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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT

Basic information

species Vitis vinifera
transcript Vv11s0016g01870.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 16
gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT
|||  || |||   |  || ||     |   || |||    |    | |||  | ||  |   ||||||  | ||  |  | | | ||||||||||| || ||  | || ||||||||||| || |||||| | || |||||||||||||| || |||||||| || || |  ||| | ||  |||| |
gtatatggattgtatggtagttaatttt---tgcatga--aacaacagcat--ttttccatgagaactt--ttat-gtggtgttttcagGGAGGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTT

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 17
gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT
                   || ||||   |||  ||  ||||||  ||  |  | ||        | ||      ||   | | ||||||| ||||| || ||||| || ||||||||||| || |||||| | || ||||| ||||||||  | |||||||| ||||| |  ||  | ||  |||| |
-----------------gtataggccg--aatatatatttgattcgatagtatttttcctttgacaatttggatgcaatgtct-tgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 11
gtaactgcattaccttctaattggccat-caatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatg-cagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT
      | ||  | | |  | | |   | | | | | |   ||    || |           ||||  |  ||  |      || |  ||||| |||||||| ||  | || ||||||||||| || || ||| |||||||||| |||||||| || |||||||| || || |  ||  | ||  |||| |
------gtatatcgtgcatactaggtgtgctaagcaggaaagaagaaatgagaaaaaaaaccatga--tatattgttgctgcatttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 16
gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT
                  ||||    |||  |   |   | ||  |||| |       ||||    ||  || ||| || | |   |||||||| || |||||||| || |||||||||||||| |||||  |||| ||||| |||||  |  | ||||| || ||| ||| ||| || |||||||| |
-----------gtgagagaattcattatc--ttactcactaatcatatctt---tcagtaaacatgcta-ataatc-tcgttttctcagGGAGGAACATTTACTGTCTCTAACTTGGGAGGACCTTTTGGCATCAAGCAATTCTGTGCAGTCGTTAATCCACCTCAAGCCGCCATTCTAGCAGTTGGAT

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: PP1S78_56V6.1 (Physcomitrella patens), 3'ss of exon 14
-----gtaactgcattaccttctaatt--ggccatcaatggatggttg-attgtatcatggtctttta---aatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT
     ||   |   | |  |    |||  |    | | |   | |||  ||| |  | | || |||||   ||||   || |    || ||  | ||||||| || || |||||  | || || ||||||||||| |||||  | |||||||||||||| || ||||||||||| ||| | | ||| || || |||||| 
attccgtgtttctgtgatttgaagattatgatttttattttttagtttcatttttccttcgttttttactaaatgttttttaactgcaacaattctgcagGGTGGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGA

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT
                               |    | ||| ||    |||| |  || ||| |  | | |    | |  | |  |||||| ||||| || || || ||||||||||| |||||||||||  |||||||||||||||| || |||||||| || || ||  |||| || || || ||  
------------------------------gtaagcgtttgcttt--gcatgatacttgaaacgctcatgagtcccttggtgt-cgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA

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|110364343|gb|EC923926.1|EC923926
EST:     ATTTAGCACAGAAGGCCAAAGATAACAGCCTGAAATCTGAAGACTATGAG                         GGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAA
genomic: ATTTAGCACAGAAGGCCAAAGATAACAGCCTGAAATCTGAAGACTATGAGgtaactgcat ... atatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAA
EST: gi|110361992|gb|EC925498.1|EC925498
EST:     ATTTAGCACAGAAGGCCAAAGATAACAGCCTGAAATCTGAAGACTATGAG                         GGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAA
genomic: ATTTAGCACAGAAGGCCAAAGATAACAGCCTGAAATCTGAAGACTATGAGgtaactgcat ... atatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAA
EST: gi|30131574|gb|CB916913.1|CB916913
EST:     ATTTAGCACAGAAGGCCAAAGATAACAGCCTGAAATCTGAAGACTATGAG                         GGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAA
genomic: ATTTAGCACAGAAGGCCAAAGATAACAGCCTGAAATCTGAAGACTATGAGgtaactgcat ... atatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT
  ggttgat  putative branch site (score: 5)
                     ttttaaatgaactt  TA-rich tract