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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accataatgcataaatgtacttcaactttggttgctctgatatagagtccttgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT

Basic information

species Vitis vinifera
transcript Vv04s0023g00370.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g21700.1 (Oryza sativa), 3'ss of exon 6
----accataatgcataaatgtacttcaactttggttgctctgatatagagtccttgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACA-ATCTGT
||| || | ||||| | | | | || || | | | || | || | | | |||| | || | |||||||||||||| | |||| || ||||||||||| ||||||||||| |||||||| | |||||| |||||||| |||||||||| | | || | ||
agtagttccaataaattataatacttgagtaatctgtaatttggtactttttgcctatcgggggat--gctaccctaac--atctatctctttcctgctaacagGGAGAACCTGTCTGCACATTCTATTCTCGTTACGGGATCTGCAAGTTTGGTCCTAATTGCAAATTTGACCATCCTATGGGAACCCTTATGTATGGAAGTG-

upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 6
accataatgcataaatgtacttcaactttg-gttgctctgatatagagtcct-tgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT
| | || | | | || ||| ||| || | | | || | || | | | || | |||| || || | ||| |||||||||||||||||| | || |||||||||||||| || ||||||||||| ||||||||||||||||||||||| |||| ||| ||| | |||||| |
-caaatatttgtgggttttttttctcttcacgttagattggtcttgtgtgttgtgattgaattagtgcaa-tctgatagaggcagtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTTACAATATCA

upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G31370.2 (Glycine max), 3'ss of exon 5
accataatgcataaatgtacttcaactttggttgctctgatata--gagtccttgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT
|| | || | | | || | ||| | || | | |||| | | | ||| | ||| |||| || || | ||| |||||||||||||||||| | || |||||||||||||| || ||||||||||| ||||||||||||||||||||||| |||| ||| ||| | | ||| | |
acaaatatttgtgttttttttttttttcacgttagtttggtcttgtgagttgtgattgaattagtgc--aatctgatagaggcagtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT

upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 6
accataatgcataaatgtacttcaactttgg--ttgctctgatatagagtccttgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT-
|| | | ||| ||| | |||| ||| | | ||||| | | || | | || || | | | || | ||||| | ||||||||| || |||| | || ||||| |||||||| || ||||||||||||||||| ||||||||||| ||||| |||||| ||||| | || || |||
--gatga-gaatatatgcaattcagtattgtcttcacactgatttgatatttttattgatttcggtacatgctaatagaggttgtgtcccattttcctacaggGAGAGCCCCTGTGTGTGTTCTATTCACGTTATGGCATATGCAAATTTGGTCCAAGCTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATGTC

upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 6
accataatgcataaatgtacttcaactttggttgctctgatatagagtccttg-tctagttatttataaatttgatggatctggt-ttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT
| ||| || | || || | || | | | ||| | | | || | ||| || | || | ||||| | ||||||||| || |||| | || ||||| ||||| || || ||||||||||||||||||||||||||||| ||||| |||||| ||||| | || || | |
--agggagatgagaatatatgcaattgtttattacagtgttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT

upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
accataatgcataaatgtacttcaactt--tggttgctctgatatagagtccttgtctagttatttata-aatttgatggat-ctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT
| | | | | | || | | | | | || ||||| | |||| |||| | || || ||| | ||| ||||||||||||| ||||| | || |||||||| |||||||||||||| ||||||||||| || || ||||| ||||| ||| || ||||| | |||||
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA

upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
accataatgcataaatgtacttcaactttggttgctctgatatagagtccttgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT
||| | || |||||| || || | | ||||| || || | | ||| | |||||| || ||| | ||| ||||||||||||| ||||| | || |||||||| |||||||||||||| ||||||||||| || || ||||| ||||| ||| || ||||| | |||||
---gtaagctaataaaagacttcagattc--tttcctt--tatagtctcattatgtggtt--tggtaaatt--------cttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA

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|156736717|gb|EV240838.1|EV240838
EST:     TCCCTACTCCAGATTGTGTTTTGAGTCCCATAGGCCTCCCTTTACGTCCG                         GGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGT
genomic: TCCCTACTCCGGATTGTGTTTTGAGTCCCATAGGCCTCCCTTTACGTCCGgtgagttgcc ... ttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtccttgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT
                       atttgat  putative branch site (score: 5)
 tttttatttttc  putative PPT
 ttgtctagttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accataatgcataaatgtacttcaactttggttgctctgatatagagtccttgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT

accataa
- - - - - - - - - -cttcaac
- - - - - - - - - - - - - - tggttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgga