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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaacttccatgaaattaaaatgtaaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatgtttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG

Basic information

species Vitis vinifera
transcript Vv04s0008g01170.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g39260.1 (Oryza sativa), 3'ss of exon 5
-aaaaacttccatgaaattaaa--atgtaaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatgtttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG
 |   |     | |    ||||   ||| |    | |  ||  || |  | | | |  || |||| | |   ||    | |     || |||| |  || ||||| || || ||||| ||||| ||||| ||||| ||||| ||||| |||||||| |||||||| || ||||||||||| ||||| ||||| ||||| ||||
tatgcatcgttaagcccataaatggtgtgaggatttacccctcattttca-tcaca--tgcatatgttatacggcaaatgacaagctgcttccttgttttcagCGTTTTACACGTCTTGGTGGAAAACTGCCAAAAGGTGTCTTGCTGGTTGGTCCTCCTGGCACTGGAAAGACCATGTTAGCAAGGGCTATTGCTGGGGAAG

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g39250.1 (Oryza sativa), 3'ss of exon 5
aaaaacttccatgaaattaaaatgtaaaccctgaagccctatctctagttagagttgt---atatc-tgaataggtttcttattttatgtttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG
    ||||  ||| |  ||  || ||     | |   |   | |     || | ||||   ||||  |||  ||   ||  |   |  |  ||| |  || ||||| || |||| ||| ||||| ||||| ||||| ||||| ||||| ||||| || |||||||| || ||||||||||| || || ||| | ||||| ||||
--gcactttaatgcatatatgatctatcatttcataactgtttttgtcatatacttgtgctatatggtgatcagaagtcacaagct--gcctccttcttttcagCGTTTTACTCATCTTGGTGGAAAACTGCCAAAAGGTGTCTTGCTGGTTGGCCCTCCTGGCACTGGGAAGACCATGTTAGCGAGGGCTGTTGCTGGGGAAG

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 5
aaaaacttccatgaaattaaaat-------gtaaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatgtttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG
     |||  |||||  | |  |         ||  |||| ||   || || || ||    || | | | |   || | | || |     |||   | |  || ||||||||||| ||||| ||||| |||||||| || || || |||||||||||||| |||||||| || || |||||| | || || ||||| ||||| ||||
---tgcttttatgaagctcatctcgtcttgacaacacctggagg--tacct-tatttttcattttgtctttcg-tatgatgctcacaaactgtgctcttgttttcagCGCTTCACACGTCTTGGTGGAAAACTTCCGAAAGGAGTCTTGCTTGTTGGTCCTCCTGGCACTGGGAAAACCATGCTAGCTAGGGCTATTGCTGGTGAAG

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G463032_T01 (Zea mays), 3'ss of exon 4
aaaaacttccatgaaattaaaatgt-aaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatgtttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG
|  | |    ||||   |     ||   | |     | | |    |||||   | || ||| | |  ||| | | || |     |||   | |  || |||||||||||  |||| ||||| |||||||| || ||||| |||||||| || || |||||||| || || |||||| | || || ||||| ||||| ||||
accatcaaatatgattgtgtgccgtcgtaacacacgggcatcgtactagtctta-ttatatgtttttataagatgctcacaaactgtgctcttattttcagCGCTTCACATGTCTTGGTGGAAAACTTCCTAAAGGTGTCTTGCTTGTGGGCCCTCCTGGCACTGGGAAAACCATGCTAGCTAGGGCTATTGCTGGTGAAG

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G10960.1 (Glycine max), 3'ss of exon 3
aaaaacttccatgaaattaaaatg--taaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatg------tttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG
      ||   |  | || | |||  |    |||||   | |||      ||  | || |    || |  |  ||| | ||| ||||      |||||||||| ||||||||| |||||||| ||||| || |||||||| || |||||||||||||||||||||||||| || || || ||||| ||||||||||| |||||||| |
-----ttttgttacattttatatgcttctttcctgactgcatatactggcttgtactttt---ccttatcatctttgtaattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 5
aaaaacttccatgaaattaaaatg--taaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatg------tttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG
     |||   |  | || | |||  |    |||||   | |||      ||  | || |    || |  |  ||| | ||| ||||      |||||||||| ||||||||| |||||||| ||||| || |||||||| || |||||||||||||||||||||||||| || || || ||||| ||||||||||| |||||||| |
-----ctttgttacattttatatgcttctttcctgactgcatatagtggcttgtactttt---ccttatcatctttgtaattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 3
aaaaacttccatgaaattaaaatgtaaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatg-----tttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG
  |   ||   | |  ||      |    |||||   | |||      ||  | || |    || |  |  ||| | ||||||||     |||||||||| ||||||||| |||||||| ||||| || ||||| || || ||||| |||||||||||||||||||| || || || ||||| || |||||||| |||||||| |
--acttttttgttacgttttttattctttcctgaccgcgtatactggcttgtactttt---ccttatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------aaaaacttccatgaaattaaaatgtaaaccctgaagccct-----atct---ctag------ttagagtt-gta----tatctgaataggtttc-ttattttatgtttc---ccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG
                                                                      | || |    |||| |||  || || ||| | |  | ||     ||||   | ||       ||||||| |||    | | |   ||||  ||  | ||| || |||    | ||  || || | ||||||||||| || || || ||||| |||||||| |||||||| ||||| ||||| || || || || ||| | || |||||||| ||||||||||
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttagagttgtatatctgaataggtttcttattttatgtttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG
                          tttcttattttatgtt  CT-rich tract
                          tttcttattttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaacttccatgaaattaaaatgtaaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatgtttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
aaaaact
- - - - - - -aaattaa
- - - - - - - - - - - - -aaaccct
- - - - - - - - - - - - - - - - - - ccctatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttcc