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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT

Basic information

species Vitis vinifera
transcript Vv12s0028g00310.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------gtatgtttatatgtt--catcttaagt-cccctttagtctttatagtttttccacctgtatgatataaatttt-ttatgagagcctcagaacctgacatcttttctctgg------------atttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
                                             ||  |||   ||||   || |  ||| |  |  |  |   || | | |       |  ||| |   || ||| |  |  |    | | |||  |     || ||  ||             ||||||| |||||||| || || ||||| || || ||  ||||||| |||||||||||| ||||||| |||||||| ||  | ||||||||||| ||||| || |||
gtatgttgatatttttttggagttagtattaatctttcctatgcttagcttttactgttggaatgtgcagtacttcgcttattcatacaatataaaattttacatgctgcgaactttgtccttcgtatattataacaggtagctttctcattgctatcattgattcatttcagGTATGTGGCCCCTGAGTATGCCAACACAGGTCTGTTAAACGAGAAGAGTGATGTCTACAGTTTTGGTGTGCTATTACTGGAAGCAGTGACTGGTAGAGAT

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g41730.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctc----tggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
                                                     |  ||| || |  | |   | ||       ||  | |||| | | | ||||  |   | ||  ||| ||   ||     |   || |  || ||  |  || |    ||  ||  || || || || || |||||||||||||||||   | |||| |||||||||||  ||||||| ||||| || || ||  |||||||||| || |||||||||
gtaagctactaagctctcgttttaagttgtaattttcctgattgagttgcaggggctgtataaa-atactgatcaacatgaaattcatgttta-actatctccaattcctttattcaaagttg--atagcgtctcaagcaattgccacttaatcccccattgttttctagGTACGTAGCCCCTGAATATGCTAATACTGGGCAGCTAAACGAGAAGAGTGACGTCTACAGTTTTGGAGTGCTACTCTTGGAAGCAGTGACCGGAAGGGAT

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------gtatgtttatatgttcatct-taagtcccc--tttagtctttatagtttttccacctgtatgatat------aaattttttatgagagcctcagaacctgacatcttttctctgga---tttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
                                                                ||||     || |  | | |  | ||       || || |||   ||||||  | | |||| |  |          ||   |||| |     ||||||   || ||||| |    |   |||||| |||||||| || |||||||| || |||||  |||||||||||| ||||||| ||||||| ||||| || || || |||||| |||||||||| ||||| 
gtatgttgtttgcttgatattctttcatttttgtagtaccttgcttgactaactggaacatgtggtattacagtaggaacctttacatgttgagggatttgtttttcatgtttttagagcagtataaagttttgtggtgcttcacatgacatgaaaagaaccattcaccttttgttgctactgtttcagGTATGTGGCCCCTGAATATGCCAACACTGGTCTGTTAAATGAGAGGAGTGATGTCTACAGTTTTGGAGTGCTACTACTGGAATCAGTTACTGGGAGGGAC

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctg----gatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
                                                         ||| || |  |    ||     |        ||       | ||||| | |  | || ||   |     | |    | |   ||     | |  | |||  |       | |||||| |||||||| || || ||||| ||||| ||  |||||||||||||||| ||| ||||||| ||||| || || || ||||||||||| ||||| ||||||
gtatgtttttttatgggaacattccgaaatatgtcttttcttcactaactggaacctgta-gtcttcacacgcagtaggaagtttacatacagagctttgttttccaatttttaagaagaattagctctgcaggggaagcaaccattcatctttttatttcaccacggtttcagGTATGTGGCTCCCGAGTATGCCAATACAGGTCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGAT

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G017386_T03 (Zea mays), 3'ss of exon 5
gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
           | ||  ||||   ||      |  | |  |  |||       ||| |  |   |||   |||| ||||  | |    |   ||||  || |      ||||| ||||| ||||| |||||||||||||||||  |||||||||| ||||||||  | ||||| ||||| |||||| || | ||| | || || |||||| ||
----------gtattattcttttttctaacccatacctgctcatttgctt---tgtgtctttacaatgacttat-agagtttaactttcct-catccatttttcttgcttcagATATGTTGCACCTGAATATGCTAATACTGGAATGTTAAATGAAAAGAGTGACGTTTACAGTTTTGGCGTTCTCTTGTTAGAAACTGTGACAGGAAGGAAT

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 4
gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
                 | |  ||     || ||| | ||   | |       | | | |   |     || ||   | | |    |  |   | || ||| |   ||||||||||||||||||| |||||||||||||| || ||||||||||||| |||||| || ||||||||||||||||||||||| |||||||||||||||||||||
----------------gtatgcagaatgtttcagtatctactatatagat-tttatttaaaggattgcattaatagaaacttactcatgttggacctgttccc--aatttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 4
gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
                       ||   |   |   |||||  | | |   | | | | |||   |     | ||    | |  ||||    ||  |||  | |||||||||||||||||||||||||||||||||| |  || |||||||||||||||||||| || |||||||||||||| ||| ||||||||||||||||||||||||| 
-----------------------gtatacagaaaa-tttattatctctttccttattttatacttaaaggatttgtacacttaggaact---cacttttgttttggatttcagTTATGTGGCACCAGAATATGCTAACAGCGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTGCTGGAAGCAGTTACTGGAAGGGAC

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 4
gtatgtttatatgttcatcttaa-gtcccctttagt-ctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT-
       |||       | | |   ||  ||| | | |||||||| ||||  |  |  | |||     |   | |  |||  || |   |||        |  ||   ||||||||||||||||||| |||||||||||||| || ||||||||||||| |||||| || ||||||||||||||||||||||| |||||||||||||||| |||| 
-------tatgcacatgtttcagtatctacttgactactttatagatttt--atttaaaggat-----tgcataaatagaaacttatt-cctattggacctgttcccaatttcagtTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTAGAAGCAGTTACTGGAAAGGATC

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 6
gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
                        | |     | |  ||||  | |||||   | | | |  ||||   ||||||     || || | || || ||| || |  |||||||||||| |||||||||||||||||||| | ||| |||||||||||||||||||| || |||||||||||||| ||| | ||||||||||||||||||||||||
---------------------gtatacagaaaatttattatc-tctttccttattttttacttaaaggatttatgca---cttaggaactcacttctgttgt--ggatttcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 4
gtat-gtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
|||  ||  | |  ||  |    |  | |||   | | |||  ||| ||       | | | || |  |  |||  |     |||     ||   | |||  | | | |||||| ||||| |||||||||||||||||||| ||  | ||||| || ||||||||||| || |||||||||||  | || || |||||  | |||||  | |||
gtaaagtccaaaactttgt----accctcctcaggccattaaggttattattatcttctcagatgatgtccttacaaagaaatcattga-tgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
                              | |||||  |   | |  || | |   ||||      ||||| |       | |  | | | ||| | |    |     |||| ||||| ||||| |||||||||||||| ||  | || |||||||||||||| ||||| ||||||||||| || ||||| ||  |  | |||||||| |||
-----------------------------gtaagtctaaaatttgtaccctctttggtgatgatgggtttttgtatacatattattaacggtcatgtgta---tatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT
                            acctgac  putative branch site (score: 3)
                                  catcttttctct  CT-rich tract
     aaattttttatgaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG