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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtacttgatccttaccatattcatgttaaatagaagcagttggtaatagtgggtgttctctaaggaactaggtgcgcactgtctatatagctgaactgtaatgtccaatctcaattcaaacaatatcagttaagtgtatttggcatattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAGGATGAAACATATTCTGGCGATGGCATTGCTCTTTTTCGAATTTCTGGAA

Basic information

species Oryza sativa
transcript LOC_Os03g24220.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G323479_T01 (Zea mays), 3'ss of exon 18
gtatggtacttgatccttaccatattcatgttaaatagaagcagttggtaatag-tgggtgtt---ctctaaggaacta-----ggtgcgcactg---tctatatagctgaactgtaatgtccaatctcaattcaaacaatatcagttaagtgtatttggcatattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAGGATGAAACATATTCTGGCGATGGCATTGCTCTTTTTCGAATTTCTGGAA
          |||| ||  |  |  | |||| |  || |   ||||  | |||  || ||| |   ||  || |||||      || ||   |||   |||||  |  ||||   |  | |  ||  | | | || | | || |||   | ||||||||  | ||  |||||||||| | ||||||||| ||  |||||| ||||||||| |||||  |||| ||||||||||||| |   |||||| | |||||  ||| |||||||||||
-------gtatgatgctcgctgtgattatgtcatgtatagtgagttaatgataaatgtgtgctggtctgcaaagaactcatattggagcattctgcattctatggaaatgaaaaatgttttgtaacgttactccagaaattaccag---aatgtatttgataaatcatgcagGGTGGTACCAGCTCTGGTTATAAGAAATATGTAGAAGAGAAGGGTCTGAAAGATGAAACATATTGTTCTGATGGCGTCGCTCTCATTCAAATTTCTGGAA

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 13
gtatggtacttgatccttaccatattcatgttaaatagaagcagttggtaatag-tgggtgtt---ctctaaggaactaggtgcgcactgtctatatagctgaactgtaatgtccaatctcaattcaaacaatatcagttaagtgtatttggcatattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAGGATGAAACATATTCTGGCGATGGCATTGCTCTTTTTCGAATTTCTGGAA
||||||| ||  |   | |  || | ||||| | |  ||   ||||  | |||  || ||| |   ||  || |||||   || |  |  |||||| |  ||||   |  | |  ||  | | | |   | | || |    | ||||||||  | ||  |||||||||| |  |||||||| ||  |||||||||||||||| |||||  |||| |||||||| |||| |   ||||||| ||||||  ||| |||||||||||
gtatggtgctc-actgtgattatgt-catgt-atagggagttagttaatgataaatgtgtgctggtctgcaaagaactcattg-gagcattctatagaaatgaaaaatgttttgtaacgttactcc---cgaaattacggcaatgtatttgtaaaatcatgcagGGTGGTACTAGCTCTGGTTATAAGAAATTTGTAGAAGAGAAGGGTCTGAAAGATGAAACGTATTGTTCTGATGGCACTGCTCTCATTCAAATTTCTGGAA
















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|58670584|gb|CK059270.1|CK059270
EST:     AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG                         GGTGGAATCAGCTCTGGATACCAGAAATGTGTAGAAGAAAAGGGCTTGAAG
genomic: AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
EST: gi|88692350|gb|CI735925.1|CI735925
EST:     AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG                         GGTGGAATCAGNTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
genomic: AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
EST: gi|12404685|gb|AU166286.1|AU166286
EST:     GGTCATTCTAAAG                         GGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
genomic: GGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
EST: gi|426363|gb|D22226.1|D22226
EST:     GGTCATTCTAAAG                         GGNGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
genomic: GGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
EST: gi|88569524|gb|CI660699.1|CI660699
EST:     AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG                         GGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
genomic: AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG

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), 70 (downstream exon)
Score: 35

GGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAGGATGAAACATATTCTGGCGATGGCATTGCTCTTTTTCGAATTTCTGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtccaatctcaattcaaacaatatcagttaagtgtatttggcatattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAGGATGAAACATATTCTGGCGATGGCATTGCTCTTTTTCGAATTTCTGGAA
            aattcaaacaatat  TA-rich tract