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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatggttgtctcgtcatgaatttttctgccagtttgatgttttatgatgcatgatagtctgtagaatcagaaattttgacttatctgcaagaacatgcagGAGGCTGCAAACAATGACAATGGGCGAGCACCTCATTCTGCCTGGAGGAACTATGACGATTTTAATGAGTATTTTTG

Basic information

species Vitis vinifera
transcript Vv06s0004g01200.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 10
-gatggttgtctcgtcatgaatttttctgccagtttgatgtttta--tgatgcatgatagtctgtagaatcagaaattttgacttatctgcaagaacatgcagGAGGCTGCAAACAATGACAATGGGCGAGCACCTCATTCTGCCTGGAGGAACTATGACGATTTTAATGAGTATTTTTG
   | |||||||    |   |  |   |    |||||    |  |  | || | |  | || |  | |||  ||| |  | | |||  | || | || | ||||| |||||||||||||| ||||||  ||||||||||||  | |||||||| ||||| ||||||||||||||||| ||
ttcttgttgtctaagtactgaaatgcattt--gtttgggactcaagtttatcctttttggttta-aaaatatgaattcattatttacattcatggactttcagGAAGCTGCAAACAATGATAATGGGAAAGCACCTCATTCCTCGTGGAGGAATTATGATGATTTTAATGAGTATTTCTG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 10
gatggttgtctcgtcatgaatttt----tctgccagtttgatgttttatgatgcatgatagtctgtagaatcagaaattttgacttatctgcaagaacatgcagGAGGCTGCAAACAATGACAATGGGCGAGCACCTCATTCTGCCTGGAGGAACTATGACGATTTTAATGAGTATTTTTG
   | |  | | ||| | | |  |    |      |||||    || |   |      | |  |  | |||  ||| |  | | |||| | || | || | ||||| |||||||||||||| ||||||  ||||||||||||  | |||||||| ||||| ||||||||||||||||| ||
---gttcatgttgtc-taagtgctgaaatacatttgtttgggacttgagtttatccttttggtttaaaaatatgaattcattatttatgttcatggactttcagGAAGCTGCAAACAATGATAATGGGAAAGCACCTCATTCCTCGTGGAGGAATTATGATGATTTTAATGAGTATTTCTG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 10
gatggttgtctcgtcatgaatttttctgccagtttgatgttttatgatgcatgatagtctgtagaatcagaaattttgacttatctgc--aagaacatgcagGAGGCTGCAAACAATGACAATGGGCGAGCACCTCATTCTGCCTGGAGGAACTATGACGATTTTAATGAGTATTTTTG
 |   |||| |    |   |   | | |    | | ||  ||| | ||| | ||   |   |  |   ||| ||||    ||||||      | |  ||||||| |||   |||||||||||||| |||||||||||||| || ||||| |||||||| ||||| ||||| ||||||||
aaatattgtgtttcaaaacagaatgcagtttttatcatcctttcttatgtacgaatattcatgca--tagacatttactgttatctaatggggtatgtgcagGAAGCTTTTAACAATGACAATGGCCGAGCACCTCATTCAGCTTGGAGAAACTATGATGATTTCAATGAATATTTTTG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 11
---gatggttgtctcgtcatgaatttttctgccagtttgatgttttatgatgcatgatagtctgtagaatcagaaattttgacttatctgcaagaacatgcagGAGGCTGCAAACAATGACAATGGGCGAGCACCTCATTCTGCCTGGAGGAACTATGACGATTTTAATGAGTATTTTTG
     | ||  |  | |  ||  |||||     |  || || | ||  || | |  ||  |  ||| |||     | ||| ||     |           ||||||||   ||    ||    |||   ||| || ||||| |||||||| ||||||||||| |||||||||| ||| ||
gtaagttgtaatggcattctgggtttttagtgaatcttaatatattccgaagta--atttttagtaaaattgtggacttttaccggctt-----------cagGAGGCCAAAATATGTGCTGGTGGAAAAGCTCCGCATTCAGCCTGGAGAAACTATGACGACTTTAATGAGTTTTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcatgatagtctgtagaatcagaaattttgacttatctgcaagaacatgcagGAGGCTGCAAACAATGACAATGGGCGAGCACCTCATTCTGCCTGGAGGAACTATGACGATTTTAATGAGTATTTTTG
                            ttttgac  putative branch site (score: 3)
                         aaattttgacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatggttgtctcgtcatgaatttttctgccagtttgatgttttatgatgcatgatagtctgtagaatcagaaattttgacttatctgcaagaacatgcagGAGGCTGCAAACAATGACAATGGGCGAGCACCTCATTCTGCCTGGAGGAACTATGACGATTTTAATGAGTATTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- tggttgt
- - - - - -cgtcatg
- - - - - - - - - - - - tctgcca
- - - - - - - - - - - - - - - - - - - - - - - - gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaga