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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgttatatgggtttgtaaatttccatacaagcttataatttgtttgcatagataatgttaaattattttttatgcaacatcttgtaacatttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA

Basic information

species Vitis vinifera
transcript Vv10s0003g03710.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 9
aatgttatatgggtttgtaaatt---tccatacaagcttataatttgtttgcatagataatgttaaattatttttta---tgcaacatcttgtaacatttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
     | ||||  | | |  |||     | |||| | | || ||   |||   |   |    || |||  | || ||   |  ||   |||      | ||  ||||||||||||||||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||| |||||| | || ||||| ||||||||||| ||  | |
-----tctatgcctctatccattggtggcgtacacgat-atcatcaatttcttttatttggatttaatactcttgtaaaataaaatgactttggtgctgttctcagGACATTGAATTATCCAAAGAAATAAATGAGTCTTTCAAGCAATCATCTCAAGCAAGGACAAAGCTTCCATCTGGCATTGAAATGAGTGTTCACGTGCTTA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 9
-----------------------------------aatgttatatgggtttgtaaatttccatacaagcttataatttgtttgcatagataatgttaaattattttttatg------caacatcttgtaa-cat--------ttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
                                   | | |||| |   ||||  ||  |   ||||    |||  || | | ||||    ||| | ||  | | |||| |       ||  ||| | ||| |||        ||||  |||||||||||||||| ||||| |||||||| || |||| ||||||||| ||||| |||||||| |||||  | || ||||| |||||||| |||||  | |
gtagcgttagctgttattactatgaatacatttttagtcttatcttattttgcgaacct--gtacagttgtatcgttaggt-gcatctgaaatatcaacatttcttttgtatagattcagtatcctttaaacatctgtctggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 8
-----------------------------------aatgttatatgggtttgtaaatttccata---caagcttataatttgtttg---catagata-------atgttaaattattttttatgcaacatcttgtaacattt-----ttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
                                   | | |||| |   |||| | |  || |||   | | | |   ||   | ||    ||  |||       || |  | | | |     |  |||||||  ||  |  |     ||  |||||||||||||||| ||||| ||||| || || ||||  |||||||| ||||| |||||||| |||||  |||| ||||| ||||||||||||||  | |
gtagtgttagctgtttctactatgatgatatttctagtcttattttattttgcacacctctatagttctatcgttagatgcatctgaaatatcaatatttctttatatagattcagtgcccttttaacatctcttattacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 9
-----aatgttatatgggtttgtaaatttccatacaagcttataatttgtttgcatagataatgttaaattattttttatgcaacatcttgtaacatttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
        || ||   | | ||  ||  |  ||  |   |||||  || | |  ||   |    ||  || | |    | |  |  | || |  | |  || ||||||||||||||||| ||||| ||||| ||||||||||| || ||||| || || ||||||||||| ||| |||| ||||| ||||||||||||||||| |
actatgccgtaatgatgatctgacaagctttatgaattattatagcttttatttatctgttgctttttataact----acgttattttttttttcctaatt-cagGACATTGAATTATCAAAAGAAATAAACGAGTCCTTCAAGCAGTCATCCCAGGCTAGGACAAAACTCCCATCAGGGATTGAAATGAGTGTTCATGTCTTGA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 9
aatgttatatgggtttgta-aatttccatacaagctt-ataatttgtttgcatagataatgttaa-attattttttatg----caacatcttgtaacattttta--cagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
       ||| | |||||   ||   |  |||| ||| || | || ||   |||| |  | |||| || |    || ||    | |  |||   |   || | |  ||||||||||||||||| ||||| ||||||||||| |||||||| ||||| || || ||| |||||||| || |||| ||||| |||||||||||||| ||||
------ttattgttttgtgtgatgatctgacaaacttcatgaattatt---atagttcttattaacatcacagcttctgacaactatgtctcaaattgttgtgaatcagGACATTGAATTATCAAAAGAAATAAATGAGTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 10
aatgttatatgggtttgtaaatttccatacaagcttataatttgtttgcatagataatgttaaattattttttatgcaacatcttgtaacattttta---cagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
     |||||| |||   |   |   | | ||  | || | ||  |        |  |  |  ||| ||||||||  |  |  || |    ||| ||   ||||||||||||||||| ||||| ||||| |||||||||||||| ||||| || || ||||||||||| ||| | || ||||| |||||||||||||| || |
-ggactatatgagttatgatgatctgaca-aacttcatgaattactatagcttttttttatccattgttttttata-actacattattttttttctaattcagGACATTGAATTATCAAAAGAAATAAACGAGTCCTTCAAACAGTCATCCCAGGCTAGGACAAAACTCCCATCCGGGATTGAAATGAGTGTTCATGTTTTGA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 9
aatgttatatgggtttgtaaatttccatacaagcttataatttgtttgcatagataatgttaa-attattttttatg-caacatcttgtaacattttta-----cagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
     | | | |  |  | |   ||     ||  | || | || ||   |||| |  | |||| || |    || || ||||  | | | | ||||||      ||||||||||||||||| ||||| |||||||| || |||||||| ||||| || || ||| |||||||| || |||| ||||| |||||||||||||| ||||
----atcttttgaatgatgatgctctgacaaacttcatgaattatt---atagttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaatcagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 9
aatgttatatgggtttgtaaatttccatacaagctt--at-aatttgtttgcatagataatgtt--aaattattttttatgcaacatcttgt--aacatttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
  ||    |||    ||      |||||||    ||  || || |||| | |||  | |||  |   ||| |  ||  |  |  | | || |  ||  ||| | ||||| |||||||| || || || || || ||||| ||||||||||| || || ||||| |||||||| ||| | ||||||||||||||||| || || ||||
--tggcggatgatcctgc-----tccatacttattttaatgaacttgtgtacatttacaataatcctaatgagcttgaactctccgttttattgaaattttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATTCAAACAATCTTCCCAGGCCAGAACAAAACTGCCATCGGGAATTGAGATGAGTGTCCACGTTTTAA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ14633 (Selaginella moellendorffii), 3'ss of exon 9
aatgttatatgggtttgtaaatttccatacaagcttataatttgtttgcatagataatgttaaattattttttatgcaacatcttgtaacatttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
                              | || | || ||| ||           | |  ||| |   | | |||      |||       ||  |||||||||||| | || |  || ||||| |||||||| || ||||| || |||||||||||||| || ||| | ||||||||||||| ||| ||||| || |
----------------------------gtacgcctgtattttttt----------gtatccaatcagcatctttgccgagcattgag-----ttcccagGACATTGAACTTTCAAGGGAAATAAACGAGTCCTTTAAGCAATCCTCACAAGCCAGGACAAAGCTACCAGCTGGAATTGAGATGAATGTGCATGTGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatagataatgttaaattattttttatgcaacatcttgtaacatttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
                                      ttgtaac  putative branch site (score: 2)
                                            cattttt  CT-rich tract
     tagataatgttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgttatatgggtttgtaaatttccatacaagcttataatttgtttgcatagataatgttaaattattttttatgcaacatcttgtaacatttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - gggtttg
- - - - - - - - - - - - ccataca
- - - - - - - - - - - - - - - - - - - - - - - tgcatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacatc