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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatatttatcattctcccattttgttcttgggactgtgatgtatttgtggtcttcaaatggatgtggttatgtttctcttcccaaaacttgcatgttt...

Basic information

species Vitis vinifera
transcript Vv01s0011g01610.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g01610.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G17330.1 (Glycine max), 5'ss of exon 4
GGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgtta-tatttatcattctcccattttgt-tcttgggactgtgatgtatttgtggtcttcaaatggatgtggttatgtttctcttcccaaaac-ttgcatgttt
||||||||| ||||| |||||||| || | || ||||| ||||| |||||||| ||||||||||||| |||||||||||||| ||||| ||||| ||||| | || | |||| || | ||| | ||| | | | || | || | | ||| || | || || || || || || |
GGATGAAAAGGTTCTTGCATTTCGTGACATTAATCCACAGGCTCCGGTTCATGTCCTAGTCATTCCAAAATTAAGAGATGGATTAACACAACTTGGGAAGgtcactaatcatcaccctttttctatgtgtacactgacaaaaagttttacatgatttttctgttta-gtgattcttttgcttttacctccacactggctac--

upper sequence: Vv01s0011g01610.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G31160.1 (Arabidopsis thaliana), 5'ss of exon 4
GGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatatttatcattctcccattttgttcttgggactgtgatgtatttgtggtcttcaaatggatgtggttatgtttctcttcccaaaacttgcatgttt---------
|||||||| ||| | ||||| | || | ||||| || ||||| ||||||||||| |||||||| ||||| |||||||| ||||| |||||| ||||| | ||| | | |||| || |||| | | | ||| |||| ||| || | | ||| | || | | ||| ||
AGATGAAAACGTTTTGGCATTCAGAGACATTAACCCTCAGGCTCCTGTTCATGTTTTGGTCATTCCCAAGTTGAGAGATGGCTTGACCTCGCTTGGCAAGgtga-----gtcagttttatgttttaacattcaatctgtt-tcttctcgtga-cttcctttggtcttgctcttagaggtct--caaagaatctcatcattgtgttctgt
















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|34362915|gb|CF404500.1|CF404500
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|110389333|gb|EC954162.1|EC954162
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|349818483|gb|FQ403118.1|FQ403118
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|110384323|gb|EC948751.1|EC948751
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|71867299|gb|DT016354.1|DT016354
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|71867022|gb|DT016077.1|DT016077
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|349818522|gb|FQ403157.1|FQ403157
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|110379724|gb|EC944942.1|EC944942
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatatttatcattctcccattttgttcttgggactgtgatgtatttgtggtcttcaaatggatgtggttatgtttctcttcccaaaacttgcatgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc