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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaaatattctaatgaaagcaccagaaataggtgccccctggtatacatgatgtctcttatatgtgataggcaattctgacatgggtttgtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTCTTGGCATCAGTAAGTGTGGATTCTATCAGAGTTTGGACGCTTGGGTCAG

Basic information

species Vitis vinifera
transcript Vv04s0008g04910.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04910.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G16040.1 (Glycine max), 3'ss of exon 16
gtcaaatattctaatgaaagcaccagaaataggtgccccctggtatacatgatgtctcttatatgtgataggcaattctgacatgggtttgtaatg---ctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTCTTGGCATCAGTAAGTGTGGATTCTATCAGAGTTTGGACGCTTGGGTCAG
      | || |  ||    || ||  |||   ||  || |  | |     | ||||  | |   | | |  | | |    |||  | || |||      |||||||||||  || | || |||||||| || |||||||||||||| |||||  ||||||| ||||||| ||| ||| |||| |||||||| ||||| ||||
---tgttgttttggtggcttcaacaataatttatgttccttcttctcttgtaagtcttgtcttattcaaactctactaatgcatttgattttaacatgattagGGACATACAAAATCGATACATTCTGTGTGTTGGGATCCTTCTGGGGAGTTTCTGGCATCTGTAAGTGAGGACTCTGTCAGGGTTTGGACTCTTGGATCAG

upper sequence: Vv04s0008g04910.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G30910.1 (Glycine max), 3'ss of exon 16
-----gtcaaatattctaatgaaagcaccagaaataggtgccccctggtatacatgatgtctcttatatgtgataggcaattctgacatgggtttgtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTCTTGGCATCAGTAAGTGTGGATTCTATCAGAGTTTGGACGCTTGGGTCAG
        ||| |   | |||  | |        | |||| |  |     ||  | ||||  ||| | |   |    |   | |||  |      |  ||  |||||||||||  || |||| | |||||| || |||||||||||||| |||||  ||||||| || |||| ||| ||| ||||||||||||| ||||| ||||
atttccaaaaacaactttatgctacctaagtgttttggtgacttcgacagtaatttatgttccttctctccta---acgtatttgattttaacacg--ataatagGGACATACAAAATCAATACGTTCTGTGTGTTGGGATCCTTCTGGGGAGTTTCTGGCATCTGTCAGTGAGGACTCTGTCAGAGTTTGGACTCTTGGATCAG

upper sequence: Vv04s0008g04910.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G07460.1 (Glycine max), 3'ss of exon 16
gtcaaatattctaatg-aaagcaccagaaataggtgccccctggtatac--atgatgtctcttatatgtgataggcaattctgacatgggtttgtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTCTTGGCATCAGTAAGTGTGGATTCTATCAGAGTTTGGACGCTTGGGTCAG
 |     |||  |||  | |||| ||  |||   |    |||  | | |  |  || || |  || ||   |     |||   |  | |   | |  |   ||||||| ||  ||||| |  ||| ||| || |||||||||||||| |||||  ||||||| || |||| ||| ||| |||| |||||||| ||||| ||||
-ttggccattacaatttacagcagcaacaattt-tatttcctactgtcccaagaatatcaccaat-tgaatttctttattggaatgttgtactatggttgcagGGACACACAAAACCAGTGGATTGTGTTTGTTGGGATCCTTCTGGGGAGTTGCTGGCATCTGTGAGTGAGGACTCTGTCAGGGTTTGGACTCTTGGATCAG

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|161719157|gb|FC066063.1|FC066063
EST:     TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAG                         GGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
genomic: TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAGgttagtatat ... gtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
EST: gi|110708875|gb|EE086916.1|EE086916
EST:     TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAG                         GGACATACGGGAAC-AATTCATTCTGTCTGCTGGGATCCTTCTGGTGATTT
genomic: TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAGgttagtatat ... gtaatgctagGGACATACGG-AACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTT
EST: gi|110703802|gb|EE080967.1|EE080967
EST:     TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAG                         GGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
genomic: TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAGgttagtatat ... gtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
EST: gi|110690242|gb|EE067180.1|EE067180
EST:     TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAG                         GGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
genomic: TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAGgttagtatat ... gtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
EST: gi|34545176|gb|CF513408.1|CF513408
EST:     TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAG                         GGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
genomic: TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAGgttagtatat ... gtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
EST: gi|110700254|gb|EE078082.1|EE078082
EST:     TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAG                         GGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
genomic: TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAGgttagtatat ... gtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
EST: gi|34546171|gb|CF514403.1|CF514403
EST:     TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAG                         GGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
genomic: TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAGgttagtatat ... gtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
EST: gi|110699780|gb|EE077080.1|EE077080
EST:     TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAG                         GGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC
genomic: TTGTATCAATACTGGATGTGGAGACACAAGCTTGTCGGCATTCATTACAGgttagtatat ... gtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatgatgtctcttatatgtgataggcaattctgacatgggtttgtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTCTTGGCATCAGTAAGTGTGGATTCTATCAGAGTTTGGACGCTTGGGTCAG
                              ttctgac  putative branch site (score: 2)
           tcttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaaatattctaatgaaagcaccagaaataggtgccccctggtatacatgatgtctcttatatgtgataggcaattctgacatgggtttgtaatgctagGGACATACGGAACCAATTCATTCTGTCTGCTGGGATCCTTCTGGTGAGTTCTTGGCATCAGTAAGTGTGGATTCTATCAGAGTTTGGACGCTTGGGTCAG

- caaatat
- - - - - - - -gaaagca
- - - - - - - - - - - ccagaaa
- - - - - - - - - - - - - - - - - -ccccctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacat