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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATTCTTGAAGCGACATATCCTGCTGTTGCAAAGAGGTTACAGGGTGATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAAgtatgcattttcccattactcatgtttaaggccatcgcgcctattcttttgcatttatgatgctgcacttgaattagatttgttatatttgtgtttatgataatgcacatcaaattgcag

Basic information

species Oryza sativa
transcript LOC_Os03g63330.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63330.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G024686_T01 (Zea mays), 5'ss of exon 5
GGACATTCTTGAAGCGACATATCCTGCTGTTGCAAAGAGGTTACAGGGTGATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAAgtatgcattttcccattactcatgtttaagg------ccatcgcgcctattct-tttgcatttatgatgctgcacttgaattagatttgttatatttgtgtttatgataatgcacatcaaattgcag
||| ||||||||||| || || ||||||||||| |||||| |||| |  || ||||| || |||||||||||||||||||| |||||||| ||||| || ||||| | ||   ||| | || |||| | ||      |  ||  |  |  | | ||||  ||| | ||| ||||| | ||||  |                                          
GGATATTCTTGAAGCCACTTACCCTGCTGTTGCGAAGAGGCTACATGAAGACTGGATGGATGACCCTGCTATTCCTATAGTCACTGGTTTTCTTGGGAAGgtatgtacttctacatgattc-tgttgagggtgtcaactgtcaagtttcctttgtttggttttgtaatgatgcacatcaatttcag-----------------------------------------
















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|33675742|gb|CF303981.1|CF303981
EST:     ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAA                         GGATGGAAATCATGTGCTGTCACCA
genomic: ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAAgtatgcattt ... caaattgcagGGATGGAAATCATGTGCTGTCACCA
EST: gi|29614036|gb|CB619049.1|CB619049
EST:     ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAA                         GGATGGAAATCATGTGCTGTCACCACTTTANGCAGAGGTGGCAGCGACTTG
genomic: ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAAgtatgcattt ... caaattgcagGGATGGAAATCATGTGCTGTCACCACTTTAGGCAGAGGTGGCAGCGACTTG
EST: gi|58686338|gb|CK075025.1|CK075025
EST:     ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAA                         GGATGGAAATCATGTGCTGTCACCACTTTAGGCAGAGGTGGCAGCGACTTG
genomic: ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAAgtatgcattt ... caaattgcagGGATGGAAATCATGTGCTGTCACCACTTTAGGCAGAGGTGGCAGCGACTTG
EST: gi|29613802|gb|CB618815.1|CB618815
EST:     ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAA                         G-ATGGAAATCATGTGCTGTCACCACTTTAAGCAGAGGTGGCAGCGACTTG
genomic: ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAAgtatgcattt ... caaattgcagGGATGGAAATCATGTGCTGTCACCACTTTAGGCAGAGGTGGCAGCGACTTG
EST: gi|29618751|gb|CB623763.1|CB623763
EST:     ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAA                         GGATGGAAATCATGTGCTGTCACCACTTTAGGCAGAGGTGGCAGCGACTTG
genomic: ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAAgtatgcattt ... caaattgcagGGATGGAAATCATGTGCTGTCACCACTTTAGGCAGAGGTGGCAGCGACTTG
EST: gi|29683343|gb|CB679618.1|CB679618
EST:     ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAA                         GGATGGAAATCATGTGCTGTCACCACTTTAGGCAGAGGTGGCAGCGACTTG
genomic: ATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAAgtatgcattt ... caaattgcagGGATGGAAATCATGTGCTGTCACCACTTTAGGCAGAGGTGGCAGCGACTTG

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: 70 (upstream exon), 73 (downstream exon)
Score: 14

GGACATTCTTGAAGCGACATATCCTGCTGTTGCAAAGAGGTTACAGGGTGATTGGATTGACGACCCTGCTATTCCTATAGTTACTGGTTTCCTTGGAAAAgtatgcattt ... caaattgcagGGATGGAAATCATGTGCTGTCACCACTTTAGGCAGAGGTGGCAGCGACTTGACTGCTACCACCATTGGCAAAGCGTTGGGATTAAGAGAGATCCAG




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