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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggaaataaatgtttttttcttggtggagttcagtttgaccatttggagatgcttatgaatttaaaatgatgtggccccttattgcattttttttttcagATTGACTGCAATTGGATCAATTCAAGTAGGTGAGTGGAATTGATCCTCTTGAAGATTTTGACCCAAGTCCAATTCACAAGTAGAATTGTGAATTCTTTAG

Basic information

species Oryza sativa
transcript LOC_Os08g06110.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g06110.5 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G175265_T01 (Zea mays), 3'ss of exon 1
----gggaaataaatgtttttttcttggtggagttcagtttgaccatttggagatgcttatg--aatttaaaatga-tgtggcccct-tattgcattttttttttcagATT--GACTGCAATTGGATC---AATTCAAGTAGGTGAGTGG---AATTGATCCTCTTGAAGATTTTGACC--CAAGTCCAATTCACAAGTAGAATTGTGAATTCTTTAG-----------------------------
    | | |||  ||  ||||    |    ||   |||||  |   |   |   | ||  ||  ||||| | |  | | ||||  || | ||   | |       || |||   |||   |  | ||    | | |  ||  || || ||   |   |   || |     | |    ||  || |||||         | ||  | || |      ||                             
gtgagtggaattgatccttttgaagtttctgaccccagttcaattctacaggttttctcgtgtaaatttgacactactttggctgctcttttaggtctgggcacacaaatttgaactattaacgcattgggagtgcttgtgtgttagAGGTCTAGGAGGAGCTATGAGGTACTACTTCCGTCAGGTCCAGCGTTTGGTTGGAGATATGGAAGGAGGAGCTCTCTTGTTTATAGATGACCTCAACTCC
















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|88720644|gb|CI743943.1|CI743943
EST:     CTGACTTGGTTTTTGTGTGCACAGACCAACTGCAGCTGAGGATTTAGTAG                         ATTGACTGCAATTGGATCAATTCAAGTAGGTGAGTGGAATTGATCCTCTTG
genomic: CTGACTTGGTTTTTGTGTGCACAGACCAACTGCAGCTGAGGATTTAGTAGgtgagtggag ... tttttttcagATTGACTGCAATTGGATCAATTCAAGTAGGTGAGTGGAATTGATCCTCTTG
EST: gi|88716737|gb|CI740247.1|CI740247
EST:     CTGACTTGGTTTTTGTGTGCACAGACCAACTGCAGCTGAGGATTTAGTAG                         ATTGACTGCAATTGGATCAATTCAAGTAGGTGAGTGGAATTGATCCTCTTG
genomic: CTGACTTGGTTTTTGTGTGCACAGACCAACTGCAGCTGAGGATTTAGTAGgtgagtggag ... tttttttcagATTGACTGCAATTGGATCAATTCAAGTAGGTGAGTGGAATTGATCCTCTTG
EST: gi|58662589|gb|CK051275.1|CK051275
EST:     CTGACTTGGTTTTTGTGTGCACAGACCAACTGCAGCTGAGGATTTAGTAG                         ATTGACTGCAATTGGATCAATTCAAGTAGGTGAGTGGAATTGATCCTCTTG
genomic: CTGACTTGGTTTTTGTGTGCACAGACCAACTGCAGCTGAGGATTTAGTAGgtgagtggag ... tttttttcagATTGACTGCAATTGGATCAATTCAAGTAGGTGAGTGGAATTGATCCTCTTG

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: 74 (upstream exon), 72 (downstream exon)
Score: 155

AGTTGAAGATAACGAAAGGAGCAAGGGTGAACTCTGCTGACTTGGTTTTTGTGTGCACAGACCAACTGCAGCTGAGGATTTAGTAGgtgagtggag ... tttttttcagATTGACTGCAATTGGATCAATTCAAGTAGGTGAGTGGAATTGATCCTCTTGAAGATTTTGACCCAAGTCCAATTCACAAGTAGAATTGTGAATTCTTTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagatgcttatgaatttaaaatgatgtggccccttattgcattttttttttcagATTGACTGCAATTGGATCAATTCAAGTAGGTGAGTGGAATTGATCCTCTTGAAGATTTTGACCCAAGTCCAATTCACAAGTAGAATTGTGAATTCTTTAG
                              ccccttattgcatttt  CT-rich tract
        ttatgaatttaaaatg  TA-rich tract