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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTTCTTAATGCTACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattcttttaattacttgtagtttttggatttccatatgttttcatgttgacattctgaatttttggttttgtgcag

Basic information

species Vitis vinifera
transcript Vv01s0010g01740.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G174286_T03 (Zea mays), 5'ss of exon 9
GCTCTTCTTAATGCTACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattct----tttaattacttgtagtttttgg----atttccatatgttttcatgttgacattctgaatttt---tggttttgtgcag
| | ||| | ||| | ||||| ||||||||||| |||||||||||||| |||||  |||| ||||||   | |    | |  |    || | |||||||    |||||  ||    || ||      ||| || ||| |   |   | | | |||
GTTGTTCATGATGTTGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttggattctgctggtctgaattttttgggggtatttctgtacaaatt-atacgctaattatgtattctgcatacctctatacag

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G174286_T02 (Zea mays), 5'ss of exon 1
------------------------------------GCTCTTCTTAATGCTACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattc----ttttaattacttgtagtttttgg----atttccatatgttttcatgttgacattctgaatttt---tggttttgtgcag
                                    | | ||| | ||| | ||||| ||||||||||| |||||||||||||| |||||  |||| ||||||   |     || |  |    || | |||||||    |||||  ||    || ||      ||| || ||| |   |   | | | |||
TTGAGATGACTTTTGATGTTCTGTCTGTTTCTGTAGGTTGTTCATGATGTTGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttggattctgctggtctgaattttttgggggtatttctgtacaaatt-atacgctaattatgtattctgcatacctctatacag
















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|349816624|gb|FQ399613.1|FQ399613
EST:     TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAG                         GTTGGCTACGTCACCGCCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
genomic: TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattctt ... ttttgtgcagGTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
EST: gi|30137883|gb|CB923221.1|CB923221
EST:     TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAG                         GTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
genomic: TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattctt ... ttttgtgcagGTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
EST: gi|22013779|gb|BQ798813.1|BQ798813
EST:     TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAG                         GTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
genomic: TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattctt ... ttttgtgcagGTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
EST: gi|110411137|gb|EC976839.1|EC976839
EST:     TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAG                         GTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
genomic: TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattctt ... ttttgtgcagGTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
EST: gi|30136439|gb|CB921777.1|CB921777
EST:     TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAG                         GTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
genomic: TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattctt ... ttttgtgcagGTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
EST: gi|349823327|gb|FQ402526.1|FQ402526
EST:     TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAG                         GTTGGCTACGTCACCGCCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
genomic: TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattctt ... ttttgtgcagGTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
EST: gi|349809177|gb|FQ398950.1|FQ398950
EST:     TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAG                         GTTGGCTACGTCACCGCCATATGTTTCTCATGTTTCCTTGTTAGATGCATT
genomic: TACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattctt ... ttttgtgcagGTTGGCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTTCTTAATGCTACAGCGCTTTCCTGTAGAGTCAAAAGGAAGACGTAAGAAGCTGCAAGAGgtaaattcttttaattacttgtagtttttggatttccatatgttttcatgttgacattctgaatttttggttttgtgcag

- - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA