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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttgtgtttttatcttctttctttggtgggttggtgctttgactgatttttttactgggtctttacgtctgtagACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTA

Basic information

species Vitis vinifera
transcript Vv08s0056g00150.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 2
-------------gtaagcttgt--gtttttatcttctttctttggtgggttggtgctttgactgattttt---ttactgggtctttacgtctgt---agACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTA
              | | ||||    |  ||| ||| |   | | || | |  ||  |  || | ||       | |||     |||   ||| |   |||| ||||| |  ||  | |||||||| || ||||| ||| | || |||||||| |||||||| ||||| || || ||| || |||||||||||||||| |
tttcgggcatattattaacttggaaatccttaccttttcattcttgtcgttatgttataagaattatcaggaagtaactcatcttttgtttctttgtcagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 2
------------gtaagcttgtgtttttatcttctttctttggtgggttggtgctttgactgattttt-------ttactgggtctttacgtctgt---agACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTA
             | | ||||    || ||   ||||   |  | | | | |   ||    || || |       | |||     |||   ||| |   |||| ||||| |  ||  | |||||||| || ||||| ||| | || |||||||| |||||||| ||||| || || ||| || |||||||||||||||| |
ttcgggcatattattaacttggaaattcattaccttttcattcttg-tcgttatgttagaagaattatcaagaagtaactcatcttttgtttctttgtcagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 2
---------------------gtaagcttgtgtttttatcttctttctttggt-gggttggtgctttgactgatttttttac--tgggtctttacgtctgtagACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTA
                       ||  || |  |   |   |  ||||||| |        ||     | || ||| |  |   |  || |||| |||   |||| ||||| ||||   | |||||| |||||||||| ||| ||||||||||||| || ||||| ||||| || || || ||| ||||||| |||||||| |
tatcatgcttattgctagcctacaaaattattgtgccagtattgttctttgctcaaaacaatgtaaaaaatgttttatccatcttttgtgtttatgtc---agACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 2
-------------------gtaagcttgtgtttttatcttctttctttgg--tgggttggtgctttgactgatttttttactgggtctttacgtc-tgtagACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTA
                   || |   |   ||  | |     ||     |  |   |||   |  |   |   |||  |  || || |||  ||  || ||||||||||||| ||| ||||||||||||||||||| ||||||||||||||||| ||||| || ||||| || |||||| || |||||||||| |||||  
cgtgatgtgattgttgagtgtcaaaataccttaatgttgaaattgcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtgcaGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC-

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G40650.1 (Glycine max), 3'ss of exon 2
gtaagcttgtgtttttatcttctttctttggtgggttggtgctttgactgatttttttactgggtctttacgtctgtagACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTA
||  | || ||  ||| | |||||  |||  |       | | || | | | ||||||  |     |||  |  || ||||||||||||| ||| | ||||||||||||||||| ||||||||||||||||| ||||| ||||| || || |||||| || |||||||||| ||||| |
gtgcgtttttgccttttttttcttcttttt-taaacccatacgtttatttaattttttttt----ttttgtgg-tgcagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCA

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|351019747|gb|FQ439564.1|FQ439564
EST:     CTGTCAAGGTTTTGAACAAGGAGGGATTTCAGGGTCATAGAGAATGGCTT                         ACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTG
genomic: CTGTCAAGGTTTTGAACAAGGAGGGATTTCAGGGTCATAGAGAATGGCTTgtaagcttgt ... acgtctgtagACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttggtgggttggtgctttgactgatttttttactgggtctttacgtctgtagACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTA
                     gactgat  putative branch site (score: 3)
                                        tctttac  putative PPT
                        tgattttttta  TA-rich tract