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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA

Basic information

species Vitis vinifera
transcript Vv13s0156g00180.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
gtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatca-tataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
    ||  || | |  |||| | ||       | |||| |  |  |||||||  |  |   | | |      |   || ||   ||         | |||||||||||||||||| || |||||||||||||| ||||| ||||| 
----gta-atgtattccatcct-tgttttgacttatatatttg--tttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 12
gtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtg-ttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
           |   ||||   ||     |  || | | ||    ||| ||  |  |  |  |     |    | ||| ||  |||      |||  |||||||||||||||||| || || ||||||||||| ||||| ||||| 
----------gtaattcattccatccttgttttagtttcta----tttatttctaaaagacttggt--ttgatttctttttcctttcacctgtgttcttccagTGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 13
gtgggtgtatatttctcatc-ttatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
||   | |  ||   ||    ||       |  | || | | |||  | ||| |||     | |  |  |||||   | | |  | ||         ||| |||||||||||||||||||||||||||||||| ||||||||||| 
gtaattttgcatccatccctgtttctatttttgttatgtctcggaagtacttgttg-----ttttcccctcatactgtgacttgtgttc--------ttctagTGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 12
gtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
||   | |  ||   || |  | ||  | |  || |||||      |||  |     || | |  |  |||||   | |    |        | | ||| |||||||||||||||||||||||||||||||| ||||||||||| 
gtaattttgcatccatccttgtttg-tacttttattatgt------ttcagaagtactcgttttcctctcatactgtgacctgtcacctgtgt-tcttctagTGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 11
gtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
         || || |      ||  | ||    || | |    || | || | | |  |  |     |      | || |      |    |||  || ||||||||||||||||||||| ||||| |||| ||||||||||| 
--------gtacttttgcatccatctctatttctatttttg---ttatgttttggaagtacttgttttttcccctcatactgtgacctgtgttgt--tctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 11
gtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgtt---ccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
||     |  |    |  | ||    | ||    || | ||   |||| ||||    |   |  ||     | | |   | |   | | |  ||||||   | ||||||||||||||||||||| ||||| |||| ||||||||||| 
gtaacaattcacgcgtacttttgcatccatctctatttctat--ttttgttatgttttggaagtacttgttttttcccctcatactgtgacctgtgttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 12
-----------------------gtgggtgtatatttc--tcatctta-tggcaatgataatatgtaggattttcttattggatcatata-acaatcatatgcttattaatttttaaaatg-----tgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
                        ||  ||| |  ||   | | |||| |     ||  ||| |||  | | || |||     | | ||| ||  |  |||     ||   ||||  | |      || || |||||||||||||| || ||||| ||||||||||||||||| || 
gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttctttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 11
--------------------------------------------------------------gtgggtgtatatttctcatcttatggcaat--gataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
                                                                  || |||| |  | |||||     | |     ||    ||  |  ||  ||| | || ||  ||   |  | |     ||   |  |    | ||||  |||||||||||||| || ||||| ||||||||| ||||||| || 
gttagtcctggttctcttcgtttcaacatgtctcattaattagaatacataagctaaagttttcttgtatataatgatgatcttcctttattttaccaactcttaccaaatttctatagcatgat-caaggtttttttttcccttgtctactggtttctgttttagTGATCATGAAGGTGGAAATGTTAGTGCTCACGCTGGTCACCTG

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|29785895|gb|CB343236.2|CB343236
EST:     ATAGTCCAAAAATGC-CGATCNTAATGAGGCTTTATGTCACCATCCATAG                         TGATCATGAAGGCGGGAATGTCAGTCGCTCACACTGGTCATCTA
genomic: ATAGTCCAAAAATGCAAGAGC-TAATGAGGCTTTATGTCACCATCCATAGgtgggtgtat ... tgtgttccagTGATCATGAAGGCGGGAATGTCAGT-GCTCACACTGGTCATCTA
EST: gi|110372355|gb|EC936513.1|EC936513
EST:     GATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAG                         TGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
genomic: GATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAGgtgggtgtat ... tgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
EST: gi|77577886|gb|DV217693.1|DV217693
EST:     GATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAG                         TGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
genomic: GATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAGgtgggtgtat ... tgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
                              tattaat  putative branch site (score: 2)
         atcatataacaatcat  TA-rich tract