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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG

Basic information

species Vitis vinifera
transcript Vv08s0007g07420.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
||||| | || | || | || | | | | | | || ||||| | || ||| || || || | | ||| | |||||||||||| ||| |||||| ||||||||||| |||||||| || |||||||| |||||||| || || ||
gtaagcacctagatttatcccattcattgctgttgcctcgtgttc-ctcat-------catttgtgtttatgtattaaaagtaataacatcat-taacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g57940.2 (Oryza sativa), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaa-cagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
| | || || | | | || || ||| | | | | | | ||| ||| || | | || || ||||||||| | ||||||| ||||||||||| || || || ||||||||||| |||||||||||| || ||
------------gtaagtttcgga-tcacctttttgcattgac---cacctgattttat-tactcctcactgaaaataacagcattggaacttgcaaacagGATGTCTGCCCATATGGTTGCTTGCATTGCTGTGGAAGCGATATCAATTCTTGAGAAGCTTCACTCTAAAGG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 6
gtaagaaatagaatctctctctctctct-ctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
|| || | ||| ||| || | | || || ||| | | | || | ||| ||| ||||||| |||| |||||||| ||||||||||| ||||||||||| || || || ||||| ||||| || ||
-------gtaagatgacatgttctgtctgctttgtttaactcatgttattctaagcagctgactgatcaccaatatttgatt----------------cagGATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 4
-------------------------------------gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
| | | || | ||| | ||| | | | | | | | | || | || | | | || ||||||||| | |||||||||| ||||||||||| |||||| ||||||||||| |||||||| ||
ggtatgttgtttatggtatttcagctgtatttaattcgatggggcaggcataagtatcttccattcttttttatg---gtatcttttgtcactcatgtatcagCTTCTAGACTAAACGAGTCAACAATCTCAAACAGGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCAATTCTTGAGAAGCTCCATTC------

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
|| | | ||| | ||| | | | | ||| || || | | || | || | | | || ||||||||| | |||||||||| ||||||||||| |||||| ||||||||||| |||||||| || || ||
-------gta-agtatcttccattctttttaa-tggtatcttttgtcactcatgta------tcagcttctagactaaacgagtcaacaatctcaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCAATTCTTGAGAAGCTCCATTCTAAAGG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaa-cagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
| | ||| | ||| | | | | | | | | || |||| || || | | || | |||| ||||||| | |||||||||| ||||||||||| |||||| ||||| ||||| |||||||| || || ||
------------gtaagtatcttccattcttttttatg-atat-cttttgtcactcatcagcttttagact------aaatggtccaactatcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacac-----acacacacacacaagtggacattttttttcctgtttttaatt--tatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
|||||| | | ||| || | | ||| | | || | | | | || | | ||| |||| | | ||| |||| ||||||||||||||||| || ||||||||||||||||||||||||||||| |||||||| ||| |||| ||
gtaagatttgtaccctcccttttgttagtataggttcacttttaatagctgcaatttatttaaactcttcctatataagccccattaacattttagttctg-gacagAATGTCACCAAATATGGTTGCGTGCATTGCAGTAGAGGCAATATCAATTCTTGAGAAGCTCCACTTGAAAGG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
| |||| ||||||| ||||| | | || | || || || || || | || ||| ||||||||| ||||| ||||| || ||||||||||| ||| | ||||| ||||| ||||| ||||| ||||| ||
---------------gtaagcactcttctcctctcac-cacacttccttctgattgcaagattcttgatttgattcatgttcgt----gtcatgtggcagGATGTCTCCAAACATGGTAGCCTGCATTGCAGTTGAGTCCATATCTATTCTTGAGAAACTTCATATGAAAGG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
||||| | | | | || ||| | | | | || || | || || | | | ||| | ||||| ||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||||| ||||| || || || || ||||||||
gtaagtact----tttatcattctatattttcttaccaaccatgctcatgcagat--atgctaaatttattattttt---ctatttgg---------tagGATGTCTCCAAACATGGTAGCATGCATTGCAGTGGAGGCGATATCTATTCTTGAAAAACTGCATATGAAGGG

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|71861339|gb|DT010394.1|DT010394
EST:     ACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGAC                         GATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCT
genomic: ACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGACgtaagaaata ... cctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCT
EST: gi|110385816|gb|EC950372.1|EC950372
EST:     GACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGAC                         GATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAA
genomic: GACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGACgtaagaaata ... cctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
                            ttttaat  putative branch site (score: 3)
 acattttttttcctgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC