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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacctacaagctcttaaactttctatgccatatcctttacctctcaggtgttactttttctgtaacaatgcaccatgtgaagttctccctccttt...

Basic information

species Vitis vinifera
transcript Vv16s0098g01040.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA06G14050.2 (Glycine max), 5'ss of exon 9
GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacctacaagctcttaaactttctatgccatatcctttacctctcaggtg-ttactttttctgta-acaatgca---ccatgtgaagttctccctccttt
||||||||||||||||| ||||| || || ||||| || ||||||||||| ||||| ||||||| | |||||| | |  || | || || |  | | | |     ||   | | ||||    || |||  | || |||| |  ||  |   |  ||||||||  |  |      
GTTCATCGCTTGAGGCTTCTTGGGGATTACCATCATTCAACTCGAATTGCATTTGTTGAGTTTGCACTGgtaatttctcactaacttttcatatgtttttttttcatgagtcaactcttgtttgcttagctattttgtatattatctatctctttgtgaagtaataacc-----

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA06G14030.1 (Glycine max), 5'ss of exon 10
GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacctacaagctcttaaactttctatgccatatcctttacctctcaggtgt---tactttttctgtaaca--atgcacca---tgtgaagttctccctccttt
||||| || |||||||| |||||||| || ||||| || ||||||||||||||||| |||||   | ||||||  ||  |  | || |  ||| || |||    |||||    |  | | ||| |   ||  | || | || ||  ||  | |    ||||||||| |         
GTTCAACGGTTGAGGCTTCTTGGAGATTACCATCATTCAACTCGAATTGCTTTTGTTGAGTTCACAGTGgtaataactcattaactttctaaccttatatttt-tatccaactctcccctggtttacatagctgttttttagcattatctatccgtttgtgaagttataa-------

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA04G40760.1 (Glycine max), 5'ss of exon 10
GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacctacaagctcttaaactttctatgccatatcctttacctctcaggtgt---tactttttctgtaacaatgca---ccat--gtgaagttctccctccttt
||||| || |||||||| |||||||| || ||||| || ||||||||||||||||| |||||   | |||||| ||| | | | || || ||| || |||    |||||    |  ||| ||| |    |  | || |||| || |      ||||  |||||||| |         
GTTCAACGGTTGAGGCTTCTTGGAGATTACCATCATTCAACTCGAATTGCTTTTGTTGAGTTCACAGTGgtaattacttgctaacttttcaaccttatatttt-tatccaactctcctctggtttacacatctattttgtagcattatctatccatttgtgaagttataa-------

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA04G40750.1 (Glycine max), 5'ss of exon 9
GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacctacaagctcttaaactttctatgccatatcctttacctctcaggtg-ttactttttctgta-acaatgca---ccatgtgaagttctccctccttt
||||||||||||||||| ||||| || || ||||| || ||||||||||| ||||| ||||| | | |||||| | |  || | || || |  | |   |  ||| |   | | | ||    |  |||  | || |||| |  ||  |   |  ||| ||||  |  |      
GTTCATCGCTTGAGGCTTCTTGGGGATTACCATCATTCAACTCGAATTGCATTTGTTGAGTTCGCACTGgtaattgctcactaacttttcatgtcttgctttcatctgagtaaaccctggtttacttagctattttgtatattatctatctctgtgtaaagtaataacc-----

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacctacaagctctt-aaactttctatgccatatcctttacctctcaggtgttactttttctgtaacaat-gcaccatgtgaagttctccctccttt-
|||  |||  | ||  || | || ||||||||||||||||||||||| || |||||||||||||| ||||||| |   ||    || ||   |  || |||    ||   |||   | ||||   | | | |||  |||||    ||  | ||   | |       || |  
GTTGCTCGGCTAAGATTGTTGGGTGACTATCATCACTCTACTCGAATCGCATTTGTCGAGTTTGTGATGgtaagt-tttatgctcttttcggagcttgtattggttagattttg--tgtcagaactaattgtttgagtaaccgcagcgacttggtcattaggataaccctga

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|110394549|gb|EC959681.1|EC959681
EST:     TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG                         GCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
genomic: TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacct ... gctctttcagGCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
EST: gi|110693868|gb|EE070476.1|EE070476
EST:     ATTGCTTTTGTCGAGTTTGTAATG                         GCTGAGAGTGCAATTGCAGCCCTTAACTGTAGTGGCGCCATTTTAGGATCC
genomic: ATTGCTTTTGTCGAGTTTGTAATGgtaactacct ... gctctttcagGCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
EST: gi|254917332|gb|GR906158.1|GR906158
EST:     TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG                         GCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
genomic: TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacct ... gctctttcagGCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
EST: gi|110406292|gb|EC971861.1|EC971861
EST:     TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG                         GCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
genomic: TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacct ... gctctttcagGCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
EST: gi|110371491|gb|EC935557.1|EC935557
EST:     TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG                         GCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
genomic: TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacct ... gctctttcagGCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
EST: gi|45770361|gb|CN006213.1|CN006213
EST:     CTATCATCACTCAACTCGAATTGCTTTTGTCGAGTTTGTAATG                         GCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
genomic: CTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacct ... gctctttcagGCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
EST: gi|27586314|gb|CB009009.1|CB009009
EST:     GCTTTTGTCGAGTTTGTAATG                         GCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
genomic: GCTTTTGTCGAGTTTGTAATGgtaactacct ... gctctttcagGCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
EST: gi|110385680|gb|EC950225.1|EC950225
EST:     TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATG                         GCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC
genomic: TTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacct ... gctctttcagGCCGAGAGTGCAATTGCAGCCCTTAACTGTAGCGGCGCCATTTTAGGATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATCGCTTGAGGCTGCTTGGAGACTATCATCACTCTACTCGAATTGCTTTTGTCGAGTTTGTAATGgtaactacctacaagctcttaaactttctatgccatatcctttacctctcaggtgttactttttctgtaacaatgcaccatgtgaagttctccctccttt

- - - - - - - - -  TTGGAG
- - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcct