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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagtgacagacatgggaaaagtttctgctgagttattcaacatatttgtctacaattcttttgtatgtaatttgacatgagtccaatttgcctgtggatcag

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 8
GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagtgacagacatgggaaaagtttctgctgagttattcaacatatttgtctacaattcttttgtatgtaatttgacatgagtccaatttgcctgtggatcag
|||| || || |||||||||||||||||||| || ||||||||||| |||||||| || | | ||| ||| ||     || |      |||   |  || || || |  || | |||  ||||  |||| | |||  |||| ||||   || ||| ||
GTAAGAAATTCTGGAACCTCTTTCACTTGCAGCCTATGCGTGATCAGAAGgtactgtaataagagatatgaga-----tttt------ttacgtagtat-ttggtttggaactatttcatatg--atttaagatgcatccattttgatggttgattag

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA12G07890.2 (Glycine max), 5'ss of exon 10
GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactata-gtgacagacatgggaaaagtttctgctgagttattcaacatatttgtctacaattcttttgtatgtaat--ttgacatgagtccaatttgcct-gtggatcag
|||||||||| |||||| | ||||| ||||| || ||||||||||| |||||||  |   ||| |   |         ||| |  | | | ||  | |  ||||  | |   ||||     |    ||  || || ||  ||   ||| | | ||  | |||
GTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAGgtacagtttatgataacaacttttgttttttgtagttaatcat--atcccatttaccaaaccttctaacagaaaccatggttaacttgtttctctttttctttgtttaacag

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G40550.1 (Glycine max), 5'ss of exon 8
GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactata-gtgacagacatgggaaaa-gtt---tctgctgagttattca---acatatttgtctacaattcttttgtatgtaatttgacatgagtccaatttgcctgtggatcag---------------------------
| || ||||| |||||||| ||||| |||||||| ||||||||||| |||||||      ||| ||   |  ||| | |||   ||   | || | ||      || ||||    | | |  ||     | || ||| |||| |    | |  |  |||                                  
GAAAGAAGTTCTGGAACCTGTTTCATTTGCAACCTATGCGTGATCAGAAGgtacagcgtatgatagttttctgaagatgttaaatcctttaagatcttggcgtgcaaatttaataatattatttccccctatattttaacattaactgagtacgagtgttagcttttgtctcttttccttcttggtttaacag

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|29624477|gb|CB629488.1|CB629488
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29681859|gb|CB678134.1|CB678134
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29624448|gb|CB629459.1|CB629459
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29641853|gb|CB646860.1|CB646860
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|2317379|gb|C22433.1|C22433
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTTGGATGGGACTGAGCATGT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATT-GGATGGAACTGAGCATGT
EST: gi|29672018|gb|CB668293.1|CB668293
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29628293|gb|CB633304.1|CB633304
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29613611|gb|CB618624.1|CB618624
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGCT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29678744|gb|CB675019.1|CB675019
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29627346|gb|CB632357.1|CB632357
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGCT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29630466|gb|CB635475.1|CB635475
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGCT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|2317377|gb|C22431.1|C22431
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGGTTCAATTGGATGGGACTGAGCATGT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGG-TTCAATTGGATGGAACTGAGCATGT
EST: gi|29624450|gb|CB629461.1|CB629461
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29630119|gb|CB635128.1|CB635128
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGCT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29646710|gb|CB651717.1|CB651717
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT

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: 50 (upstream exon), 74 (downstream exon)
Score: 34

GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTTCAGGATGATGCTGCAAAAGAGGGAGTCGTGCTG




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