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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacataaaatatttactattgagcttagctttccgctgtattttctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA

Basic information

species Vitis vinifera
transcript Vv13s0019g04470.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 4
gtacataaaatatttactattgagcttagctttccgctgtattttctaattaagaaattgcattcat-tttctcaccttgccttgtgtg--tgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
             | |    |||    |      |  ||         |  || ||  || ||  ||  || |   ||| |  | ||    || ||||||||||||||||||||  ||||| |||||||| || ||||| |||||||||||||| |||||||| ||||| |||||||| ||  |  ||  |||||||||||
------------gtaagctctgaatccactaaaaccatgagcaagagcaacaaaaacctgtatatatacttgtttgcttactgtatgccattgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTA

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 4
----gtacataaaatatttactattgagcttagctttccgctgtattt---tctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
    || || |||||| | | |  |    |||  ||     |||         | | ||  | ||  ||  || | |      ||    |   | | | |||||||||||||| || || ||||| |||||||| || ||||| |||||||| ||||||||||| || ||||| ||||||||| || || ||   ||||||||||
gtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttactactagatcacaa-cactcttgattattattattaatatttattgcagTGGATGCTCCAGATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTA

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
----gtacataaaatatttactattgagcttagctttccgctgtattt---tctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA--
    || || |||||| | | |  |    |||  ||     |||         | | ||  | ||  ||  || | |      ||    |   | | | |||||||||||||| || || ||||| |||||||| || ||||| |||||||| ||||||||||| || ||||| ||||||||| || || ||   ||||||||||  
gtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttactactagatcacaa-cactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 4
---gtaca-taaaatatttactattgagcttagctttccgctgtattttc--taattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
     ||    |  | ||||  | |   |    | ||| | |   | |||  |   |  | | || |||  ||||  | |   || | |||   |||||| ||||||||||||||||  ||||| |||||||| || ||||||||||||||||||||||||||||| |||||||||||||||||| |  ||  ||| || ||||
tatccacggcgagctctttatcaatattccactccttcaggtccctcttcactgcctctgtagttacatcaatttgttga---tgacatgtcattgtttt-cagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGAAAGGACAAGTTTGGTGAGGAAATGAAGAAAAACGCTCAAGCTGCAGGAGTTA

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 4
gtacataaaatatttactattgagctta-gctttccgctgtattttcta-attaagaaattgcattcattt---tctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
  | |    ||  |    |  |  |||      ||  ||  |   |  | |   | ||| || | | |  |   | | |    | | |||   |||||| ||||||||||||||||  ||||| |||||||| || |||||||||||||| |||||||||||||| ||||| |||||||||||  |  ||  ||| || ||||
--aaactgcatcatcgaaacaggccttttataatctactaaaccgtgaacaaccaaaaactgtagttacatcagtttgatgacggcatgtccttgtttt-cagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGGAAGGACAAGTTTGGTGAGGAGATGAAGAAAAATGCTCAAGCTGCAGGAGTTA

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G089767_T01 (Zea mays), 3'ss of exon 2
---------gtacataaaatatt-tactatt--gagct--tagctttccgct-gtattttctaattaagaaattgcattcattttctcaccttg----ccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
         | | | |||  |   || ||||   ||||  |||| |    |  ||  |   |  |||   ||   |||      |   | | |      | ||    |  ||| ||||||||||||||||| ||||| ||| |||| || || || ||||| || ||||| |||||||| ||||| ||||| |||||  || ||  ||||||| |||
gtaagctctgaagaaaaaccacaataatattcaaagctattagcctatgaccagtcctgattggttacataaactcataagaaattaaaacataacaatcctgacattacttttcagTGGATGCTTCAAATTCCTGGTGCATCAAGTTACATTGGTTGCATCGGGAAGGATAAGTTTGGTGAGGAGATGAAAAAAAATGCACAAGCTGCTGGTATTA

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
gtacataaaatatttactattgagcttagctttccgctgtattttctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
|||  ||      ||  || ||  |||||   | | ||| || |  || |        |  |  || |||  | | || | ||   ||  | ||| |||||||||| ||| | ||||| |||||||| || |||||  |||| |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| |
gtatgtatctaccttgttagtg--cttagtaatactctgaatcta-tattagctttggtcaaagcaatttacc-ctttacttt---tgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G33910.2 (Glycine max), 3'ss of exon 3
gtacataaaatatttactattgagcttagctttccgctgtattttctaattaagaaattgcattcattttctcaccttgccttgtg----tgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
                 ||| |    || |||     |  ||  ||| | |  | | | || ||  |     ||  || || | |     ||  | ||| |||||||||| ||| | ||||| |||||||| || |||||  |||| |||||||| ||||||||||| || |||||||| |||||||  ||||||||||| |
----------------gtat-gcatctaccttgttagta-atactctgaatctgtagtagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAGGCTTGCTGGTGTAA

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 1
gtacataaaatatttactattgagcttagctttccgctgtattttctaattaagaaattgcattcattttctcaccttgccttgtg----tgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
  |   |   |  | |    ||    || |||     |  ||  ||| | |  | | | || ||  |     ||  || || | |     ||  | ||| |||||||||| ||| | ||||| |||||||| || |||||  |||| |||||||| ||||||||||| || |||||||| |||||||  ||||||||||| |
-aatcaaggttgctcaagtatgcatctaccttgttagta-atactctgaatctgtagtagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAGGCTTGCTGGTGTAA

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
gtacataaaatatttactattgagcttagctttccgctgtattttctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
    ||  | | | |  |||  |||| ||  |   |  || | |  || ||  | |  |  ||   || |||   |||  ||  |          |||||||||||||||   || || || ||||| ||||| || ||||| ||||||||||| ||||| ||||| |||||||| || |  | ||| | |||||| |
--gtatgcactttcttttat-aagctgagtctggagtagt-tgtgttacttgtgtagcta-atcatttgtcttcacttcactcata--------acagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA
                         ttctcac  putative branch site (score: 2)
     attaagaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacataaaatatttactattgagcttagctttccgctgtattttctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA