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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCCTGCCCAACATGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcattcagccaagtcaatattactttttgtttgagcctcctcctgagtttgtagctgaatatttttatttatacccttttatttaattttaaattcttttccattctggtttacag

Basic information

species Vitis vinifera
transcript Vv14s0083g01160.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 5'ss of exon 4
GTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCCTGCCCAACATGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcattcagccaagtcaatattactttttgtttgagcctcctcctgagtttgtagctgaatatttttatttatacccttttatttaattttaaattcttttccattctggtttacag
|||| || ||||| || || |||||||||||||||||   ||||||||||||| | ||||| ||||| |||||    |||   || |||||||||||| ||| |||| | | |||   || | | ||| ||                                                                                           
GTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACTAGTCCTGGGAGCTGTGTAAAgtgagtt-actaagct--gttattgttatttcag----------------------------------------------------------------------------------------

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 2
GTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCCTGCCCAACATGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcattcagccaagtca---atattactttttgtttgagcct--cctcctgagtttgtagctgaatatttttatttatacccttttatttaattttaaattcttttccattctggtttacag
|||| || |||||||| || || ||||||||||||||   ||||||||||||| | ||||| ||||| |||||    ||    || || ||||||||| ||| |||| ||  | ||||  |    |  |  ||| |||||   |||   | |          | ||| |  | ||  ||  ||  ||                                        
GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttctgcaaaattgctaacaagttccatgcatttccacag------------------------------------

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G22410.1 (Glycine max), 5'ss of exon 4
---GTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCCTGCCCAACATGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttc---attcagcca--agtcaatatt----actttttgtttga-gcctcctcctgagtttgtagctgaatatttttatttatacccttttatttaattttaaattcttttccattctggtttacag
   |||| || |||||||| ||||| ||||||||| | |||  ||||||||| ||||||||||||||||  ||||| |      | || || |||||||||||||||||     ||| | |      |  |||||    ||| | | |||        ||||  ||  |||  |  | ||  |||  | || |  ||     |  |  | | || |||| |    ||   | |||
GCTGTGTTTCCCTCTCATCCTTCTATAATGACACAGTAGTAAACTGCCCAACCTGCACCTGTGGTTGCCGAAACAAAACAG---AACCTGGCAGCTGTGTAGAgtaagtctccaatttatctttccatagatatttgaaactgtctattttttagtgtctccaaagaatgttccaaagtaacttttgtcat-catttccccattctgatgatttgtttttctgaatgtcctgcag

upper sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G32130.1 (Glycine max), 5'ss of exon 4
---GTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCCTGCCCAACATGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttc---attcagcca---------agtcaatatta-ctttttgtttgagcct------cctcctgagtttgtagctgaatatttttatttatacccttttatttaattttaaattcttttccattctggtttacag
   |||| || |||||||| ||||| ||||||||  |||||  ||||||||| ||||||||||||||||  ||||| |      | || || |||||||||||||||||     ||| | |           | |  | | |  |||||| |||| | ||         ||  ||| ||   |  | ||  |||  | || |  ||     |  || | | || |||| |    ||  || |||
GCTGTGTTTCCCTCTCATCCTTCTATAATGACACCGTTGTAAACTGCCCAACCTGCACCTGTGGTTGCCGAAACAAAACAG---AACCTGGCAGCTGTGTAGAgtaagtctccaatttatcttttcatagatatttgaaactgtctttttttttgtgtctagtagtttgccaaagtatgctccaaagtaacttttgtcat-catttccccattcttatgatttgtttttctgaatgtcttgcag

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|30128146|gb|CB913485.1|CB913485
EST:     TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGA                         GGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG
genomic: TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcat ... tggtttacagGGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG
EST: gi|110371120|gb|EC934895.1|EC934895
EST:     TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGA                         GGAAGACTCGCCATATTTGGCTTC
genomic: TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcat ... tggtttacagGGAAGACTCGCCATATTTGGCTTC
EST: gi|30137657|gb|CB922995.1|CB922995
EST:     TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGA                         GGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG
genomic: TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcat ... tggtttacagGGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG
EST: gi|32269012|gb|CD718171.1|CD718171
EST:     TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGA                         GGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG
genomic: TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcat ... tggtttacagGGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG
EST: gi|30127202|gb|CB912541.1|CB912541
EST:     TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGA                         GGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG
genomic: TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcat ... tggtttacagGGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG
EST: gi|30128277|gb|CB913616.1|CB913616
EST:     TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGA                         GGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG
genomic: TGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcat ... tggtttacagGGAAGACTCGCCATATTTGGCTTCAGTTGTCTCAGGTTCTGGGAAGAATAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCCTGCCCAACATGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcattcagccaagtcaatattactttttgtttgagcctcctcctgagtttgtagctgaatatttttatttatacccttttatttaattttaaattcttttccattctggtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT