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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcatttttctaattttctctctcatggatttgctcatgttttattaaccatttgttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA

Basic information

species Vitis vinifera
transcript Vv06s0004g01200.t01
intron # 43
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 43
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 3'ss of exon 12
--------gtaagtatcatttttctaattttctctctcatggatttgctc-atgttttattaaccat--ttgttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA
         |||| ||  | |   |   || ||||  | |   | |  |  |  ||  | | | ||   ||    |||| || | |||   || ||||| ||  | || ||||| || ||||| |||||| ||||||| ||||| |||||||||| |||||| ||||| || |||||||||||||||
gtaagctgctaagcattctatgcatgtgttactctg-cgtaattatatttgaaattcgaattatcaggattaaaatacctctctcagGGTCGTTGAGGATTTCAGAGACTGGACGAATTGGCTGTTTTACCGAGGTGGTATTGGGGTTAAGGGAGAAGAAAGTTGGGAAGCCTGGTGGGATGAAGAA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
--------gtaagtatcatttttcta-attttctctctcatggatttgctcatgttttattaaccatttg--ttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA
          ||| ||  | | | |  || | || |    |  | |||    | |   ||||    |       ||  |||| |||||| ||| ||||| ||  | || |||||||| ||||| |||||  ||||||| ||||| ||||| |||| |||||||||||| ||||||||||| ||||||
gtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcattatgagattagatttcaaacccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 48
gtaagtatcatttttctaattttctctc--tcatggatttgctcatgttttattaaccatttgttttac----cccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA
|||||||| || | | ||  ||| | |   || |||  |  ||||||  | || |    |||  || ||    |  |||||||   ||||| || ||  | ||||||||||| |||||  | ||| ||||||||||||| |||||||||| |||||||||||| ||||||||||| ||||||
gtaagtattatctatttatctttgtattcttcctggcatgtctcatgagtcatgattattttccttcacggtgcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
lower sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 46
gtaagtatcatttttctaattttctctctcatggatttg-ctcatgttttattaaccatttgttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA
|||||||| || | | ||  ||   || | |  |   || |||||| ||  ||  ||        |     |||||||   ||||| || ||  | ||||||||||| |||||  | ||| ||||||||||||| |||||||||| |||||||||||| ||||||||||| ||||||
gtaagtattatctatttatcttgaactttgacaggcatgtctcatgattattttccctcacacagtgttt-ttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 45
gtaagtatcatttttctaattttctctc-----tcatggatttgctcatgttttattaaccatttgttttaccc--cttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA
||||||     | |  || || | ||          | || |  |   | | | ||| | ||    |   |     |||| ||    |||||||||||    || |||||||| ||||| |||||||||||||||||||| || || ||||  ||||||||||| || |||||||| ||||||
gtaagtggtgctatcttatttatatcatgttgagtgttgagtaacgtgtttctcattgaacaacaataaaattatgctttcagAGTCGTGGAGGACTTCAAAGAATGGACAAATTGGCTCTTTTACAGAGGTGGAATTGGTGTGAAAGGAGCTGAAAGCTGGGAAGCATGGTGGGAAGAAGAA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
lower sequence: EFJ05083 (Selaginella moellendorffii), 3'ss of exon 45
gtaagtatcatttttctaattttctctctcatggatttgctcatgttttattaaccatttgttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA
||||| |  | | |    | ||| ||| |  | ||||        ||  | |  |  || || ||| |   || || |||||||| |||||    || ||||| ||||||||||| || | ||||||| | ||||| || |||| ||| |||||||| || |||||||||||||| 
gtaagcacaactgt----aatttttctatggttgatt-------attccactgtc--ttcgtcttaac---ttcagAACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
lower sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 45
gtaagtatcatttttctaattttctctctcatggatttgctcatgttttattaaccatttgttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA
||||| |  | | |    | ||| ||| |  | ||||        ||  | |  |  || || ||| |   || ||||||||||| |||||    || ||||| ||||||||||| || | ||||||| | ||||| || |||| ||| |||||||| || |||||||||||||| 
gtaagcacaactgt----aatttttctatggttgatt-------attccactgtc--ttcgtcttaac---ttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctctcatggatttgctcatgttttattaaccatttgttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA
                           tattaac  putative branch site (score: 1)
                                    tttgttttaccccttt  putative PPT
                        ttttattaaccatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatcatttttctaattttctctctcatggatttgctcatgttttattaaccatttgttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA