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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatcatgtggctccatataattttgttgatcaagttggttctgatacttgtagtttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC

Basic information

species Vitis vinifera
transcript Vv05s0020g01890.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os07g47180.1 (Oryza sativa), 3'ss of exon 6
---------tttcatcatgtggctccatataat--tttgttgatcaagttggttc-tgatacttgtagtttgtagattttgattgctgt----cttatatctc---catttctaaa-----cagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
         |||  |    ||  | ||  |  |  |||||| ||     || | |   | | |   |     ||    | ||    |||    || | | |||   |  |  || |     ||||   || | |||||||| ||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||  | ||||| || || ||||||| |||| 
gtatgtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaac-atactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
-----tttcatcatgtggctccatataat--tttgttgatcaagttggttc-tgatacttgtagtttgtagattttgattgctgt----cttatatctc---catttctaaa-----cagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
     |||  |    ||  | ||  |  |  |||||| ||     || | |   | | |   |     ||    | ||    |||    || | | |||   |  |  || |     ||||   || | |||||||| ||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||  | ||||| || || ||||||| |||| 
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaac-atactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
tttcatcatgtggctccatataatttt--gttgatcaagttggttctgatacttgtagtttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC------
     |||| ||  |   |||         | || |  |    |      |  |  | |||| |   | |      ||||  || | |  || ||| | ||||   |  |  || |||| ||||||||||| || ||||||||||||||||||||||| || || ||||||||  |  |      | | |||| |||| ||       
-ggtctcatttgatttactatggcccaaaatggagcccggcactctcttaatgtaaattttgcaatgtctctaatttgtcccatttatttatatctta-cagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGT------CTCTTTGGTTTCTACAAATCACA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: 13113.m00244 (Oryza sativa), 3'ss of exon 8
------tttcatcatgtggctccatataattttgttgatcaagttggttctgatacttgtagtttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
        |  |  ||||  ||  | | || |   |  |||   |   | | |   ||  ||         |  | |     | | | || | ||||   || |||||||||||  | ||||| ||||| |||||||||||||| ||||| ||||| || || || || ||||||||| |  | ||  |||||||||| ||    |
aactagcgttgttctgtg-ttctctctgatctcact--tca--ctatctttaaccattcaagacaaacatgtacgttgaacttttcaaattttcattaacaa-cagAGGCGACGCATGATAACGCATGCCAATGCCAAGAGCAAAAGTGAGAAGTTCCCCCCACCTCATCAGGATGGAGCTATGGGTAACCCATTGGGATCCAGTC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 6
-tttcatcatgtggctccatataatttt---gttgatcaagttggttctgatacttgtagtttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
 |    |   || | ||  | |  | |      | |      |   | | |   ||  ||         |  | |     | | | || | ||||   |  |||||||||||  | ||||| ||||| |||||||||||||| ||||| ||||| || || || || ||||||||| |  | ||  |||||||||| ||     
gtaaactagcgttgttctgtgttctctctgatctcacttcactatctttaaccattcaagacaaacatgtacgttgaacttttcaaattttcattaacag-

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g27020.1 (Oryza sativa), 3'ss of exon 7
------tttcatcatgtggctccatataattttgttgatcaagttggttctgatacttgtagtttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
        |  |  ||||  ||  | | || |   |  |||   |   | | |   ||  ||         |  | |     | | | || | ||||   |  |||||||||||  | ||||| ||||| |||||||||||||| ||||| ||||| || || || || ||||||||| |  | ||  |||||||||| ||    |
aactagcgttgttctgtg-ttctctctgatctcact--tca--ctatctttaaccattcaagacaaacatgtacgttgaacttttcaaattttcattaacag-cagAGGCGACGCATGATAACGCATGCCAATGCCAAGAGCAAAAGTGAGAAGTTCCCCCCACCTCATCAGGATGGAGCTATGGGTAACCCATTGGGATCCAGTC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G873277_T01 (Zea mays), 3'ss of exon 6
---------------------------------------tttcatcatgtggctc-catata--attttgttgatca----agttggttctgatacttgtagtttgtagattttgattgct-gtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
                                       |  ||| |  | | |  ||||||   | |||   ||||        ||| |  |  |||||   |||   |     |||  |  |||| | ||||   || |  |||||   || |  ||||||||||||||||||| |||||||||||||||||||| ||||| || || ||||||||  | ||||| |  || ||||| | |||  
gtacattcctatatttatttgagttacttagcagttcattggcatgaactcgtttgcatatactgtgttgcgtatcatctggaagggtgccaaatcttgtctcttggctaacacaattcttcatcttttctctc---ttatctacagAAAAGAAGGTTAATAACTCATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCGCATCAGGATGGCGCACTTGGATTTCCCTTGGGCTGTTCGA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
---tttcatca--tgtggctccatataattttgttgatcaagttggttctgatacttgtagt-ttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
   | | ||||    |||  | | |  |      | |  |   |    |  |   ||| ||| | |  |||||    |  |  ||| | | |||   |  | |||||   || |  | || |||||||||||||| ||||||||||| |||||||| ||||||||||| || |||||  |  ||||   ||| |||| | ||||| 
gagtcttatcagccatggtccaaaaggaagcccat-actaccataaagcaaac-tttgcagtatcgctgatttgtgctaat-ccttttttttcc---ttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 6
tttcatcatgtggctccatataattttgttgatcaagttggttctgatacttgtagtttgta-gattttgattgctg----tcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
      |||    |   |   || |  |    |        |||  ||  |  |  ||  || |||  ||| |  ||    |   | |||||   ||   | |||||||||||  | ||||||||||||||||| ||||| || ||||| ||||||||||| || || |||||||||      ||  | ||  | || || |   
--gtgccatagcccataagtaaactcaggctgtttgtcactttcaaatgttattgcttaatatgatactgaatattgaggtttccaaatctcttattaacagCAGAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCT---

