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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTTCAAGATATTGAGAAGGTTTTGGAACCATTGTTTTCCTATTGGAACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatctttctgcaaatactcgtgaatgattttcgagatgaatcatttggaacctcacatgtagattggccactcaatggttcccaaaagatatct...

Basic information

species Oryza sativa
transcript LOC_Os05g42350.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G090338_T01 (Zea mays), 5'ss of exon 7
GAAGCTTCAAGATATTGAGAAGGTTTTGGAACCATTGTTTTCCTATTGGAACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagta-atctttctgcaaatactcgtgaatgattttcgagatgaatcatttggaacctcacatgtagattggccactcaatggttcccaaaagatatct
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GAAGCTTGATGACATCGAGAAGGTTTTGGAACCTCTCTTTACCTATTGGAATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggattcttctttttttttctgcatatggtgttcctg-tcaataatttagtccatttggaggtggtgaatcgtttaggatttcactctcaggactg
















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|24468759|gb|CA305708.1|CA305708
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|88544519|gb|CI472623.1|CI472623
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|10794927|gb|AU108893.1|AU108893
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACATATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|58691385|gb|CK080072.1|CK080072
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|29621655|gb|CB626666.1|CB626666
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|58694341|gb|CK083028.1|CK083028
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|5002798|gb|AU067907.1|AU067907
EST:     AGCACACGTCAGGAAGGTGAATCTTNTTGGTAGCTTCACACGCCGGAACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATC
genomic: AGCACACGTCAGGAAGGTGAATCTT-TTGGTAGCTTCACACGCCGGA-CGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATC
EST: gi|2311250|gb|C27405.1|C27405
EST:     ACAGCACACGTCAGGAAGGTGAATCTNTTGGTAGCTTCACACGCCGGACG                         GGATTTGACATATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|58694439|gb|CK083126.1|CK083126
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|88216162|gb|CI216011.1|CI216011
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|86495058|gb|CI137691.1|CI137691
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|89176027|gb|CI043048.1|CI043048
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|88214761|gb|CI214610.1|CI214610
EST:     ACAGCTCACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
EST: gi|29625861|gb|CB630872.1|CB630872
EST:     ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACG                         GGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA
genomic: ACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCA

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: 74 (upstream exon), 59 (downstream exon)
Score: 16

GAAGCTTCAAGATATTGAGAAGGTTTTGGAACCATTGTTTTCCTATTGGAACAGCACACGTCAGGAAGGTGAATCTTTTGGTAGCTTCACACGCCGGACGgtgagtaatc ... ataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCAGCTGCATGATGGACTGCTTTCGCTGAACAAGTTGATAACAATTCTGACC




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