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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATAGCACCTACCTCTGGTTTGAGAGAACCTAGTGGCCACAATGCCGGTGTTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagggactggtctaatgcttctgtttcttcgtgttactgttccttgtcttttgcctgcacttaattgattattgatcatttgcattggttactgaagacagttcttgatttttcag

Basic information

species Vitis vinifera
transcript Vv14s0060g00600.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G41420.2 (Glycine max), 5'ss of exon 2
---------CATAGCACCTACCTC---TGGTTTGAGAGAACCTAGTGGCCACAATGCCGGTGTTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagggactggtctaatgcttc-tgtttcttcgtgttactgttccttgtcttttgcctgcacttaattgattattgatcatttgcattggttactgaagacagttcttgatttttcag
           | ||||| || ||    || ||||||||| | |||||            |||||||||||||||||| ||||||||||| |||| |||||||||||| ||||||||| |   ||||   |||| ||   |      |||| ||  | |      |  |||        || |||  |||    |      ||||| || || | | |    ||| ||  |  ||
TTCAGTTGGTGTGGCACCAACATCATCAGGCTTGAGAGAATCCAGTGG------------TGTTGATAGGTTGCCAGAGGAGATGAATGATATGAGAATTAGGGATGATAAAgtatgtcacacactg--ttaattctcaatacaatatcgtttttttttgtgggataattttttgttgtttgatttttta--agtttgagacattg-ttgcttacggcttgcctt-atcgtgtag

upper sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G28530.2 (Glycine max), 5'ss of exon 2
CATAGCACCTACCTCTGGTTTGAGAGAACCTAGTGGCCACAATGCCG---GTGTTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagggactggtctaatgcttctgtttcttcgtgttactgttccttgtcttttgcctgcacttaattgattattgatcatttgcattggttactgaagacagttcttgatttttcag
    ||||| || || |||||||||||| | ||||| ||    || |   |||||||||| |||||||| |||||||| || ||||||||||||||||| | ||||||| |          |  |    | | |  ||  | ||   |||  ||   | ||   |  | ||  |  ||    |  ||| |   ||||||||| |      | ||| |||||  ||
---GGCACCAACTTCGGGTTTGAGAGAAGCCAGTGGGCATGGAGCAGCAGGTGTTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaa---------tttgtaaccccgctctttgatattttcgtttttttcatgttagttttattttctctat----gtccatgt-tgttggttacttacagtt-tgcttcattttgtag

upper sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA03G38850.2 (Glycine max), 5'ss of exon 2
---------CATAGCACCTACCTCT---GGTTTGAGAGAACCTAGTGGCCACAATGCCGGTGTTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagggactggtctaatgcttctgtttcttcgtgttactgttccttgtcttttgcctgcacttaattgattattgatcatttgcattggttactgaagacagttcttgatttttcag
           | ||||| || ||    || ||||||||| | |||||            ||||||||| ||||| || ||||||||||| |||| ||||||||| || ||||||||| |    |||            ||||  |||    |||  |  | | | |||||   |   |   |   || ||||       ||||| || || |   || | ||  || || |||
TTCAGTTGGTGTGGCACCAACATCATCAGGCTTGAGAGAATCCAGTGG------------TGTTGATAGATTGCCTGAGGAGATGAATGATATGAGAATTAGGGACGATAAAgtatgtcatacgctg------------tgttaattctcaatacaatatcat-ttttttgggggggatacttcttttgttgag-----acattg-ttgcttacagca-tgctccatcttgcag

upper sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA20G22600.3 (Glycine max), 5'ss of exon 2
CATAGCACCTACCTCTGGTTTGAGAGAACCTAGTGGCCACAATGCCGGTGTT---GATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagggactggtctaatgcttctgtttcttcgtgttac---tgttccttgtcttttgcctgcacttaattgattattgatcatttgca---ttggttactgaagacagttcttgatttttcag
    ||||| || || |||||||||||| | ||||| ||    || |  | |   ||||| |||||||| |||||||| || ||||||||||||||||| | ||||||| |         |   |  ||    || ||| | ||     ||||  || | ||||  |||    |   || ||  | || | || ||   |  |||||| |      ||||| |||||  ||
---GGCACCAACTTCGGGTTTGAGAGAAGCCAGTGGGCATGGAGCAGCAGCTGCGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatttgtaaacccgctcttttaaatttttcattttttccatgttagttttattttctctgtgtctgtgtggttggttataaatttcaggctcagttacttacagtt-ttcttcattttgtag

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|46917569|gb|CN546898.1|CN546898
EST:     TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|71858122|gb|DT007177.1|DT007177
EST:     TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|161718942|gb|FC067353.1|FC067353
EST:     TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACGGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|30256245|gb|CB972088.1|CB972088
EST:     TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACGGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|110689423|gb|EE065633.1|EE065633
EST:     TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACAGTTGTTGACGGTAATGGTACAGAGACAGGTCATATA
genomic: TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|30327244|gb|CD010506.1|CD010506
EST:     GAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACGGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: GAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|161713248|gb|FC063076.1|FC063076
EST:     TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|161718839|gb|FC065074.1|FC065074
EST:     TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|33405711|gb|CF211338.1|CF211338
EST:     TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|110687881|gb|EE065793.1|EE065793
EST:     TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: TTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|30325747|gb|CD009009.1|CD009009
EST:     GAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACGGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: GAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|30325454|gb|CD008716.1|CD008716
EST:     GAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACGGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: GAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|71859213|gb|DT008268.1|DT008268
EST:     ATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACGGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: ATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
EST: gi|30323811|gb|CD007073.1|CD007073
EST:     GAATGACATGAAAATTAGGGATGACAAA                         GAGATGGAAGCAACGGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA
genomic: GAATGACATGAAAATTAGGGATGACAAAgtatgtgagg ... gatttttcagGAGATGGAAGCAACAGTTGTTGACGGTAATGGAACAGAGACAGGTCATATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAGCACCTACCTCTGGTTTGAGAGAACCTAGTGGCCACAATGCCGGTGTTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagggactggtctaatgcttctgtttcttcgtgttactgttccttgtcttttgcctgcacttaattgattattgatcatttgcattggttactgaagacagttcttgatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG