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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtggtgtgtttgtgtgtatgaaatcatattgggcatttgcttttatttatttatttttatttttatttttttgaacattcacttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG

Basic information

species Vitis vinifera
transcript Vv06s0009g00960.t01
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 26
gtgtggtgtgtttgtgtgtatgaaatcatattgggcatttgcttttatttatttatttttatttttatttttttgaacattcacttgcaaa-----cagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG
|| | || || ||| | || | ||| || |||| || | | | | ||| | ||| || | ||||| |||||||| ||||| || ||||||||||||||||| | |||||| |||| ||||| || |||||||| || |||| ||||||
--gtaaattatt-gtttgttccctacaggcttctctagttgtgcccataaatttgttgtgttctatgatttacaaagttttctgttctgatttcttcagAGGAGAGATGTCTATGGAGCCTGGGAGCAGTATCTTGGTTTGGAGCATGCTGATACTGCACCAAAAAGGGCCTACACAGCCAATCAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 30
---------------------gtgtggtgtgtttgtgtgtatgaaatcatattgggcatttgcttttatttatttatttttatttttatttttttgaacattcacttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG
| | | ||| || | ||| | | | | |||| |||| ||| | | ||||| || | | | |||| | |||| ||||||||||||||||||||||||||||||||||| | |||||| |||||| |||||||||||| | ||||| | ||| |||
gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaatttatgctt--gcattgtatcttgtga-tagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 11
-------gtgtggtgtg-tttgtgtgtatgaaatcatattgggcatttgcttttatttatttatttttat-ttttatttttttgaacattcacttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG
| ||| ||| | | | ||| ||| | | | | | ||||||| | ||| || | || ||| || | | | ||||||||||||||||||||||||||||||| |||||||| | |||||| |||||| |||||||||||| | ||||| | || |||
gttgagacttcattgtaattttttttcttaaaaagttatccactgtattcatgtttttatttgtgattacattgcacttgttttggtatcctat----gatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 22
-------gtgtggtgtg-tttgtgtgtatgaaatcatattgggcatttgcttttatttatttatttttat-ttttatttttttgaacattcacttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG
| ||| ||| | | | ||| |||| | || | | | | | |||| | ||| || || || ||| || | | | ||||||||||||||||||||||||||||||| |||||||| | |||||| |||||| |||||||||||| | ||||| | || |||
gttgagacttcattgtaattttttttcttaaaaagatatccgctatattcatgtttgaatttgtgattacattgtacttgttttggtatcctat----gatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGTTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 30
----------------gtgtggtgtgtttgtgtgtatgaaatcatattgggcatttgcttttatttatttatttttatttttatttttttgaacattcacttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG
|| | ||| | | | ||| | | | | |||| | |||| | ||| | | ||||| || | | | |||| | |||| |||||||||||||||||||||||||| |||||||| | |||||| |||| | |||||||||||| | ||||| | ||| |||
gtacattcatttatacttggattccttttttttttgtgataattcaattgatatttagcatcatttttatatgtctgaatttatgctt--gcattgtatcttgtga-tagAGGAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGTTTGGAGCATACTGATAATGCTCCTAAAAGATCATATGCTGTTAACCAG

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|71857046|gb|DT006101.1|DT006101
EST:     GTCGCCCAGAGTACCTTCAAGACTCTGACATTGTCTCCAGTCGTTTTCAG                         AGAAGAGATGTTTATGGTGCTTGGGAGCAGTATC
genomic: GTCGCCCAGAGTACCTTCAAGACTCTGACATTGTCTCCAGTCGTTTTCAGgtgtggtgtg ... ttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATC
EST: gi|71865499|gb|DT014554.1|DT014554
EST:     GTCGCCCAGAGTACCTTCAAGACTCTGACATTGTCTCCAGTCGTTTTCAG                         AGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCT
genomic: GTCGCCCAGAGTACCTTCAAGACTCTGACATTGTCTCCAGTCGTTTTCAGgtgtggtgtg ... ttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCT
EST: gi|110374900|gb|EC939841.1|EC939841
EST:     AAGACTCTGACATTGTCTCCAGTCGTTTTCAG                         AGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCT
genomic: AAGACTCTGACATTGTCTCCAGTCGTTTTCAGgtgtggtgtg ... ttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCT
EST: gi|110383584|gb|EC947963.1|EC947963
EST:     GTCGTCCAGAGTACCTTCAAGACTCTGACATTGTCTCCAGTCGTTTTCAG                         AGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCT
genomic: GTCGCCCAGAGTACCTTCAAGACTCTGACATTGTCTCCAGTCGTTTTCAGgtgtggtgtg ... ttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCT
EST: gi|71857119|gb|DT006174.1|DT006174
EST:     GTCGCCCAGAGTACCTTCAAGACTCTGACATTGTCTCCAGTCGTTTTCAG                         AGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCT
genomic: GTCGCCCAGAGTACCTTCAAGACTCTGACATTGTCTCCAGTCGTTTTCAGgtgtggtgtg ... ttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttttatttatttatttttatttttatttttttgaacattcacttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG
                                        ttcactt  CT-rich tract
 ttatttatttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtggtgtgtttgtgtgtatgaaatcatattgggcatttgcttttatttatttatttttatttttatttttttgaacattcacttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT