGAGTAACCAAGACCATGATT

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 25
acaatctctggcttaatcttg-taactggaattctatttgtagcaccaactaaatattcatattaattacttgtacctaattaatatttgttg--aaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT
 |  |||     ||  | ||| |   || |    ||||  | | |  |  |  ||   |   |  |||  ||  |  | | |  | | ||||       | ||||||||||||| || ||||| ||||||||||||||||||||||||||||| || ||||| || ||||||||||| ||||||||||| |||||||| ||||
-ctttcttgcagttgctattgctcgatgaacaagtattacttgta--agttgtatcaccgattacattgttttaattttaattgtttgtgttattgtgattagATTGCACGTCGATTATTGGGCAAAATTTTAATTGATCTGAGGAACACTCGCGAGGAAGCCATTAGTGTTGCTGAGTTAAAGAGTAACCAAGACCATGATT

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 23
acaatctctggcttaatcttgtaactggaattctatttgtagcaccaactaaatattcatattaattacttgtacctaattaatat-ttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT
  |||  |||     |      || |  ||| | |||  |   ||| |   |||    |   ||   || ||    || ||  | |  ||||  || ||||||||| ||||| || ||||| ||| |||||||||||||||| |||||||| || ||||| || | |||||||||  | |||| ||| || |||||    |
tgaataactgaacacagtacacaaattaaatgc-attgcttctacctatgtaattaaaagtctagccacctgattatattttttttactgtttcaattcagATTGCTCGTCGGTTATTGGGAAAACTTTTAATTGATCTGAGAAACACTCGAGAGGAAGCCATTACTGTTGCTGAGCTGAAGAATAACCATGACCATTCAT

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 39
acaatctctggcttaatcttgtaactggaattctatttgtagcaccaactaaatattcata---ttaattacttg--tacctaattaatatttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT
   ||   |  || ||    ||| |   ||||  ||   | || | |  ||  || | | |    ||   || ||  ||| |  ||  || | |||  || ||||||||| ||||| || ||||| ||| |||||||||||||||| |||||||| || ||||| || | |||||||||  | |||| ||| || |||||    |
---atgaataactgaactcagta-cacaaattaaatgcattgctctacatatgtacttaaaagtctagccacctgattacattgtttttact-gtttcaattcagATTGCTCGTCGGTTATTGGGAAAACTTTTAATTGATCTGAGAAACACTCGAGAGGAAGCCATTACTGTTGCTGAGCTGAAGAATAACCATGACCATTCAT

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 26
-----------------------------------acaatctctggcttaatcttgtaactggaattctatttgtagcaccaact------aaatattcatattaattact-tgtacctaattaatatttgttg---aaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT
                                   | |   |||| |||   ||      |||||||    |    |  |    |      | ||  ||  |  | ||||  | |   | |||  | ||||||    |||   |||||||||| ||  || ||||||||||  | |||||  ||||||||||||| ||||| || || |||||||||||||| ||||  | |||||| ||||  |
gtgtgtgttctcagcttggccttctaagttccacaatagcatctgacttttcctctc--ttggaatttccctgagggtccagggttttctcagatgatctcacaacttaccattttttttatttttttttgttttctaaataaagATTGCACGGCGCCTGCTGGGTAAAATCCTTATTGACTTGAGGAACACTCGAGAAGAGGCCATGAGTGTTGCTGAATTGAAGAACAGTCAAGATCAAGTCT

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 25
acaatctctggcttaatcttgtaactggaattctatttgtagcaccaactaaatattcatattaattacttgtacctaattaatatttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT-
                              | ||  || | |     |||  |||  | | ||||| |||    |||  ||    |||||    ||  |||||   ||||| ||| |||| || ||||| || ||||||||||||||  | ||||| |||||||||||||| || || || |   |  |||   || ||  
-----------------------------gtactgcttattga---tactttatacgcgttttaatcactc--tcctgctt--cctttgt----acctagATTTGCCGTCGATTGCTGGGGAAGATTTTGATAGATCTGAGGAACACCAGAGAAGAGGCTATCAGTGTTGCAGAGTTGAAAAACGAAGAAG-TTAAAATAA

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: EFJ19878 (Selaginella moellendorffii), 3'ss of exon 25
acaatctctggcttaatcttgtaactggaattctatttgtagcaccaactaaatattcatattaattacttgtacctaattaatatttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT-
                              | ||  || | |     |||  |||  | |  |||| |||    |||  ||    |||||    ||  |||||   ||||| ||| |||| || ||||| || ||||||||||||||  | ||||| |||||||||||||| || || || |   |  |||   || ||  
-----------------------------gtactgcttattga---tactttatacgcgttctaatcactc--tcctgctt--cctttgt----acctagATTTGCCGTCGATTGCTGGGGAAGATTTTGATAGATCTGAGGAACACCAGAGAAGAGGCTATCAGTGTTGCAGAGTTGAAAAACGAAGAAG-TTAAAATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactaaatattcatattaattacttgtacctaattaatatttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT
     aaatattcatattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaatctctggcttaatcttgtaactggaattctatttgtagcaccaactaaatattcatattaattacttgtacctaattaatatttgttgaaactcagATTGCACGTCGTTTGTTGGGTAAAATTTTAATTGATCTGAGGAACACTCGTGAAGAAGCTATCAGTGTTGCTGAATTAAAGAGTAATCAAGACCAAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
-caatctc
- - - - tggctta
- - - - - - - - - - - - - - - - - - - - - caccaac