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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagtgaaaaaaggttaccttctaggtgtcatcaagatcatgtcccctttcttattgctagttggtgatctagtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG

Basic information

species Vitis vinifera
transcript Vv11s0016g00170.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 17
ttgagtgaaaaaaggttaccttctaggtgtcatcaagatcatgtcccctttcttattgcta-gttggtgatctagtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
                       || |||| || |||      | |   || |  |||  | ||     |       |   | || | || |  || |||| |||||||| || || || |  ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||| || || || || |||
----------------------gtatgtgt-ataaagtcttaatgctacttttatttgacatgtcaaccactggtctcaaatggtatattatgacttgcagGTACTGTGCTGATAACCCTGGACTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGACGCCCACAACCCAATG

upper sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 18
ttgagtgaaaaaaggttaccttctaggtgtcatcaagatcatgtcccctttcttattgctagttggtgatctagtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
            |||||    | ||  | |    || |  |  | |  |    | ||||             ||    |  | |||||  |     |||| |||||||| || ||||| || ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||| ||||| |||
----------gtaggtttatatgtacttatagaaaacacaaatttctttaagattttgcccccgtcaccctcagatactgatatgtttattt----gcagGTACTGTGCTGATAATCCTGAGCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGATGCACACAATCCAATG

upper sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 20
----------ttgagtgaaaaaaggttaccttctaggtgtcatcaagatcatgtcccctttcttattgctagttggtgatctagtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
          |     |     | | |||||| ||  |||  | |  ||  |     ||||  || |  |||   |||   | || ||| ||||       || |||||| ||||||||||||||||| |  ||||| |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||||||||| ||||| || |||
ttatactttatatttcgtgggcatgataccttgtacctgtactgataat--ttatatcttttgtactaataga-agtgtcttggtgcttgttgt-------ctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG

upper sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 20
-------------------------------------------------------------------------------------------------ttgagtgaaaaaaggttaccttctaggtgtcatcaagatcatgtcccctttcttat-tgctagttggtgatctagtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
                                                                                                 ||  |||   |            | | |||        | ||      | |||| | | ||| |  |   | |    |||| ||  | |||||| || ||| ||||||||||||||||| |  ||||| |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||||||||| ||||| || |||
gtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaatcttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgataccttgcatggttgtacctgtactgataatttatatcttttgtactaat-agcagtgt----ctttgtgcatgttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG

upper sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 19
------------------------------------------------------ttgag--tgaaaaaaggttaccttctaggtgtcatcaagatca-----tgtcccctttcttattgctagttggtgatcta---gtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
                                                      || ||  ||  |     ||      ||||||     || |||      ||   | | || | || | ||||  | |   |    |  | ||    | ||| ||   | || || || ||||||||||| | ||||||||| ||||||||||| || || ||||| || ||||||||||| ||||| ||||| ||||| |||||||| |||
gtaagggcgccatgtattattctctgagatcattatatgaatctagtacaaatattaagcttggtagttatttgtggattaggtgaatggaaaatctatatttggttcttatcattttcccagttaataactaacatattatgttccactgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG

upper sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------ttgagtgaaaaaa-ggttaccttctaggtgtcatcaag-atca----tgtcccctttcttattgctagttggtgatctagtcctttt-tgtgttttgtctctg-----gcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
                                                                                || |  |  |       ||||||| || |     ||   ||||    |||  | |  | ||   |  |  ||  || |  ||    | |||  ||||  |  |      ||| ||||||  ||| |||    | ||||||||||||||||| || |||||||| || || ||||||||||| ||| | || || ||||| ||||||||   |
gttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgccggctatttcttctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG

upper sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ32651 (Selaginella moellendorffii), 3'ss of exon 18
ttgagtgaaaaaaggttaccttctaggtgtcatcaagatcatgtcccctttcttattgctagttggtgatctagtcctt-tttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
                                                     ||    | |    ||  |  || | |  ||     | |  | |  ||| |||||      ||| || |  || ||||||  ||| || || ||||||||||| |||||||||||||| ||| | || || ||||| |||||||| |||
----------------------------------------------------gtacgatttgccaatgcccgtgtgcatgcttcaaactagagtgttccagGTACTGCCGTTGCAACCCGGGGCTCTTCAAATCTGCCGACACAGCTTATGTTCTGGCATATGCAGTTATTATGCTCAACACGGATGCCCATAATCCTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctttcttattgctagttggtgatctagtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
                             tcctttttgtgttttg  CT-rich tract
     tcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagtgaaaaaaggttaccttctaggtgtcatcaagatcatgtcccctttcttattgctagttggtgatctagtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG

- - - gaaaaaa
- - - - - - - - - ccttcta
- - - - - - - - - - - - - - -tcatcaa
- - - - - - - - - - - - - - - - - - gatcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttggtg