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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg...

Basic information

species Oryza sativa
transcript LOC_Os05g28180.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G416667_T01 (Zea mays), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgtt-----gacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
|| |||||||||||||||||||||||||| || || |||||||| ||||||||||||||||||||||| |||||||||||||| || |||||||| |||||||| | |||||  || |  | | ||      |    ||| |  ||    |||||| ||    | |         ||   || | |  ||  ||| |  |  || 
AGCACATTTCATCGTTTTGACAAATTCAATCTAAAATACAATCCATGTGGCCAAAGTAGGCTCAGAGAAATTTTCCTCAAACAAGATAATCTTATTCAAGgtattggttgttataagtcctatattccttaaaagtcttttttgattgggccttttatgcaaattcc---tttatttattgtatat--tatcatgctcattgttc

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA03G07460.1 (Glycine max), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaat-gtttgtccttg-
||||| |||||||| ||||| || ||||| ||||| |||||||| ||||| ||||||||||| || ||||| || || || ||||| ||||| || ||||||| |  || |||    |||     || | || |    | | |      || |  |     | || |||   | | | ||   |    | ||    | ||  
AGTACTTTTCATCGCTTTGATAAGTTCAATCTTAAATACAATCCTTGTGGTCAAAGTAGGCTGAGGGAGATATTTCTGAAGCAGGATAATCTCATACAAGgtaacattt-ttttgggtataacactgtc-ctatcacacctgtgtttacttgtaatcaaattcaaaggggcagaaatatcctatggttttgtgcagctttct

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G29470.1 (Glycine max), 5'ss of exon 10
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttca----attattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
||||| |||||||| ||||| || ||||| ||||| |||||||| || || |||||||||||||| ||||| || || || ||||| ||||| || ||||||| |  || |||      || |   |  |  ||| | |||   | | | |   ||    || ||| ||    |     ||||     |  || |||       
AGTACTTTTCATCGCTTTGATAAGTTCAATCTTAAATACAATCCTTGCGGTCAAAGTAGGCTCAGGGAGATATTTCTTAAGCAGGATAATCTCATTCAAGgtaacatttttttttgggtataacagtcctatcacctgtgttactttaatcaaattcaaagtggctgaaatatcccatggttttgtgcagtatttttact----

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G38280.2 (Arabidopsis thaliana), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgta-tcgcttgtttcaattatt-ttgttgacactttt-gtgcatct--taccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
||||| |||||||||||||| || |||||||| ||||| || || ||||| ||||||||||| || ||||||||||| |||||||| ||||| |||||||||| | |  |  | || | | | || ||  |  |||| || ||| |  | | |   || |     || |   | ||  || ||  |        ||||       
AGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGTAGGCTTAGGGAGATTTTCCTTAAACAGGATAATCTCATCCAAGgtaattgaatactccagtcactcttattaccgtttttagttcatttgatgcatcagttatgcactctcagttgcctgacatttattttcgtttggtttaag----

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattat-tttgttga--cacttttgtgcatcttac-cttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
|| ||||||||||||||||| || ||||| || ||||||||||| || || |||||||||||||| || |||||||| || ||||| ||||||||||||||||| || || ||    ||| ||| ||     |   ||| | |       ||     |    |  | |||  | ||        | | |||   ||  |     
AGCACATTTCATCGTTTTGATAAGTTCAATCTCAAGTACAATCCCTGCGGTCAAAGTAGGCTCAGGGAAATTTTCCTTAAGCAGGATAATCTTATCCAAGgtatggcgtgcttgttatatgtttattaggttaagcttgaggaaaaagtgctaaacagacccttttgaacaagtttttttcaatttccaaatacttcatt----

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaat---tattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
| ||| ||||||||||| ||||| |||||||| || |||||||| |||||||| |||||||| || ||||||||||| || || |||||||||||| ||||||  |||  | ||||     ||||| |  ||| |    || |   ||  | || |  | | |    ||    |    || | |   |  ||||| ||     
AATACGTTTCATCGTTTCGACAAGTTCAACCTGAAATACAATCCTTGTGGCCAGAGTAGGCTAAGGGAGATTTTCCTGAAGCAAGACAATCTTATCAAAGgtagtgctcttatcaaaaagcattttctcaacattcgaatg-acgctagatcttgtactctggagccacattttgcttgtatttgaaaggatgttggttga--

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgtt--gttgctaaacgggcttgcagtttctcctaaaat-gtttgtccttg
|  ||||| || |||||||| || |||||||||||||||||||| || ||||||||  | || || |||||||| || ||||| ||||| ||||| |||||| |   ||   ||| ||   ||    | || |||   | ||| ||   |  |  |     | ||  |    || ||  |  |  |||||| |||||| ||  
AACACATTCCACCGTTTTGATAAGTTCAACCTTAAGTACAATCCATGCGGCCAAAGCCGACTAAGGGAGATTTTTCTGAAACAAGACAACCTTATTCAAGgt-taaattacatcatttcagttacacaaacatttacacctctaacacatgatacttcacagatattcaacttttca--tggtgttaaaatagtttgtactat

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ17267 (Selaginella moellendorffii), 5'ss of exon 8
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgttgttgc-taaacgggcttgcagtttctcctaaaatgtttgtccttg
| ||| || ||| | || || ||||| ||| | || |||||||| ||||| |||||||||||| |||| || ||| | || ||||||||||| || ||||||||        | ||||  |  |   |  ||||    | ||||   ||||   |  || |     | || || |||                        
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtatg-------ttaatttctccgcctattcttt----cttctttttttttccatcattacgcttgctggtttacag------------------------

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 8
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
| ||| || ||| | || || ||||| ||| | || |||||||| ||||| |||||||||||| |||| || ||| | || ||||||||||| || ||||||||        | ||||  |  |   |  ||||  |   | || || |  ||    |||||     || || |||                        
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtatg-------ttaatttctccgcctattctttcttctttttttccatcattacgcttgct-----ggtttacag------------------------

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|29638452|gb|CB643461.1|CB643461
EST:     CCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAG                         GTCGTTTTCTTGCCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAA
genomic: CCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttg ... tttaaactagGTCGTTTTCTTGCCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAA
EST: gi|29637474|gb|CB642483.1|CB642483
EST:     CCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAG                         GTCGTTTTCTTGCCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAA
genomic: CCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttg ... tttaaactagGTCGTTTTCTTGCCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAA

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: 61 (upstream exon), 63 (downstream exon)
Score: 14

AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttg ... tttaaactagGTCGTTTTCTTGCCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAAGTAAATACCAG




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