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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCAAGTCAATGAAGTTTAAGGATGGGTACATGATCTCCTCTGGTCAACCTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgctataatgtctcctggttttggttgaattgttagctgccacatcttgatttcatcattttatttgttgaatcccggctgattttccttttctatggtgtatag

Basic information

species Vitis vinifera
transcript Vv04s0008g01750.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01750.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G093902_T02 (Zea mays), 5'ss of exon 5
TGCCAAGTCAATGAAGTTTAAGGATGGGTACATGATCTCCTCTGGTCAACCTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgctataatgtctcctggttttggttgaattgttagctgccacatcttgatttcatcattttatttgttgaatcccggctgattttccttttctatggtgtatag
||| ||||| |||||||| ||||||||||||||||| || |||||||| ||||| ||    |||||||| ||||||||||| ||||||||  | ||||||||           ||   | |||| |  | ||   | |||     || |  |  |    |  |  |  || ||   |  |  | ||| ||  |||               
TGCTAAGTCTATGAAGTTCAAGGATGGGTACATGATTTCTTCTGGTCATCCTGTCAACCTATACATTGATTCAGCTGTGAGACATGTTCTATTGAGACAGgtt----------tggtgcttggtatcagatgttatcttattatgcaaacatataacaaaatagct-gttagtaatactctagttgacttggcttcag------------

upper sequence: Vv04s0008g01750.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCCAAGTCAATGAAGTTTAAGGATGGGTACATGATCTCCTCTGGTCAACCTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgctataat-gtctcctggttttggttgaattgt--tagctgccacatcttgatt--tcatcattttatttgt--tgaatcccggctgatt--ttccttttctatggtgtatag
||| ||||| |||||||| |||||||| ||||||||||| |||||    ||||| || |||||||| |||   || ||  | || ||| |  |  | ||||||||    ||  | |    | |    | | |   || |  ||   |  | || ||||||  |  ||  | |    |   ||||||     ||     || ||||  |||| | || ||
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGATCTCATCTGGGAGCCCTGTCAACGATTACATCGACAGTGCCGTCCGACACGTTATGTTGCGTCAGgtacacaagatgcttgatgtccgtcagtagctcctttttcgtactagaaagatattgattgatagtcggtgttcccgaagtgaatctgaagtggaggattactttggtatg-tttacag
















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|30295730|gb|CB972524.1|CB972524
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|110375300|gb|EC940275.1|EC940275
EST:     GCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: GCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|32247633|gb|CD713452.1|CD713452
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGAT
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGAT
EST: gi|32270022|gb|CD719181.1|CD719181
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|33401617|gb|CF207244.1|CF207244
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTAGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|30301307|gb|CB978101.1|CB978101
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|110728527|gb|EE104173.1|EE104173
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTAGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|352773252|gb|FQ470839.1|FQ470839
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|110690223|gb|EE067133.1|EE067133
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTAGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|110732469|gb|EE107785.1|EE107785
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAAGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|110688348|gb|EE066796.1|EE066796
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTAGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|77578758|gb|DV218182.1|DV218182
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|27582088|gb|CB004783.1|CB004783
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGA
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGA
EST: gi|110709636|gb|EE085271.1|EE085271
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|32272105|gb|CD721264.1|CD721264
EST:     CTGTTAAGGATTACATTGACTCANCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|30253062|gb|CB970613.1|CB970613
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|27586377|gb|CB009072.1|CB009072
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|352782408|gb|FQ470311.1|FQ470311
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|32245818|gb|CD711637.1|CD711637
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|30326710|gb|CD009972.1|CD009972
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGG
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGG
EST: gi|32460064|gb|CD801238.1|CD801238
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAGGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
EST: gi|110708853|gb|EE086870.1|EE086870
EST:     CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAG                         GGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC
genomic: CTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgcta ... tggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCAAGTCAATGAAGTTTAAGGATGGGTACATGATCTCCTCTGGTCAACCTGTTAAGGATTACATTGACTCAGCTGTGAGGCATGTTCTCCTCAGACAGgtacatgctataatgtctcctggttttggttgaattgttagctgccacatcttgatttcatcattttatttgttgaatcccggctgattttccttttctatggtgtatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC