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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA

Basic information

species Vitis vinifera
transcript Vv01s0011g02460.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g02040.1 (Oryza sativa), 3'ss of exon 5
cagagggcacttactatttagggatgaattgt--ccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaa---ttgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
                        | ||||    || |  | ||| ||           |   | ||  ||| |||| |   || ||   ||  |||   | ||| ||| ||||||| |||||||| || ||||||||||| ||||||| ||||||||| ||||||||||| ||||| ||  | ||||||||||| ||  | || 
-------------------gtaagtaaattactgcctgccttactgagggcacaagagaacatcgta--cattttcatatgatctaatgattatttgttatgcagTTATCTGGCTCCGGAGTATGCTTCGAGTGGCAAGTTGACTGAGAGATCTGATGTATTCTCTTTTGGCGTTGTTCTCTTAGAGCTTATTACCGGTAGAAAG

upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g01040.1 (Oryza sativa), 3'ss of exon 5
cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
              || | | | |       |    |    |  |||| |||  |  ||   | |   ||  | ||  |      ||  ||   || ||| || |||||||| ||||||||||||||||| || || ||||||| ||||||||| ||||||||||| ||||| ||  | |||||||| |||||  | |||
------------gttagtgaagtactggcaattttcagaagc--agatctgtcgtg-atcttacagagataattaataaaattcgtt--tttccttgcagGTACATGGCTCCAGAGTATGCATCAAGTGGGAAATTGACTGAGAGATCTGATGTGTTCTCTTTTGGTGTTGTTCTCTTAGAGCTTATCACTGGTAGAAAA

upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G355636_T01 (Zea mays), 3'ss of exon 6
cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
          |    |   || ||  | |     |||     ||| |  || ||   ||   |    ||||||      |   ||||           || ||  | ||||| |||||||| |||||||||||| | || |||| ||||||||| ||||| ||||| ||||| ||  ||||||||||||||||  | || 
--------gttagtaaagcagcgacaagtccaagagagcagttaaaacatgcttgtaatctgacg--catgtt------tcttaatt-----------agGTACCTTGCTCCGGAGTATGCCTCAAGTGGCAAGCTGACCGAGAGATCTGATGTATTCTCATTTGGTGTTGTTCTCTTGGAGCTTATTACTGGTAGAAAG

upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G872442_T02 (Zea mays), 3'ss of exon 6
cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
          |    |   || |   | ||    ||||    ||| |  || ||   ||   | |  |   |   |                   || || ||  | ||||| ||||| || ||||| |||||||| ||||||| ||||||||| ||||| || || || |||||  ||||||||||||||||  | || 
--------gttagtaaaacagcggcaagttcaagagaacagttaaaacctgcttgtaatctgacacacgcttctta-------------------tttagGTACCTTGCTCCAGAGTACGCGTCAAGCGGCAAGTTGACTGAGAGATCTGATGTATTCTCATTCGGTGTCGTCCTCTTGGAGCTTATTACTGGTAGAAAG

upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G458548_T01 (Zea mays), 3'ss of exon 7
cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatg-----ttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
                 |  | |||||   |||     | || |||        || ||| |||| ||||      ||||  |    ||  |  ||   |||||| || |||||||| ||||||||||| ||||||||  | ||||||| ||| ||||| ||||||||||| || ||  |  | |||||||||||||| ||||||
----------------gtgggtgatgagccgtcatatctcacaaagtacatcaatatatgacataaccatacggaattcatggtagacatcttgtttcttttcagGTACATGGCTCCAGAGTATGCATCGAGTGGCAAACTGACTGAGAGATCAGATGTGTTCTCTTTTGGTGTAGTTTTGTTAGAGCTTATTACTGGCCGGAAA

upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G23180.1 (Glycine max), 3'ss of exon 5
-------------------------------------cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
                                            |||||  |  ||| |    |  | |    | ||   || | | | |||| ||      ||| |   |       ||   |   | ||    || |||||||| || |||||||| ||||||||||| || |||||||| |||||||| |  ||||||||||| || ||| ||||||| ||||| ||| |||| 
gttggtattcatcaatatgtctccaaacttctctttttctttttcactttttcattaagaccaagatatttt-agtgcaaaaaactggattta-atattgattccctcccccccccccccccctttcttaa----agGTATATGGCCCCTGAGTATGCGTCAAGTGGCAAATTGACTGAGAAGTCTGATGTATATTCTTTTGGAGTCGTGCTTTTGGAGCTAATTACCGGAAGGAAG

upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G14310.1 (Glycine max), 3'ss of exon 5
-----------------------cagagggcacttac--tatttagggatgaattgtccagaatgactaagatttgttttacatgccata---tccatgttcaaagatt---------ccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
                       || |   | |||    | ||||    |  ||| | || |  |||||| || | |||||  ||| | |   |  ||   ||  ||||         ||           ||  || |||||||| || || ||||| ||||||||||| || |||||||| || ||||| |  |||||||||||||| ||| |||| || |||||||||||||| 
gtgggtattcatcaatatgtctccaaacttctcttttcttttttactttttcatttttcata--gactaaaatatatttta-gtgcaaaaaactttattaacattgatttcccccccccccccccccccccttatagGTATATGGCCCCTGAATATGCGTCAAGTGGCAAATTGACTGAGAAGTCCGATGTATATTCTTTTGGAGTTGTGCTTTTGGAACTAATTACTGGACGGAAG

upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 5
cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
                      | ||  ||| |  |  ||| ||   || ||   | ||        |  ||| | |  || || |    |  | || || ||||||||||| || |||||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||| || |||||| | || |||||||| |||
-------------------gtaggtgc-ttgccttgtttgattag--ttagtcgcatattttggcatctagttgatatttttcattcatct--actttagCTATATGGCTCCTGAATATGCATCAAGTGGAAAATTAACAGAGAAATCAGATGTATTCTCCTTTGGGGTTGTTCTGCTGGAGTTAATCACTGGACGTAAA

upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G26150.1 (Arabidopsis thaliana), 3'ss of exon 5
-cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
  ||  |    |||   |          ||||  ||   |||  || | || |||    |      ||||| ||  ||        |  ||    |||||| || |||||||| || ||||||||||||||||| ||||| |||||||| || || ||||| ||||| ||||| || |||||| | || |||||||| || 
gtaggtgctggttaaggtcccatatgacattgctca---tgagcaaaacttctttc-tgtatatgttccatcttataaacgattggtaaat--gttttcagCTACATGGCTCCGGAATATGCATCAAGTGGCAAATTAACCGAGAAATCAGACGTATTCTCCTTTGGGGTTGTTCTACTGGAGTTAATCACTGGACGTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA
                                      aattgat  putative branch site (score: 4)
                                      aattgattgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - -cagaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgtt