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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCCCACAAGCTTTTGCAGCCAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAGgtattctttagctcttaaggtgcttgatgtacatgtattttggtggtgacacatcattgttgtattctccccttttcag

Basic information

species Oryza sativa
transcript LOC_Os11g29200.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29200.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G019236_T04 (Zea mays), 5'ss of exon 1
----------------------------GAACCCCACAAGCTTTTGCAGCCAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAGgtat----tctttagctcttaaggtgcttgatgtacatgt--------attttggtggtgacacatcat-tgttgtattctcccct-tttcag
                            ||| |||| || ||||||||||| |||||||| || ||| |||| |||||||||||||||||||||||||||| ||    | ||  || |||  | |  ||  | |    ||         |  || || ||  |||| || | || | ||||||||| ||||||
AACACTAATAATCTTGTGTGGTTTACAGGAAGCCCATAAACTTTTGCAGCCTGTTGACAATACCCTCCAGACAATGGCACTAGAATTTGCTGAATATCAGgcatgtcatgttcggcgcttctgatttttattttctgggttaagagctgtcatgttgttgttacattatgttttattttctcccctctttcag

upper sequence: LOC_Os11g29200.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G019236_T06 (Zea mays), 5'ss of exon 13
GAACCCCACAAGCTTTTGCAGCCAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAGgtat----tctttagctcttaaggtgcttgatgtacatgt--------attttggtggtgacacatcat-tgttgtattctcccct-tttcag
||| |||| || ||||||||||| |||||||| || ||| |||| |||||||||||||||||||||||||||| ||    | ||  || |||  | |  ||  | |    ||         |  || || ||  |||| || | || | ||||||||| ||||||
GAAGCCCATAAACTTTTGCAGCCTGTTGACAATACCCTCCAGACAATGGCACTAGAATTTGCTGAATATCAGgcatgtcatgttcggcgcttctgatttttattttctgggttaagagctgtcatgttgttgttacattatgttttattttctcccctctttcag

upper sequence: LOC_Os11g29200.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G075680_T01 (Zea mays), 5'ss of exon 11
----------------------------GAACCCCACAAGCTTTTGCAGCCAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAGgtattct----ttagctcttaaggtgctt-----gatgtacatgtattttggtggtgacacatcat-tgttgtattctcccct-tttcag
                            ||| |||| || ||||||||||| |||||||| || |||||||| |||||||||||||||||||| ||||||| || ||    | | |  || || || ||     | |  | |  |    || || ||  | || || | || | ||||||||| ||||||
AATACTAATAACCTTGTGTGATTCATAGGAAGCCCATAAACTTTTGCAGCCTGTTGACAACACCCTCAAGACAATGGCACTAGAATTTGCTGAGTATCAGgcatgctatgttcatcatttgagttgtttttctgggttaagagttgccatgttgctgttatatgatgttttattttctcccctctttcag

upper sequence: LOC_Os11g29200.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT4G32640.2 (Arabidopsis thaliana), 5'ss of exon 14
GAACCCCACAAGCTTTTGCAGCCAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAGgtattct-------ttagctcttaaggtgcttgatgtacatgtattttggtggtgacacatcattgttgtattctccccttttcag-------------------------------------------
||  |||| ||  |  | || ||||  ||||||||||| ||||| |||||  | |||||||||||||| ||||||| |        |||  |   ||  |   ||||   | |    | ||    | |   |||     |||||  | |  | ||||                                            
GAGGCCCATAAATTACTACAACCAGCAGACAAAACTCTAAAGACCATGGCTATTGAATTTGCTGAATACCAGgtataccaatagaattatgttcgaatttaactgataatctttccatctgcgtatcagtaatctacaatgtatcattctttcttcattgcaatagttcgtccatgtctaagccatccataaatgtctcag

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|29631170|gb|CB636179.1|CB636179
EST:     CAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAG                         GTCTGCGTGGATGTGTTCCTTACTACACAATCATATGTTGATATTGCTTCG
genomic: CAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAGgtattcttta ... cccttttcagGTCTGCGTGGATGTGTTCCTTACTACACAATCATATGTTGATATTGCTTCG
EST: gi|86908985|gb|CI302673.1|CI302673
EST:     ACGATGGCACTAGAATTTGCTGAATATCAG                         GTCTGCGTGGATGTGTTCCTTACTACACAATCATATGTTGATATTGCTTCG
genomic: ACGATGGCACTAGAATTTGCTGAATATCAGgtattcttta ... cccttttcagGTCTGCGTGGATGTGTTCCTTACTACACAATCATATGTTGATATTGCTTCG
EST: gi|29634970|gb|CB639979.1|CB639979
EST:     CAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAA                         GTCTGCGTGGATGTGTTCCTTACTACACAATCATATGTTGATATTGCTTCG
genomic: CAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAGgtattcttta ... cccttttcagGTCTGCGTGGATGTGTTCCTTACTACACAATCATATGTTGATATTGCTTCG

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: 74 (upstream exon), 73 (downstream exon)
Score: 20

GAACCCCACAAGCTTTTGCAGCCAGTTGACAAAACTCTCAAGACGATGGCACTAGAATTTGCTGAATATCAGgtattcttta ... cccttttcagGTCTGCGTGGATGTGTTCCTTACTACACAATCATATGTTGATATTGCTTCGATATCTGTTGTTCCCAATACTACAGGAGGCCGG




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