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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcatttcatgcagcatctctctgctatgtgattcattataaggtgttacaggaaatgactttatctttgttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCT

Basic information

species Oryza sativa
transcript LOC_Os01g01307.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G376727_T05 (Zea mays), 3'ss of exon 2
gtgagtgcatttcatgcagcatctctctgctatgtgattcattataaggtgttacaggaaatgactttatctttgttgcttct--agTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCT
|||||| |||||  |   ||||||||||||| | ||  |   | ||      ||||| |||||| || ||  || |  || ||  ||||||| ||||||| | ||  ||| |||| |||||||||||  |||||||||||| || |||||||| ||  ||||||| || ||||||||||||||| ||
gtgagtacattttgtaatgcatctctctgctttatgtgttcatgtagatcagtacagaaaatgatttcattattttgactccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACT

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G067476_T03 (Zea mays), 3'ss of exon 2
gtgagtgcatttcatgcagcatctctctgctatgtgattcattataaggtgttacaggaaatgactttatctttgttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCT
|||||| |||||  |   |||| || ||||| |     |   | ||  ||   | ||  |||||  ||| |||   | |||  ||||||| ||||||||| ||  ||| |||| |||||||||||  |||||||||||| || |||||||| ||  | ||||| || ||||||||||||||| | 
gtgagtacattttgtaatgcatatcactgctttacatgttcatgtacagt---aaagttaatga--ttaccttgact-ctttcagTGGTGCCACTGCTTCACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATCATTACATACCGTGTTCCCACAAAGACA
















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|5002911|gb|AU068020.1|AU068020
EST:     TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCCACTG-TTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCA
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGT-CACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCA
EST: gi|87032410|gb|CI264191.1|CI264191
EST:     TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|25807463|gb|CA763424.1|CA763424
EST:     TNTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|86416814|gb|CI030825.1|CI030825
EST:     GGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: GGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|88975507|gb|CI021589.1|CI021589
EST:     GCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: GCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|87027081|gb|CI261528.1|CI261528
EST:     AAAGGCTTGACNC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: AAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|2797245|gb|AA750539.1|AA750539
EST:     TTTAAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTATCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|33660042|gb|CF291009.1|CF291009
EST:     GATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: GATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|58594778|gb|CF993086.1|CF993086
EST:     TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGAGGC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|86415979|gb|CI029990.1|CI029990
EST:     GATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: GATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|427829|gb|D23969.1|D23969
EST:     TTGAGCTTGATCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTGAGCTTG-TCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|5004937|gb|AU070175.1|AU070175
EST:     TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG

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: 75 (upstream exon), 75 (downstream exon)
Score: 121

AACTGCCTATGATGTGAGCATTAATGATGATACTTGGCCAAAGGAGGCATTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgattcattataaggtgttacaggaaatgactttatctttgttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCT
                                       tctttgttgcttct  CT-rich tract
      attcattataa  TA-rich tract