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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagcttatcaaatgttgttgtgtttttcagtgctctttagatagatctgaaatgtacgtatgctcttatattgtttggctcattggtattggcatttccttag

Basic information

species Vitis vinifera
transcript Vv15s0048g00370.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 5'ss of exon 3
TTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagcttatcaaatgttgttgtgtttttcagtgctctttagatagatctgaaatgtacgtatgctcttatattgtttggctcattggtattg-gcatttccttag
|||||||||||||||| ||||| |||||  |||| ||||| |||| |||| |||||||||| |||||||| || ||||  ||||||||||||||||||||||||     || |    | || |  ||  |  |  |  | || |  |   |     |||   ||     |||   |    ||  |||| | | ||| |||         
TTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCACTACACgtaa----tttttt---ttttatcatgaatacctttagttttcactttagtt----atggtggtgcaaccttg-gtaacatgattcatggattttgtgcag--------

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 3
TTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaa-acagcttatcaaatgttgttgtgtttttcagtgctctttagatagatctgaaatgtacgtatgctcttatattgtttggctcattggtattggcatttccttag--
||||||||||||| |||||||| ||||| ||||| ||||| |||| |||| ||||||| || |||||||| || |||| |||||| || || |||||||||||| ||  || ||  || |     |||         ||| ||   | ||   ||   |     | ||   |   |  |||| | | |   || | |    | |  ||   
TTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCACTACACgtaatacttctaat--aacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtg---tggcacagttttggtaacatgtttcgtggatcctgtacag

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 5'ss of exon 3
TTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagcttatcaaatgttgttgtgtttttcagtgctctttagatagatctgaaatgtacgtatgctcttatattgtttggctcattggtattggcatttccttag
|||| || |||||||| ||||||||||| || ||||||||||||| ||| ||||||||| |||| |||||||| ||||||||||||||||| ||||||||||||  |  ||  |   |      |   |||| | || | | |   | |   ||  ||||  |||  ||      |  ||||| | |                     
TTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCACTACACgtaag-attttgactccttcaacggcactttt-attgttatctttcttggattgtgatgt-tgtaaactgac---tgctttggattag--------------------

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 3
TTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaa-acagcttatcaaatgttgttgtgtttttcagtgctctttagatagatctga-aatgtacgtatgctcttatattgtttggctcattggtattggcatttccttag
|||| || || || || ||||||||||| || |||||||| |||| ||| ||||||||| ||||||||||||| ||   |||  | || || |||||||||||| | |  | | | |  ||| |  |||  |||  || | | || |||| ||||| |||  |  ||   | ||  |||| ||| ||                       
TTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGAGAAGCATTTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCACTACACgtaatatatataacccatagttatgttgtcgttct-tggtttgtatatagctctgataatagaaatactgtttttgattgattgtctag---------------------

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|110689991|gb|EE066698.1|EE066698
EST:     TTGGCTGCTCGATTCA-CAAACCAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGGAGGGT-GTCAAATGGANGGTGTTGCACATGAAG
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGG-ATGGTTGTCAAATGGAGGGTGTTGCACATGAAG
EST: gi|351013311|gb|FQ425016.1|FQ425016
EST:     TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
EST: gi|161705830|gb|FC057107.1|FC057107
EST:     TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGATGGTTGTC
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGGATGGTTGTC
EST: gi|110689389|gb|EE065571.1|EE065571
EST:     TTGGCTGCTCGATTCA-CAAACCAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAAC
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
EST: gi|161714022|gb|FC064097.1|FC064097
EST:     AAACCAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
genomic: AAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
EST: gi|110687702|gb|EE065414.1|EE065414
EST:     TTGGCTGCTCGATTCAACAAAACAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGGTGCACATGAAGC
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
EST: gi|110700650|gb|EE077489.1|EE077489
EST:     TTGGCTGCTCNATTCA-CAAAACAGACAATGAGATTGTTGATCACTAC-C                         ATACGTGATACTGGGGGGATGGTTGTCCAATGGAAGGTGGTGCACATGAAA
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGG-ATGGTTGTCAAATGGAGGGTGTTGCACATGAAG
EST: gi|110686000|gb|EE063214.1|EE063214
EST:     TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
EST: gi|161718402|gb|FC065025.1|FC065025
EST:     TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
EST: gi|34548489|gb|CF516721.1|CF516721
EST:     TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
EST: gi|110689357|gb|EE065511.1|EE065511
EST:     TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACAC                         ATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC
genomic: TTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagct ... atttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCACTACACgtaaacagcttatcaaatgttgttgtgtttttcagtgctctttagatagatctgaaatgtacgtatgctcttatattgtttggctcattggtattggcatttccttag

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