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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattctgattgctctgtgtgtttaagcttacattttattgtaataattgcagaagttacatctctaatttaactgtcagATTGCAAAGCTGAGTATGATCCCTGTGTCCTGCCTTTTGGAAGTTGTCTTGGACAAGATCCGGTATTCAAGAGACACAAAGCTCAGCATATCAGTTGTTC

Basic information

species Vitis vinifera
transcript Vv18s0072g00080.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G08700.1 (Glycine max), 3'ss of exon 3
gtatattctgattgctctgtgtgtttaagcttacattttattgtaataattgcagaagttacatctctaattta---actgtcagATTGCAAAGCTGAGTATGATCCCTGTGTCCTGCCTTTTGGAAGTTGTCTTGGACAAGATCCGGTATTCAAGAGACACAAAGCTCAGCATATCAGTTGTTC
||   ||  |  ||  || | | | |  | | |   || |||  |||   | ||||||||| ||      ||||   | || |||||||| ||| | |||||||||||||| || ||||| |||||||||||  | |||||||| |||||||||||||||||||| || ||||||   |||||||
gtgagttg-ggctgagctttatctattggttaa---ttcatt--aatgccttcagaagttatattcactttttagccattgacagATTGCGAAGTTAAGTATGATCCCTGTATCATGCCTATTGGAAGTTGTTCTCGACAAGATTCGGTATTCAAGAGACACAAAACTGAGCATAGGTGTTGTTC

upper sequence: Vv18s0072g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G36620.1 (Glycine max), 3'ss of exon 2
gtatattctgattgctctgtgtgtttaagcttacattttattgtaataattgcagaagttacatctctaatttaactgt---cagATTGCAAAGCTGAGTATGATCCCTGTGTCCTGCCTTTTGGAAGTTGTCTTGGACAAGATCCGGTATTCAAGAGACACAAAGCTCAGCATATCAGTTGTTC
||   || | ||||   | |   | |  |   |   |  |||  |||   | ||||||||| || |     |||||  |   |||||||| ||| |||||||||||||||| |||||||| ||||||||| | || ||||| || |||||||||||||| ||||| || ||||||   ||||| |
gtgagttgt-attgaattttcactattggtccaaggtccatt--aatgcattcagaagttaaattttcttcttaaccattggcagATTGCTAAGTTGAGTATGATCCCTGTATCCTGCCTGTTGGAAGTTTTTTTCGACAACATTCGGTATTCAAGAGATACAAAACTGAGCATAGGTGTTGTAC

upper sequence: Vv18s0072g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G27820.1 (Glycine max), 3'ss of exon 2
gtatattctgattgctctgtgtgtttaagcttacattttattgtaataattgcagaagtta-catctctaattta---actgtcagATTGCAAAGCTGAGTATGATCCCTGTGTCCTGCCTTTTGGAAGTTGTCTTGGACAAGATCCGGTATTCAAGAGACACAAAGCTCAGCATATCAGTTGTTC
||   ||  |  ||  || | | | |  | | |   || | |  |||   | |||||||||  ||      ||||   | || |||||||| ||  | |||||||||||||| || ||||| |||||||||||  | |||||||| |||||||||||||||||||| || |||||||  |||||||
gtgagttg-ggctgagctttatctattggttca---ttcact--aatgccttcagaagttaatattcactttttagccattgacagATTGCGAAATTAAGTATGATCCCTGTATCATGCCTATTGGAAGTTGTTCTCGACAAGATTCGGTATTCAAGAGACACAAAACTGAGCATATGTGTTGTTC

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|161709701|gb|FC060180.1|FC060180
EST:     TTGTTGGAATGAATGTTAGTTTAATGTGGAACTCAGTAGGGTTCTATCAG                         ATTGCAAAGCTGAGTATGATTCCTGTGTCCTGCCTTTTGGAAGTTGTCTTG
genomic: TTGTTGGAATGAATGTTAGTTTAATGTGGAACTCAGTAGGGTTCTATCAGgtatattctg ... taactgtcagATTGCAAAGCTGAGTATGATCCCTGTGTCCTGCCTTTTGGAAGTTGTCTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttacattttattgtaataattgcagaagttacatctctaatttaactgtcagATTGCAAAGCTGAGTATGATCCCTGTGTCCTGCCTTTTGGAAGTTGTCTTGGACAAGATCCGGTATTCAAGAGACACAAAGCTCAGCATATCAGTTGTTC
                                          atttaac  putative branch site (score: 3)
     acattttattgtaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattctgattgctctgtgtgtttaagcttacattttattgtaataattgcagaagttacatctctaatttaactgtcagATTGCAAAGCTGAGTATGATCCCTGTGTCCTGCCTTTTGGAAGTTGTCTTGGACAAGATCCGGTATTCAAGAGACACAAAGCTCAGCATATCAGTTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA