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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagatgtttgatgagatatcaaccacatgttccattgcagagatttcgcttcatgtgcatcctctgcccacaacacacatatgcatgcttattcgcgcgcacacatttatgctacttcctaagttcaatttttcccattgctgtagGCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG

Basic information

species Oryza sativa
transcript LOC_Os12g01922.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G460090_T01 (Zea mays), 3'ss of exon 12
gtaagtagatgtttgatgagatatcaaccacatgttccattgcagagatttcgcttcatgtgcatcctctgcccacaacacacatatgcatgcttattcgcgcgcacacatttatgctacttcctaagttcaatttttcccattgctgtagGCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG
                                             |  |   |   | | | ||||||||| ||         ||   ||| ||  ||   ||  ||  | ||||  |   ||  ||  |   ||| || |    | ||||||  || |||   || || || |||||||||||| ||||||||||||| || ||||| |||||||||||||||||||| ||| ||
-------------------------------------------gcaagtacagtagcgtctacatcctctggccttgcatttgatgcacattctcttttctgccaacttaattattttttctctgaatatt--tttctctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAG

upper sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G048067_T03 (Zea mays), 3'ss of exon 15
gtaagtagatgtttgatgagatatcaaccacatgttccattgcagagatttcgcttcatgtgcatcctctgcccacaacacacatatgcatgcttattcgcgcgcacacatttatgctacttcctaagttcaatttttcccattgctgtagGCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG
                             ||||  ||        |  |   || |    | |||      |  |  | |      ||| |   | |     |   ||| || ||  |   ||  ||    | | |||  |  | ||||||| | || ||||| || || ||||| || |||||| ||||||||||||| || ||||| ||||| |||||||||||||| ||||||
--------------------------gttacatcctctggcctgcatttgatgcataggatccatatgtgccttatgaaatgt-cctgcttctctttcttttctggcaccttaattgtttctctgaa---tattctttttctatactgtagGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAG
















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), 54 (downstream exon)
Score: 19

TCTGCATCTCAGGTTCGATGTGGCCAATTCGCTGCTGGTTTTCTTGATGCATCTGTTAGGATATTTGACGTGCGTACACCTGATAGgtaagtagat ... attgctgtagGCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgcgcgcacacatttatgctacttcctaagttcaatttttcccattgctgtagGCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG
                                     tttttcccattgct  CT-rich tract
                            taagttcaattttt  TA-rich tract