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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGGATTGACTGGTGGGATTGCGTCTGGAAAGAGCACCATCTCCAACCTGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaaccagagctccatcacatcaaactcacaattcttctgtttgtgtgtgtatatttcatgagtggaagactatgagcaagttactgaatgatgaa...

Basic information

species Oryza sativa
transcript LOC_Os01g25880.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25880.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA19G39680.1 (Glycine max), 5'ss of exon 1
GGTTGGATTGACTGGTGGGATTGCGTCTGGAAAGAGCACCATCTCCAACCTGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaaccagagctccatcacatcaaactcacaattcttctgtttgtgtgtgtatatttcatgagtggaagactatgagcaagttactgaatgatgaa
 |||||| |||| ||||| || |||||||||||||||||| | ||||| ||||||||| |    |   ||||  |||| ||||| ||| |||| ||||| ||||||  |     |||| |    ||||  ||        |     | ||||| | |   | || | ||||| ||||||                     
CGTTGGACTGACGGGTGGAATAGCGTCTGGAAAGAGCACCGTTTCCAATCTGTTCAAGTCCCATGATGTTCCCATTGTAGATGCTGACGTTGTCGCTCGCgtaagttcctt---ctcccttttttcaatttcg-gtcaaattaaactctgtgtctgtgagtgattactggaatactatgcag------------------

upper sequence: LOC_Os01g25880.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G27490.2 (Arabidopsis thaliana), 5'ss of exon 2
GGTTGGATTGACTGGTGGGATTGCGTCTGGAAAGAGCACCATCTCCAACCTGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaaccagagctccatcacatcaaact--cacaattcttctgt---ttgtgtgtgtatatttc----atgagtggaagactatgagcaagttactgaatgatgaa----------------------------------------
 || || || || || || || |||||||| ||||| ||  | || ||||| ||||||||||| |||||||| |||||||| || ||  |||||||||| ||||| ||| | |  ||  ||   || |  |     ||||||| |||   |  |||||     || |    |    || |   |||   |||| |||    | ||  |                                         
AGTCGGGTTAACGGGAGGCATAGCGTCTGGGAAGAGTACAGTGTCTAACCTCTTCAAGGCTAGTGGCATTCCCGTTGTTGACGCTGATGTTGTTGCTCGAgtaaggaac-aaacatctctcttttctacttgctggaattcttttgtaactattgtgtcaccgttgctaagagagatgtactcctagatgcaatttagctcaagagaagtttagtaaaagatgtggaaatgtgttgttttactatatag
















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|33805659|gb|CF328708.1|CF328708
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|88314179|gb|CI602511.1|CI602511
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|88301045|gb|CI592225.1|CI592225
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTACAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|88313188|gb|CI594818.1|CI594818
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|38473157|gb|CF957289.1|CF957289
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTGGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGTACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|88300648|gb|CI587452.1|CI587452
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|58595486|gb|CK006014.1|CK006014
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|88387818|gb|CI587906.1|CI587906
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|88386515|gb|CI575293.1|CI575293
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|33689062|gb|CF317301.1|CF317301
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
EST: gi|88312093|gb|CI580258.1|CI580258
EST:     TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGG                         AATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT
genomic: TGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTT

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: 58 (upstream exon), 73 (downstream exon)
Score: 16

GGTTGGATTGACTGGTGGGATTGCGTCTGGAAAGAGCACCATCTCCAACCTGTTCAAGGCTAGCGGCATTCCTGTTGTTGATGCCGACATTGTTGCTCGGgtaagtaacc ... acatttgcagAATGTGGTACAGAAAGGCACTGGAGGTTGGAAGAAGATTGTAGAAGCTTTTGGAAATGATGTTCTGTTAGAAAATGGAGAAATTGACCGAGCTCGCTTAG




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