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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggcagtatttatagagaatttcagttgctagccaactccttgggctgtttccgtaacctttactgctgcttggtttcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG

Basic information

species Vitis vinifera
transcript Vv08s0058g01360.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 4
gtttgtgg--cagtatttatagagaatttcagttgct-agccaactccttgggctgtttccgtaacctttactgctgcttggtt-tcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG
|||||||      |||  ||    | |   ||  |   | |  | |  |  || |  ||  ||  | | | |   |  ||| || ||||| || || || |||||||| ||||| ||||| |||||||| ||||| | ||| |||||||||||| |  ||||  | ||||| |
gtttgtgctctgctatccatcataactacaagaagtagaacgcaattttgaggttccttgtgtg-cttatccaaatctttgtttgtcagGGAAACTTGATAAAGGAGCGGTTCTTAAGGCAATTTGTGCTGGTTTTCGAGAAACCACTGAACCAGCTGTTTGCTTGAGTGAAG

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 4
gtttgtgg--cagtatttatagagaatttcagttgctagccaactccttgggctgtttccgtaacctttactgctgcttggttt--cagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG
|||||||      |||  ||  | || | ||     |||    |   || |    |    ||   |||  |     ||| ||||  |||| || || || |||||||| ||||| ||||| |||||||| ||||| | ||| |||||||||||| |  ||||  | ||||| |
gtttgtgctctgctatccatc-ataactacaagaagtagaatgcaattttgaggttcctggtgtgcttatccaaatctttgtttgtcagGGAAACTTGATAAAGGAGCGGTTCTTAAGGCAATTTGTGCTGGTTTTCGAGAAACCACTGAACCAGCTGTTTGCTTGAGTGAAG

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 5
gtttgtggcagtatttatagagaatttcagt--tgctagccaactccttgggctgtttccgtaacctttact-gctgcttggtttcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG
|| |||| | || | |||  |   ||| |||  || ||      | ||  |           ||  | | |  |||  |   | ||||||||||| ||||||||||||||||| || ||  ||||||| |||||  | || || ||||| ||| || ||||  | ||||| |
gtatgtg-ctgt-tctatctatcctttaagtcatgataagggtttgctgagatcaccagatgaatttatccgagcttatgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 4
gtttgtggcagtatttatagagaatttcagttgctagccaactccttgggctgtttccgtaacctttactgctgcttggtttcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG
|| || | ||   ||| | || | | |   | | |       || |||  ||| |    |||  |||| |  |   || ||| ||||||||||   |||| |||||| |||||||| || ||| | |||||||||||||||||||| ||| | |||||| | | |   |
gtctgagacaaactttctggaca-tcttgatggttttttttatctttgttctgctgt-ataatttttatttttaactgcttttagGTAAGCTGTCAAAAGCAGCAGTACTCAAGGCAATCTGTTCAGGTTTCCAAGAGACCACTGAGCCATCAATTTGTTTAACTCCAG

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 4
gtttgtggcagtatttatagagaatttcagttgctagccaactcc-ttgggctgtttccgtaacctttactgctgcttggtttcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG
|| || | ||   ||| | || | | |   | | |    ||||   ||  ||||| |   |    |||| |  |    | ||| ||||||||||   | || |||||| |||||||| || ||| | |||||||||||||||||||| ||| | |||||| | | |   |
gtctgagacaaagtttctggaca-tcttgttggtttttaaactttgttctgctgtataattttattttatttttaaccgcttttagGTAAGCTGTCAAGAGCAGCAGTACTCAAGGCAATCTGTTCAGGTTTCCAAGAGACCACTGAGCCATCAATTTGTTTAACTCCAG

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|33405593|gb|CF211220.1|CF211220
EST:     GGATGTGACTATATTGCCCACACTTGTAATAAACAATAGACAGTACAGAG                         GTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAG
genomic: GGATGTGACTATATTGCCCACACTTGTAATAAACAATAGACAGTACAGAGgtttgtggca ... ttggtttcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAG
EST: gi|29781753|gb|CB346482.2|CB346482
EST:     ACTTGTAATAAACAATAGACAGTACAGAG                         GTAAGCTGGACAAAGGAGCAGTCCTCAAGGCCATTTGTGCCGGTTTCCAAG
genomic: ACTTGTAATAAACAATAGACAGTACAGAGgtttgtggca ... ttggtttcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctagccaactccttgggctgtttccgtaacctttactgctgcttggtttcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG
                          ccgtaac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtggcagtatttatagagaatttcagttgctagccaactccttgggctgtttccgtaacctttactgctgcttggtttcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA