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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAGgtacgccttaaacaattcctgttccgctaggttgtcgaaagtgaacatggtagcttttcaccaatagtttacctgcttaactgtaaatcaagtttggact...

Basic information

species Oryza sativa
transcript LOC_Os07g40510.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g40510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G132810_T01 (Zea mays), 5'ss of exon 3
GTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAGgtacgccttaaacaattcctgttccgctaggttgtcgaaagtgaacatggtagcttttcaccaatagtttacctgctta--actgtaaatcaagtttggact--
|||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||| |||||||| |||||||||||||||||||||||  | |    ||           |  ||  ||  |     |||||      |   |   |||||  |  |  |||  |     | ||   |      |  
GTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTTACAGATACCCGGGCAACAAATAATAAGATGACACTAATGCACTACCTCTGCAAGgtacggttgaccttatgttgaaat--ttgagtactcacatagtcacatgtccatgtactat--atagtacattttgttatgataactattcggttcccagttag

upper sequence: LOC_Os07g40510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G414002_T02 (Zea mays), 5'ss of exon 11
GTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAGgtacg-----ccttaaacaattcctgttccgctaggttgtcgaaagtgaacatggtagcttttcaccaatagtttacctgcttaactgtaaatcaagtttggact
| ||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||| |||||||| |||||||||||||| |||||| |     ||||   | |   | |     ||    |||  |      | || |||  ||||        | |||   | ||  | || | |   | ||     
GGGCTGCGGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTTACAGACACCCGAGCAACAAATAATAAGATGACACTAATGCACTACCTCTGTAAGgtatggttcaccttctgctaaaaccggagtactcacatgtgcatgtactatatagtacattttgttatgatggttattcggttcccagttagtt--gcttaa---
















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|396941169|gb|HO188378.1|HO188378
EST:     ATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAG                         GTACTTGCTGCAAAATCATCACAGCTTCTGGACTTCTACATGGATCTTGTT
genomic: ATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAGgtacgcctta ... gtaatatcagGTACTTGCTGCAAAATCATCACAGCTTCTGGACTTCTACATGGATCTTGTT
EST: gi|88329532|gb|CI648594.1|CI648594
EST:     ATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAG                         GTACTTGCTGCAAAATCATCACAGCTTCTGGACTTCTACATGGATCTTGTT
genomic: ATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAGgtacgcctta ... gtaatatcagGTACTTGCTGCAAAATCATCACAGCTTCTGGACTTCTACATGGATCTTGTT
EST: gi|29631370|gb|CB636379.1|CB636379
EST:     ATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAG                         GTACTTGCTGCAAAATCATCACAGCTTCTGGACTTCTACATGGATCTTGT
genomic: ATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAGgtacgcctta ... gtaatatcagGTACTTGCTGCAAAATCATCACAGCTTCTGGACTTCTACATGGATCTTGT

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: 71 (upstream exon), 62 (downstream exon)
Score: 21

GTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAGgtacgcctta ... gtaatatcagGTACTTGCTGCAAAATCATCACAGCTTCTGGACTTCTACATGGATCTTGTTAGTTTAGAAGCTACATCAAAG




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