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G156251_T02 (Zea mays), 3'ss of exon 6
tttcatcatgtggctccatataattttgttgatcaagttggttctgatacttgtagtttgta-gattttgattgctg----tcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
      |||    |   |   || |  |    |        |||  ||  |  |  ||  || |||  ||| |  ||    |   | |||||   ||   | |||||||||||  | ||||||||||||||||| ||||| || ||||| ||||||||||| || || |||||||||      ||  | ||  | || || |  |
-----ccatagcccataagtaaactcaggctgtttgtcactttcaaatgttattgcttaatatgatactgaatattgaggtttccaaatctcttattaacagcagAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCTATC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
---------------------------------------tttcatcatgtggctc----catata--attttgttgatcaagttggttctgatacttgt--agtttgtagattttgatt---gctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
                                         |   ||||    ||    ||||||   | |||   | ||  | |     ||    ||   |  ||     | |||  |   ||  |  | | ||| |  | ||  |||||   || |  | ||||||||||||||||| ||||||||||| |||||||| ||||| || || ||||| ||  | || ||||  || ||||| | |||  
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G052206_T02 (Zea mays), 3'ss of exon 6
tttcatca--tgtggctccatataattttgttgatcaagttggttctgatacttgtagt-ttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC---
| | |||     |||  | | |  |      | |  |   |    |  |   ||| ||| |    || ||    |  |  ||| | | |   | |    |||||  ||| |  |  | |||||||||   || ||||||||||| |||||||| ||||||||||| || |||||  |  ||||   ||| ||||   |||||    
tcttatcggccatggtccaaaaggaagcccat-actatcataaaacaaac-tttgcagtatcactgacttgtgcttat-ccttttttttttgtcttaccacagAAACGAAGGTTCGTCACTCATGCA---GCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCTTTGGACACTTCAAATC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
tttcatcatgtggc-tccatataattttgttgatcaagttggttctgatacttg-tagtttgtagattttgattgctgtcttatatctccatttctaa-acagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
   ||| | ||||| || |||||  | | |  ||  |||||||||  ||      |   || ||  | || ||       | ||   |  | |  ||  ||||||  | || ||  |||| ||||||||||| |||||||||||||| ||||||||||| || ||| | |||||||| |||||||| || |||||||||||||
---cataaagtggcatcaatatatatatatacatggagttggttcatatctcaacttacttttatgtcttaatattgtagtaatggtttaactcttattacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
tttcatcatgtggctccatataattttgttgatcaagttggttctgatac-ttgtagtttgtagattttgattgctgtcttatatctccatttctaa--acagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
    ||  | |   |  | ||  |   |||   |||| |  || || ||  ||  || || |     |  |   | || ||| || | ||  ||| |   ||||| || || || || || ||||||||||| |||||||||||||| ||||||||||| || ||||| |||||| | || ||||| || |||||||||||||
--gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagcttttcttagtgtagaacagtgtta-atgttcagctcttactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
--tttcatcatgtggctccatataattttgttgatcaagttggttctgatac-ttgtagtttgtagattttgattgctgtcttatatctccatttctaa--acagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
  | ||  | |||||     | |      | |   |||| |  || || ||  ||  || || ||    |  |   | || ||| || | ||  ||| |   ||||| ||||| || || || ||| ||||||| |||||||||||||| ||||||||||| || ||||| |||||| | || ||||| || |||||||||||||
attctccccttgtggaattttttgg----gctatccaagataattgtgttatattacagcttctattcgtatagaacagtgtta-atgttcagctcttactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
tttcatcatgtggctccatataattttgttgatcaagttggttctgatacttg-tagtttgtagattttga--ttgctgtcttatatctccatttctaa--acagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
       || |   |  |||||  | | |  ||   ||||||||  ||    | |   || ||  | || |  |||  ||  |   |    |  ||| |  ||||||  | || ||  |||| ||||||||||| ||||||||||| || ||||||||||| || ||  | |||||||| || ||||| || |||||||||||||
-----atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttgtagtaatggttgcttaactcttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|77586479|gb|DV222360.1|DV222360
EST:     GGGCAATGCCTGCTCCAGAAGCCAATGCTGAGCTGCAAGCCAATCTTGAT                         AGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTT
genomic: GGGCAATGCCTGCTCCAGAAGCCAATGCTGAGCTGCAAGCCAATCTTGATgtatgtcaga ... ttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacttgtagtttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC
                                      tctccatttct  CT-rich tract
                  attttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcatcatgtggctccatataattttgttgatcaagttggttctgatacttgtagtttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - catgtgg
- - - - - - -ctccata
- - - - - - - - - - - - - - - - - - - - - -ctgatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atctcca