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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgctagtaaatattcttggaaagaacttcaaggatacattcaatgctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC

Basic information

species Oryza sativa
transcript LOC_Os03g18970.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
-----gtaagctgctagtaaatattcttggaaagaacttcaaggataca-------ttcaatgctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC
     |    |||||     || ||  || | |    ||| ||||||||        || ||||| |  || |||||||    ||||| |||  |    ||| |  |  || ||||||||||| |||||| ||||||||||||||||||||||||||||||| || |||||||||||||| || || ||||||||||| || ||||||||||||||||
gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctg--catgggattttttaattaatttctccctt-ttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC

upper sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G41810.2 (Glycine max), 3'ss of exon 4
gtaagctgctagtaaatattcttggaaagaacttcaaggatacattcaatgctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC
                     |  ||   ||   | |   | | |||  |  |   | |    ||    |||   |||||| | ||    |||  ||||  | ||||| || |||||  | ||||||||||||||||||||||| || ||||| || || || || ||||| || || || ||||||||||| |||||||| ||||
--------------------gtatgatgcaatcaccattgtgctttc--taataa-agattgcttaaacttagtagttttggtttg----ctttatgtt--tatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC

upper sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 4
gtaagctgctagtaaatattcttggaaagaacttcaaggatacattcaatgctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC
                           | ||  | |    |  ||||  | ||    | |  ||| ||| ||       || | ||    |||  |     | ||||| || |||||  | || ||||| ||||||||||||||||| ||||| ||||| || || ||||| || || || ||||| ||||| |||||||||||||
-------------------------gtacaatgtaatctttctattcctttctaatcaggactttttcactag----cctgttttggttccttaatacatctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC

upper sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4
gtaagctgctagtaaatattcttggaaagaacttcaaggatacattcaatgctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC
                           |     | |    || ||||  | ||    | |  ||| | | ||       || | ||    |||  |    || ||||| || |||||  | |||||||| ||||||||||||||||| ||||| ||||| || || ||||| || || || ||||||||||| |||||||| ||||
-------------------------gtatggtgtaatctttatattcctttctaatcaggactttttaactag----cctgttttggttccttaatacatttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC

upper sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 4
gtaagctgctagtaaatattcttggaaagaacttcaaggatacattcaatgctgtcaaagcatttctca--ttatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC
                |||  |  | ||  || |   |    ||| |  | ||   ||||  | | | |  |||   |||||| | ||       | | |  || ||||| || |||||  | ||||||||||||||||||||||| || ||||| || || || || || || || || || ||||||||||| |||||||| ||||
---------------gtatgat--gcaatcaccttttgcgctcatgct-ttctaataaagattgtttaaacttagtagttttggtttg------cgttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC

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|56158518|gb|AU093318.2|AU093318
EST:     CCGCGAGTGGAGGGGAGGTCAGCCGGCTCAACCTGTGTGGTGGACAGGAG                         GTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATT
genomic: CCGCGAGTGGAGGGGAGGTCAGCCGGCTCAACCTGTGTGGTGGACAGGAGgtaagctgct ... gttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATT




















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: 49 (upstream exon), 45 (downstream exon)
Score: 14

AACCGTGGACCATCGTCTCGAGGAGAATGTAGAGGAGCGGGAGCGCGTCACCGCGAGTGGAGGGGAGGTCAGCCGGCTCAACCTGTGTGGTGGACAGGAGgtaagctgct ... gttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC
                         ttttgat  putative branch site (score: 14)
                                              ttgtttt  putative PPT
                                              ttgtttta  TA-rich tract