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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgagacttgtgttacagcatctgatatgtttctccttcagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG

Basic information

species Vitis vinifera
transcript Vv15s0046g03390.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 10
attg-agacttgt-gttacagcatctgatatgtttctccttcagttattatatgaagtacagcc-tgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
| || | | || | |     |   |   | || |  | || |  |    |  |  | || | |  | |   ||| |  |  |  |||  || |   |   ||| | ||| | |||||||| ||||||||||||||||||   || || ||||||||||| || ||||| || |||||||| || || || ||||| || ||||
actgcacatttatagcccttgttgcctgtgtgctcattctgctctctagaatttgattataactgttcgatttgtaagttatcctttttatgt---tgaacagTTGCTTCGTCCAATTTACAAGCAAATTGCTGAAAATAGGAACGCTGAGATATTTTCAGCAAATACTCTCCTTGTTATTTTTGGAACAAGTCTTCTCACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------------------------------------------------attgagacttgtgttacagcat-ctgatatgtttct-ccttcagttattata-tgaagtacagcctgcacct-tgcacttatttttttgcatctgctttt--gcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
                                                                                      |    | ||||| |    || | |    |||||||    ||   |  ||  |    | |  |  ||||| || || | | |    ||| ||| |  | |    ||| | ||| | || ||||| |||||||||||||||||||| ||||| ||||||||||| || |||||||| |||||||| || || || ||||| |||||||
gtgagtttactgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactctaggctcagctggacatgggcttgtttctttgcttgcatgcatgtttcagttttttctccttgcagctgaatttaatctgcaactatgtaatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 10
------------------------------------------------------------------------------------------------------attgagacttgtgttacagcatctgatatgtttctccttcagttat-tatatgaagtacagcc-tgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
                                                                                                          | |    |||| |||  | |      || |  || ||  ||| |  || |  |||| |  |  |   |||| || |  ||||| |||        ||| | ||  | || ||||| || ||||||||||||||||| ||||| ||||||||||| || |||||||| |||||||| || || || ||||| |||||||
gtgagttgactgttcatttacattattttgcttatcctttctggtactttttgtatgccatacgtagactctgggcccagctggacataggtttggttccttgcatacatgcatgtttcagtttttttccccttgcagctgcatgtatctcaattatctacaactatttaatgtgcaattttcgttttgtatcaa-----acagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G01600.1 (Glycine max), 3'ss of exon 3
--attgagacttgtgtt-acag---catctgatatgtttctcctt-cagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
    | ||   | | || |  |   |||  |  | |  | |  |  || || ||   || | || | | |   |  || |   |||||    | |||    |||||||| ||| |||| || |||||||| ||||| || |||||||||||||| ||||||||||||||||||||  |||||||  | ||||| || || || ||||
aggataagctctatatttatgggtacattaggaaggcatgttataacaattcttgattgcactataacttttgctatgta---attttcccacttct----ttgcagCTCCTTCGACCTATATATAAGCAGATTGCAGAGAATCAAAATGCAGAAATATTTTCTGCCAATACACTCTTTGTTATTCTTGGGACCAGCCTTCTCACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 9
------attgagacttgtgttacagcatctgatatgtttctcctt-cagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
       |  | | || ||      |||  |  | |  | |  |  || || ||   || | || | | |   |  || | ||     ||  ||| |   | | ||||| ||| | || || |||||||| ||||| || |||||||||||||| ||||||||||||||||||||  |||||||  | |||||||| || || ||||
ttccccctctatatttttggatt--cattaggaaggcatgttttgacaattcttgattgcactataacttttgctatgtaatt-----ttcccatttctctgtacagCTCCTTCGGCCCATATATAAGCAGATTGCAGAGAATCAAAATGCAGAAATATTTTCTGCCAATACACTCTTTGTTATTCTTGGGACTAGCCTTCTCACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
---------attgagacttgtgttacagcatctgatatgtttctccttcagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
          ||| |  |    ||  |     |   ||| |  | ||||| ||        |  |  ||  |   | |||  || | |||  ||    |   ||| ||||| ||| ||||||| || |||||  |||| ||||||||||||||||| || || || ||||||||||| ||||||||  | || || ||||| |||||||
tgatatcattttggggttcac-ttggaaggcattgcatggtggtacttcaattgc------agatgtagagtatgctttgtgctgagtttcctgttctt--ctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 17
----attgagacttgtgttacag--catctgatatgtttctccttcagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
    | ||| | |  | ||   |  ||| ||  | |  |  | | |    |||  | || ||| ||  |||   |||  || | |||| ||    |   ||| ||||| ||| ||||||| || |||||  |||| ||||||||||||||||| || || || || |||||||| ||||||||  | || || ||||| |||||||
gataagtgata-tcattttggggttcatttggaaggcattgcatgcttcaattgca-gatgtagagtatgc--tttgtgctgagttttctgttctt--ctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCTAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
---------attgagacttgtgttacagcatctgatatgtttctccttcagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
               || | |  |  | |     |  |  | || |||| |   |  |  |||  | ||  |  ||  |||| | ||||| | | |    |      |||| ||  | || || || ||||||||||| ||||| | |||||| |||||||| || |||||||||||||| |||||  | ||||||||| | |||||||
aatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgct--gaatcatagttt-tacaatgcattgattttctggtacacac------agCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 10
--attgagacttgtgttacagcatctgatatgtttctccttcagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
  ||  |   |     | |     ||| ||  |       ||| ||  ||||||    |  |     |   |  |   | |||      |       |  |||| ||| ||||||| || ||||||||||| ||||||| ||| || |||||||| |||||||| || ||||| |||||  | ||||||||| | || ||||
tcatgaaagttaactgtgctatcactgctacttccggtactcaatt--tatatgtttcaatggagttataatataaggaatttacactcttgttgcatatagCTTCTTCGACCAATCTACAAGCAAATTGCAGAAAATCGAAACGCCGAGATATTCTCTGCCAACACGCTTCTCGTTATTCTTGGGACTAGTTTACTGACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 9
----------------------------------------------------------------------------------------------------------------------attgagacttgtgttacagcatctgatatgtttctccttcagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
                                                                                                                            || | |  |  | |     |  |  | || |||| |   |  |  |||  | ||  |  ||  |||| | ||||| | | |    |      |||| ||  | || || || ||||||||||| ||||| | |||||| |||||||| || ||||||||||                                 
gtaagtctcaatggttttctagtttctgttttgagactcatatccgaataagttaaacaacaaaagagagatccatataagtgatgagaaaacattagattttctatagaatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgct--gaatcatagTTT-TACAATGCATTGATTTTCTGGTACACAC------AGCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACAC---------------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG
                                          tctgctttt  CT-rich tract
                             ttatttttttgcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgagacttgtgttacagcatctgatatgtttctccttcagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG

- - - - - - - - - gcatctg
- - - - - - - - - - - - - - - - -ctccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgcac