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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagatactatctatagggcctgcccagctgagctggctgcaactgcatcacagccagctgctgcccgaagcagcaatgccagtggcttgctcctgc...

Basic information

species Oryza sativa
transcript LOC_Os02g31290.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g31290.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G459746_T01 (Zea mays), 5'ss of exon 13
AACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagaga-tactatctatagggcctgcccagctgagctggc-tgcaactgcatcacagccagctgctgcccgaagcagcaatgccagtggcttgctcctgc----------------------------------------------------------
|| || || ||||| ||||||||||||||||| ||||||||| |||||||||||||||||||||||||||| ||| | |  |  | || |     |  |  |||   ||   |  |  || |    ||||    |    |  |    ||  |||||      | ||                                                               
AATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAGgtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatat-gccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcag

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 3
AACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagatactatctatagggcctgcccagctgagctggctgcaactgcatcacagccagctgctgcccgaagca---gcaatgccagtggcttgctcctgc-------------------------------------------------------------
|| || || ||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||  || |  | ||       |  |  |||    |  ||||  |    |        ||  ||  | |   |   |   |||||      | || |                                                                
AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaattatt--caattaaataagtgctactgtatcg--tgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgtttttcag
















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|58687890|gb|CK076577.1|CK076577
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|58691922|gb|CK080609.1|CK080609
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|58657140|gb|CK045820.1|CK045820
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|58696242|gb|CK084929.1|CK084929
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|56158059|gb|C72031.2|C72031
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTACCAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|66930475|gb|CX117323.1|CX117323
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA

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: 69 (upstream exon), 74 (downstream exon)
Score: 93

AACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC




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