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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattagatgtataattaattatgtgctgtaaacatttgtttcagtcctaatgattcatgcactaaatgatcgcctctggttgaatctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTCATTTGCATCTGACAATG

Basic information

species Oryza sativa
transcript LOC_Os04g32330.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 3
----------------------------gtgagtattagatgtataattaattatgtgctgtaaacattt---gtttcagtcc-taatgattcatgcactaaatgatcgcctctggttgaatc--tcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTCATTTGCATCTGACAATG
                             ||| ||        || |||||     |||   | |  |||   || ||  ||| |  | || |||| |   |   ||  | |    |  | ||  | || |||||||||||||||||| || ||| | |||| ||||||| | ||||||||||||||||| || ||||  |
gtaattatcagatagcatgctctagttgatgaatacggatgccattattaacctaatgcctaatattttttatgtctctttccctttttatacatgtatgtatgcattacattatttcaattcaattttgtagaagACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTCATTTGCCTCAGACAGCG

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 3
----------------------------gtgagtattagatgtataattaattatgtgctg------taaacatttg----tttcagtcctaatgattcatgcactaaatgatcgcctctggttgaatctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTCATTTGCATCTGACAATG
                             ||| |||       || | | |     |||         ||| ||||     || || |  ||   ||| ||| | || || || ||      ||||||   || ||||||| |||||||||| || ||| ||||||| |||||| | ||||||||||||||||| || ||||| |
gtaattatcagatagcatgctctagttgatgaatatggatgccattactgacctcatgccaaataatcaaatattttctctttccatttttagacatttatgtattacattattgc----aattgaatt--ttgtagaagATGCTATTACTTACCTAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG
















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|58590899|gb|CF989207.1|CF989207
EST:     CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
EST: gi|58676164|gb|CK064851.1|CK064851
EST:     CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
EST: gi|58670038|gb|CK058724.1|CK058724
EST:     CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
EST: gi|88356597|gb|CI626212.1|CI626212
EST:     CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
EST: gi|218479259|gb|FG949034.1|FG949034
EST:     CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
EST: gi|58592377|gb|CF990685.1|CF990685
EST:     CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
EST: gi|218481751|gb|FG959381.1|FG959381
EST:     CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAG                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
EST: gi|58659078|gb|CK047758.1|CK047758
EST:     CTCTTATTCCAATTGGTGCCCAGAGCTCAAAGCTTACAAG                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
EST: gi|58659774|gb|CK048454.1|CK048454
EST:     CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTAC---                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
EST: gi|58689671|gb|CK078358.1|CK078358
EST:     CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTAC---                         AAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC
genomic: CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTC

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: 40 (upstream exon), 73 (downstream exon)
Score: 51

CTCTTATTCCAATTGGTTCCCAGAGCTCAAAGCTTACAAGgtgagtatta ... tctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTCATTTGCATCTGACAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtcctaatgattcatgcactaaatgatcgcctctggttgaatctcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTCATTTGCATCTGACAATG
                    cactaaa  putative branch site (score: 51)
                                             tctcttat  putative PPT
        taatgatt  TA-rich tract