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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACTACACTCAACTCTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAGGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtgaatatcaatcccaaacttcatcttctagttttagttctatgtagataaaataatacaggatttgagatgattgataatcatggtgtttctaatgtga...

Basic information

species Vitis vinifera
transcript Vv04s0023g02750.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os02g01070.1 (Oryza sativa), 5'ss of exon 8
AAACTACACTCAACTCTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAGGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtg--aatatcaatccca-----aacttcatcttctagttttagttctatgtagataaaataatacaggatttgagatgattgat--aatcatggtgtttctaatgtga
||||| |||||| | ||||||||||||||||||||||| || || ||| ||||| ||||| |||||||| | | |||| || || ||||| ||||| || || ||| || | | | ||| || | | | | || || | || || | || ||| || | || | ||| |
CAACTATACTCAAGTTTGGTGGGTTCCTAATGTTGTTGTTGCCCACGAAAAAGAAGGGATAGAGGCTGTTCATCTAGCTTCTGGACGTACAATCTGCAAGgttgcaagatatatctcagtgatatttgtgttttcacgtccctgccaaagcttgtctaattagttca---ttgtaaattatttatttgtttatagaattttca------

upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA01G37580.1 (Glycine max), 5'ss of exon 10
AAACTACACTCAACTCTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAGGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtgaatatcaatcccaaacttcatcttctagttttagttctatgtagataaaataatacaggatttgagatgattgataatca-tggtgtttctaatgtga
|||||||||||| | |||||||||||||||||||||||||||||||| | ||| || ||||||||| |||| ||| | ||||||| || || || ||||| || || || || | | | | | || || | ||| | ||| ||| | | | | | | | | | | | || |
CAACTACACTCAAGTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAGAAGGAGGGCATAGAAGCTCTTCATTTGGCATCTGGTCGAACAATATGCAAGgtaaacataaagcctacggtcaacttgaacctatttatttaccatgcatatcttgata-aggttacaacacaactttttctaaataatctaggccattgaa

upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA11G07720.1 (Glycine max), 5'ss of exon 10
AAACTACACTCAACTCTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAGGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtgaatatcaatccca--aacttcatcttctagttttagttctatgtagataaaataatacaggatttgagatgattgataatcatggtgtttctaatgtga
|||||||||||| | ||||||||||| |||||||||||| ||||||| | ||| || ||||||||| |||| | | |||||||| || || || ||||| || | || || | | | |||| ||||| || | | | | || | | | || || |||| ||
CAACTACACTCAAGTTTGGTGGGTTCCCAATGTTGTTGTGTCTCATCAGAAGGAGGGCATAGAAGCTCTTCATCTAGCAACTGGTCGAACAATATGCAAGgtaaacttaaaatatgataaggttacaacacaatttt--ttctaaataatctattgaggcccaagtctgcaagtagttgtatggctgcatcttctgatactt

upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT3G51050.1 (Arabidopsis thaliana), 5'ss of exon 10
AAACTACACTCAACTCTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAGGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtgaatatcaatcccaaa--cttcatcttctagttttagtt-ctatgtagataaaataatacaggatttgagatgattgataa--tcatggtgtttctaatgtga
|| ||||| | || |||||||||||||||||||||||||||||||||| ||||||||| |||||| |||| ||||| |||||||| || | || ||||| | | | | ||||| | | ||| |||| | | || ||| || | | || |||| || | |||| |
TAATTACACGAAGCTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAAGGAAGGAATTGAAGCTATTCATTTGCCTACTGGTCGAACACTTTGCAAGgttggtcctagtggctgttccttcagatcatgaacaaggttactatttcacgtacctattacttacttagtcagcgtttataaattcttcctgttcgcag-----

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|110709284|gb|EE084611.1|EE084611
EST:     AGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAG                         CTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTT
genomic: AGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtgaatatca ... atccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTT
EST: gi|33403432|gb|CF209059.1|CF209059
EST:     GGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAG                         CTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTT
genomic: GGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtgaatatca ... atccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTT

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACTACACTCAACTCTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAGGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtgaatatcaatcccaaacttcatcttctagttttagttctatgtagataaaataatacaggatttgagatgattgataatcatggtgtttctaatgtga

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa