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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAAGGGCCTTGCAGGGAGTGTTGCAACCCTTTCCAACTGGTTCTTTTCCTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgtctgtctgtctctctcacacacacacacacaatatgccccatgcaattacatggtggaataacagtttgtttgcataaagaacatgttggcatcagaaaataccctttatttgttcccaactaattggccttgtcttgctgcctccttcaacag

Basic information

species Vitis vinifera
transcript Vv18s0001g12560.t01
intron # 17
splice site 5'
intron type U2

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|349811010|gb|FQ405998.1|FQ405998
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|110384138|gb|EC948555.1|EC948555
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|28968713|gb|CB347746.1|CB347746
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|33404093|gb|CF209720.1|CF209720
EST:     CTTTGTGGTTACCACGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGATTGTGAGTGCTTTCACAGTT
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTT
EST: gi|27579979|gb|CB002674.1|CB002674
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|110382391|gb|EC939356.1|EC939356
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|30322190|gb|CD005452.1|CD005452
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|30295718|gb|CB972512.1|CB972512
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|110362730|gb|EC926280.1|EC926280
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|33404176|gb|CF209803.1|CF209803
EST:     CTTTGTGGTTACCACGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|351014223|gb|FQ434812.1|FQ434812
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|33402192|gb|CF207819.1|CF207819
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG
EST: gi|33402179|gb|CF207806.1|CF207806
EST:     CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAG                         GAACCTTCACCATTTACATGGTTGTGAGTGCTTTCACAGTTGTGTTTGCGG
genomic: CTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgt ... ccttcaacagGAACCTTCACCATTTACATGGTTGTGAGTGTTTTCACAGTTGTGTTTGCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAAGGGCCTTGCAGGGAGTGTTGCAACCCTTTCCAACTGGTTCTTTTCCTTTGTGGTTACCATGACTGCAAACTTGCTCTTGACTTGGAGCAGTGGAGgtctgtctgtctgtctgtctctctcacacacacacacacaatatgccccatgcaattacatggtggaataacagtttgtttgcataaagaacatgttggcatcagaaaataccctttatttgttcccaactaattggccttgtcttgctgcctccttcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG