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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccctcttccttatatcatattttggctcctaagctaggtgggaccgtgggatagttaatgaccctatatttcaactttgtttgccattgatttcagGGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCAACAGCATTCCTATGACATTCAAACTGGTGAACAG

Basic information

species Oryza sativa
transcript LOC_Os01g03144.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03144.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G119345_T02 (Zea mays), 3'ss of exon 4
--gtaaccc--tcttccttatatcatattttggctcctaagctaggtgggaccgtgggatagttaatgaccctatatttcaactttgtttgccattgattt-cagGGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCAACAGCATTCCTATGACATTCAAACTGGTGAACAG
   |    |  | || ||| |   ||||  | |   |||   |||   | |  |    ||   |||  ||   ||  |   |||    |||||||| |||| ||||||||| ||||||||||||||||| |||||||| ||| |||||||||||||||| ||||| |||||||||||||| |||||||||
gtattgttcattttttcttgtgatatatagttgagtctagtgtagtaagcattgcatcat--ctaactactagatgct---act---cttgccattaattttcagGGCCTTTCAAGGGCTTTGCATTAACGAGTTCAAGGGTCTGCAATTTGAGCAACAACATTCATATGACATTCAAACGGGTGAACAG
















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|27545598|gb|CA763811.2|CA763811
EST:     AATACCCCCGTCATTTTTCGCTGGATCCCAAAAGTATCCCTAATTAGATG                         GGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCA
genomic: AATACCCCCGTCATTTTTCGCTGGATCCCAAAAGTATCCCTAATTAGATGgtaaccctct ... ttgatttcagGGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCA
EST: gi|157650480|gb|EX450114.1|EX450114
EST:     AATACCCCCGTCATTTTTCGCTGGATCCCAAAAGTATCCCTAATTAGATG                         GGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTCGCAATTTGAGCA
genomic: AATACCCCCGTCATTTTTCGCTGGATCCCAAAAGTATCCCTAATTAGATGgtaaccctct ... ttgatttcagGGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCA
EST: gi|87038312|gb|CI192934.1|CI192934
EST:     ATCCCTAATTAGATG                         GGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCA
genomic: ATCCCTAATTAGATGgtaaccctct ... ttgatttcagGGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCA
EST: gi|87039299|gb|CI193921.1|CI193921
EST:     ATACCCCCGTCATTTTTCGCTTGGACCCCAAAAGTATCCCTAATTAGATG                         GGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCA
genomic: ATACCCCCGTCATTTTTCGC-TGGATCCCAAAAGTATCCCTAATTAGATGgtaaccctct ... ttgatttcagGGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCA
EST: gi|38565862|gb|CK085315.1|CK085315
EST:     AATACCCCCGTCATTTTTCGCTGGATCCCAAAAGTATCCCTAATTAGATG                         GGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCA
genomic: AATACCCCCGTCATTTTTCGCTGGATCCCAAAAGTATCCCTAATTAGATGgtaaccctct ... ttgatttcagGGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCA

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: 56 (upstream exon), 51 (downstream exon)
Score: 9

CCCTTATGACAGTTTTCATTGTATTTGGAGGATACTATGTTAACCCTGATAATACCCCCGTCATTTTTCGCTGGATCCCAAAAGTATCCCTAATTAGATGgtaaccctct ... ttgatttcagGGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCAACAGCATTCCTATGACATTCAAACTGGTGAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccgtgggatagttaatgaccctatatttcaactttgtttgccattgatttcagGGCCTTCCAAGGGCTTTGCATTAATGAGTTCAAAGGTTTGCAATTTGAGCAACAGCATTCCTATGACATTCAAACTGGTGAACAG
                                           cattgat  putative branch site (score: 9)
                       tatatttcaacttt  TA-rich tract