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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTCAAGGAGCAGAGCGACCTCATCGAGGACGTCGTCGACGAGGTCGTCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccccctcccattcttgcccgtattgtggtctcgtttggtttaatgatgaatatctttgcactgtgcggtgggctatgtatatatatatatatatatatatatatatatatatatag

Basic information

species Oryza sativa
transcript LOC_Os08g22864.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g22864.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G327394_T01 (Zea mays), 5'ss of exon 2
GTTCCTCAAGGAGCAGAGCGACCTCATCGAGGACGTCGTCGACGAGGTCGTCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccccctcccattcttgcccgtattgtggtctcgtttggtttaatgatgaatatctttgcactgtgcggtgggctatgtatatatatatatatatatatatatatatatatatatag--------------------------------------
||||||||| ||||||||||||||||||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||| || || |  |||    |   |||   | |   || | || | |||  | ||     |  | |    |  ||  | ||  | ||   || | ||  || |   | ||   | ||  | ||                                       
GTTCCTCAAAGAGCAGAGCGACCTCATCGAGGACGTCGTGGACGAGGTCGTGCACGCCTACCACCACGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgttcg-tcgcagtcc---gcccacccacctaggaatccctttcgttttgtttatttccctgatggtgaggaccgaggagccctctagccatgtgtacctaaagtcaaatggctgtaggtttaatttccgttttcctcttcattcatgcgccgtggctacag
















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|88327675|gb|CI657409.1|CI657409
EST:     TCCACGCCTACCACCATGGCTTCAACAAGGGCATCCAGAACTACTCCCAG                         ATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
EST: gi|88444107|gb|CI594480.1|CI594480
EST:     TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAG                         ATC-TGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
EST: gi|88719596|gb|CI743106.1|CI743106
EST:     CCACGCCTACCACCATGNGCTT-AACAAGGCCATCCAGAACTACTCCCAG                         ATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGC
genomic: CCACGCCTACCACCATG-GCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGC
EST: gi|88365075|gb|CI616494.1|CI616494
EST:     TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAG                         ATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
EST: gi|88727239|gb|CI750894.1|CI750894
EST:     TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAG                         ATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
EST: gi|88431150|gb|CI574321.1|CI574321
EST:     TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCC-AG                         ATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
EST: gi|88306004|gb|CI635004.1|CI635004
EST:     TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAG                         ATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
EST: gi|88391505|gb|CI598323.1|CI598323
EST:     TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAG                         ATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
EST: gi|58669732|gb|CK058418.1|CK058418
EST:     TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAG                         ATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGG
EST: gi|88358732|gb|CI649281.1|CI649281
EST:     TCCACGCCTACCANCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAG                         ATCCTGCGGCTGTTCAGCGAGTTTGCGGAGAGCATCAC
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCAC
EST: gi|88719158|gb|CI742668.1|CI742668
EST:     TCCANGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAG                         ATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCA
genomic: TCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCA

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: 50 (upstream exon), 64 (downstream exon)
Score: 24

GTTCCTCAAGGAGCAGAGCGACCTCATCGAGGACGTCGTCGACGAGGTCGTCCACGCCTACCACCATGGCTTCAACAAGGCCATCCAGAACTACTCCCAGgtccgatccc ... atatatatagATCCTGCGGCTGTTCAGCGAGTCTGCGGAGAGCATCACCGGGCTCAAGGGGGAGATGGCCGAGGCCAAGAAACTGCTTGGGAGGAAGAACAAGCACCTCG




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