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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccccttttctttttggtcgaaatgaagaaaccatgtatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG

Basic information

species Vitis vinifera
transcript Vv18s0001g08610.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 2
---------gtaagcccccttttctttttggtcgaaatgaagaaaccatgtatg-agtatattctgttcgtgtttata-----tttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
          | |    |||  | |  |   |  | |||   |||   |    |  ||| |   |     |   || |     ||   ||  ||        |    | ||| |||||||| ||||| |||||||| || ||||| || || |||||||| ||||| || ||||| ||||| || || ||||||||||||
gtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattagGTGGGTATGACATGGAGGAGAAAGCGGCGAGAGCGTATGACCTGGCGGCGCTCAAGTATTGGGGCCCTTCCACACACATCAACTTCCCG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
----------gtaagcccccttttctttttggtcgaaatgaagaaacca-tgtatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
          || ||  ||  |       |  | |  |||||   |  | | | ||   | |     ||  |  | | |||  | ||    || ||   | |   ||| |||||||| ||||| ||||| ||||| || || || ||||| || || ||||| |||||||| ||||| || || ||||||||||||
gtgtatcttggtgagtaccagtacacaagtacttgggatgaattgattagtttttggaaacaaagatttgattgtgagattgcaatg----taacc---tttgctagGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G008234_T01 (Zea mays), 3'ss of exon 1
------------------------------------------gtaagcccccttttctttttggtcgaaatgaagaaaccatgtatgagtatat---tctgttcgtgtt-tatatttaattgattctacccatgtct-ttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
                                            | |   ||          ||| ||||  || |||  |   |||    ||    | |  | |  || | | | ||  ||    |  || ||  | || ||| ||||| ||  |||| ||||| || || ||||| ||||| |||||||| ||||| |||||||| ||||| || || ||||||||||||
gtaagcagagcactcacacattcacgcagatgcagctctactagagggggccggccggccggggtagaaagtaaaaaaaaaaacatggtggtaaagatttccttgcattgtgtgtgtatgtggccgtggccgtgggtgtttagGCGGGTACGACGTGGAGGAGAAGGCGGCGAGAGCCTACGACCTGGCGGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G146688_T01 (Zea mays), 3'ss of exon 4
gtaagcccccttttctttttggtcgaa-----atgaagaaaccatgtatgagtatattctgttcgtgtttatatttaat----tgattctacccatgt-ctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
|||||| | |||| ||        | |     |||  ||||   |  |  |  |  | |     | | | |    | |     || |        | |  ||| ||| ||||| || ||||| ||||| || || || || ||||| |||||||| ||||| |||||||| ||||| || || ||||||||||||
gtaagcactctttgctgcacataagcacattgatggtgaaaaagtaaaaaaaaaactgcgagctgagctgactgctgagagcgtggtcggtattgtatatttttagGCGGGTACGACATGGAGGAGAAGGCGGCGAGGGCCTACGACCTGGCGGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 4
--------gtaagc---ccccttttctttttggtcgaaatgaagaaaccatgtatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
        |||||    | ||    ||||||| | | |||    | ||  | |   | | | || |  | ||     ||  |  |  ||| |     ||   |  |||||| ||||||||||| ||||||||||||||||| || ||||| |||||||| || |||||||||||||| || ||||| |||||  ||
gtatttgggtaagtattctcccacactttttgtttgcaatttcaacactct-tgctactgt-ttataattgt-----tacgtggtcaattttgtttttgaactaaagGGGGTTATGATATGGAGGAGAAAGCTGCAAGAGCCTATGATCTCGCGGCCCTTAAGTACTGGGGACCTTCAACGCATATAAACTTTTCG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
-gtaagcccccttt-----tctttttggtcgaaatgaagaaaccatgtatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
    ||  |  ||      | |    | |   | ||   | ||  | | | | || || ||  |  || |||    | |||  || |     ||   |  ||| || |||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||| || || || |||||||||
tactagttcttttccaaagtgtccgcgttttcagtgctcatacttttttt-actaaatgctaatt-tgattagtggtgattttttttgtttgtgaactgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 5
-gtaagccccctttt---ctttttggtcgaaatgaagaaaccatgtatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
 ||||| |  ||      |||   |||     | |  |        |    |       ||||   ||  ||  |  |  ||| |     ||   |  ||| || |||||||||||||| |||||||||||||| || ||||| ||||| || || |||||||||||||| || || || |||||  ||
ggtaagtcttctcccacacttcaaggtttttgttagcattttcaacactcttgctactggttctaattgttacgtggtcaattttgtttgtgaactaaagGAGGTTATGATATGGAAGAAAAAGCTGCAAGAGCCTATGATCTCGCGGCTCTTAAGTACTGGGGACCTTCAACGCACATAAACTTTTCG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 6
-gtaagcccccttttctttttggtcgaaatgaagaaaccatgtatgagtata---ttctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
  ||     |||||||     ||||   ||    ||  |   ||    || |   | ||  |    |      | ||||  || |     ||   |  ||| || ||||| |||||||||||||| ||||| ||||| ||||| ||||| ||||| || ||||||||||| || || || |||||| ||
gctacaagtccttttccaaagggtctgcattttcaatgctcatacttttacagaatactaatttgatgaggggtgaattttttttgtttgtgaactgaagGTGGTTATGACATGGAAGAGAAAGCCGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACGCACATAAACTTCTCG

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcccccttttctttttggtcgaaatgaagaaacc--------atgtat-gagtatattctgttcgtgttta---tatttaattgattctacccatgtcttt--cagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
|||||  | |  |||  | |    | | | | ||   |        || | | | | | ||  || | |  |||    | |||| ||   | |    |  |||||   ||| || ||||||||||| |||||||||||  |||| || ||||| || || ||||| |||||||| || |||||||| | ||| ||| | 
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT

upper sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 3
gtaagcccccttttctttttggtcgaaatgaagaaaccatgtatgagtatattctgttcgt--gtttatatttaattgattctacccatgtct-----ttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
   |   | |  ||    | |||     | |        |||  | |  |    ||||  |  |||  |  || | || ||||  ||  |  |       ||||||| ||||| | |||||||||||| ||  |||| || ||||||||||| ||||| || ||||||||| | ||    |||||||| || 
---aatgcgcagtttacctgggtgagtgtcactctttgttgttcgtgcttgaagtgttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAGGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT

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|34542668|gb|CF510900.1|CF510900
EST:     GGAAAGGAAGACAAGTTTATCTNN                         NNNNNTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCT
genomic: GGAAAGGAAGACAAGTTTATCTGG
EST: gi|110700948|gb|EE078047.1|EE078047
EST:     GGAAAGGAAGACAAGTTTATCTNN                         NNNNNTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCT
genomic: GGAAAGGAAGACAAGTTTATCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG
                              aattgat  putative branch site (score: 4)
                                             tgtctttc  putative PPT
                   tgtttatatttaattg  TA-rich tract