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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttcactttacccatccttctgtttcttttgtcctttttcttttccttttttcctttttttcctttttcctttgaaaaacagaattgggtgattc...

Basic information

species Vitis vinifera
transcript Vv09s0002g00880.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 5'ss of exon 6
GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagc-ttcactttacccatccttctgtttcttttgtcctttttctt-ttccttttttcctttttttcctttttcctttgaaaaacagaattgggtgattc
|| ||||| ||||||||||||||||| ||||| |||||||||||| | |||| ||||||| ||| |||| | | ||||||| ||||||| || | | |||| || | || || | || | || ||||||| |||| | | | | | | ||
ACCATTTCAATATTTTTGTTGGTGATCTTAGCCCAGAGGTTACTGATTCCGCATTATTTGCATTCTTCTCTGGATATTCCAGTTGCTCgtaagtatttattacctttatccactagtgttttctgccattggcccaatttggcttttcctaccccagctttataatattttgtgcgttgtcagctgtc--

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 6
GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttcactttacccatccttc-----------tgtttcttttgtcctttttcttttc---cttttttcctttttttcctttttcctttgaaaaacagaattgggtgattc--------------------------------------------------------------------------------------
|||||| ||| || |||||||| ||||| || |||||||||||||||||||| |||||||||||||||||||| | ||||||||||||||||| |||||| | || | | ||||| | ||| | |||| ||| || | | | | || |||| | ||||| |
GTCACTACAATATATTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGTTGTTTGCATGCTTTTCTGTCTATCCCAGTTGTTCgtaagtttcactctcatgatttcttagtaaaacagtcgcctctttctttatttgtagtttcggacttgaatcaatctctgttcatccaaaatggaaaaaaaaattgtactgtctcaaaggatagttgtacggtatgttctttgcaattatgttggtaacttagattggctcatcatatttattttttctggcggctccag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 6
GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttcactttacccatccttctgttt--cttttgtcctttttcttttccttttttcctttttttcctttttcctttgaaaaacagaattgggtgattc
|||| | ||||||||||||||| ||||| || |||||||||||||||||||| ||||||||||||||||||| | ||||| ||||||||||| |||||| | || | || | | ||| ||||| | | | | || || | | | || | | |
GTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTCgtaagtttcactctcatgatttcttagtaaagcagtcatccactttctgtatttggagttttggacttgaaccaatctctattcatcgaaaatagaaaaa--

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 6
GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttcactttacccatccttctgtttcttttgtcctttttcttttccttttttcctttttttcctttttcctttgaaaaacagaattgggtgattc
|||| ||||||||||||||||| |||||||| || ||||| |||||||| ||||| | | | |||||||||| ||| ||||||||||||||| | || | | || || | ||| |||| | || | | | | || | ||| |||
GTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTCgtaagttctg--ttgcttgatcagctccttttaactaacttattctacttggttgtaaaacaaatatcataatctctgactgtgtctaatattttgaag-

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G54080.1 (Arabidopsis thaliana), 5'ss of exon 6
GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttcactttacccatccttctgtttcttttgtcctttttcttttccttttt----tcctttttttcctttttcctttg-aaaaacagaattgggtgattc----------------------------------------------------------------------------------
|||| ||||||||||||||||| ||||| || || |||||||||||||| ||||||||| ||||||||| |||| ||| || ||||||| | | | | |||||| || | | | | || | || | || | | | | | | | | | ||| | |
GTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTCgtaagttct--tgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagttcttattatag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 5'ss of exon 6
GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttcactttacccatccttctgtttcttttgtc---ctttttcttttccttttttcctttttttcctttttcctttgaaaaacaga--attgggtgattc----------------------------------------------------------------------
|||| ||||||||||||||||| ||||| || || |||||||||||||| ||||||||| ||||||||| |||| ||| || ||||||| | | | | |||||| || | | | || || | ||| || | | | | | | | | | | ||| | |
GTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTCgtaagttct--tgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatag

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|71890328|gb|DT039383.1|DT039383
EST:     TCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: TCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
EST: gi|161716028|gb|FC065534.1|FC065534
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
EST: gi|349811318|gb|FQ407544.1|FQ407544
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
EST: gi|161705670|gb|FC055790.1|FC055790
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
EST: gi|161721264|gb|FC069684.1|FC069684
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTA
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTA
EST: gi|110694202|gb|EE071104.1|EE071104
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
EST: gi|110696392|gb|EE072470.1|EE072470
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
EST: gi|351031018|gb|FQ439054.1|FQ439054
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTCC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
EST: gi|161707025|gb|FC055133.1|FC055133
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
EST: gi|77582239|gb|DV220083.1|DV220083
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
EST: gi|110357183|gb|EC920553.1|EC920553
EST:     GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC                         AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG
genomic: GTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttca ... ctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCgtaagcttcactttacccatccttctgtttcttttgtcctttttcttttccttttttcctttttttcctttttcctttgaaaaacagaattgggtgattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaca