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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctcccttttcccttgcgcccataatttgttgttgcgtccccaaaatatttgtaacatctttttcattgcatcag

Basic information

species Oryza sativa
transcript LOC_Os06g43140.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g43140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G890647_T02 (Zea mays), 5'ss of exon 3
GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctcccttttcccttgcgcccataatttgttgttgcgtccccaaaatatttgtaacatctttttcattgcatcag
| || || ||||||||||||||||| ||||| || |||||||||||| |||||| ||||||   | | ||||       ||  ||| || ||| || ||||     |||||| |||||  |  |  ||||| ||||
GACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGATgtatgtagactcctttcatcctttccattaactt-ttgatgtgtccaagttatatttataacacttggtctattgcctcag

upper sequence: LOC_Os06g43140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G141241_T03 (Zea mays), 5'ss of exon 3
GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctcccttttcccttgcgcccataatttgttgttgcgtccccaaaatatttgtaacatctttttcattgcatcag
| || || ||||||||||||||||| ||||| || |||||||||||| |||||| ||||||   | | ||||       ||  ||| || ||| || ||||     |||||| |||||  |  |  ||||| ||| 
GACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGATgtatgtagactcctttcatcctttccattaactt-ttgatgtgtccaagttatatttataacacttggtctattgcctcat

upper sequence: LOC_Os06g43140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 5
GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatg---tgctcccttttccc-----------ttgcgcccataatttgttgttgcgtccccaaaatatttgtaacatct-ttttcattgcatcag
||||||| ||||||||||| ||||||||||| ||||||||||||||| | || ||||  |   | || || |||  |           |   ||  | || || | ||   ||     || || | | | | | | |||| | |   | ||
GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaatacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgttat-gaactactggcatcttatatttttacttttttag

upper sequence: LOC_Os06g43140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G17340.2 (Glycine max), 5'ss of exon 3
GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctcccttttcccttgcgcccataatttgttgt-tgcgtccccaaaatatttgtaacatctttt-tcattgcatcag
||||||| |||||||| |||||||||||||||||||||||||||||||| ||  | | || | |   | |||   |      || ||  |  |  |   |   ||  |      | | || || | |  ||   | ||
GGCCAGATGACATGCCGGCACATATTAAATCGTCGATGTTTGGTTGTGCACT--CATgtgagttatttgttcaaattgatttattatgcgaggaatatattatcatcaatccactgatatattgtgtttttaatttag

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|88323371|gb|CI553616.1|CI553616
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|38480833|gb|CF964922.1|CF964922
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|88214425|gb|CI214274.1|CI214274
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|88962751|gb|CI023851.1|CI023851
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|88209727|gb|CI209576.1|CI209576
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|88214454|gb|CI214303.1|CI214303
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|86530349|gb|CI170555.1|CI170555
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|88489362|gb|CI426634.1|CI426634
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|88691507|gb|CI733585.1|CI733585
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|86417278|gb|CI031487.1|CI031487
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|86511784|gb|CI154417.1|CI154417
EST:     GATGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|88503328|gb|CI430834.1|CI430834
EST:     GAGGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGNACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|88465002|gb|CI514774.1|CI514774
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|86523980|gb|CI164186.1|CI164186
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
EST: gi|88475322|gb|CI412593.1|CI412593
EST:     GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC                         GATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG
genomic: GACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 55 (upstream exon), 43 (downstream exon)
Score: 112

GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatgtgctc ... attgcatcagGATTCCTATCACTGATGGGCGTCTCAACATGGGAACTTGGCAG




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