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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttctctcatcaataataatagtaaaatcctaattctgtaattatctctacaactaaatacttaggcatcctggttcataaagatttgcaaggtt...

Basic information

species Oryza sativa
transcript LOC_Os08g39420.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g39420.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G126517_T01 (Zea mays), 5'ss of exon 11
ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttctctcatcaataataatagtaaaatcctaattctgtaattatctctaca--actaaatacttaggcatcctggttcataaagatttgcaaggtt-
||||||| ||||| ||||||||||||||| ||||||| || |||||||| ||||||||| | ||||| ||||||| || || ||||||| | || |||    |||||  ||   |  |||  |    |  | |   |||    ||  | |   ||||  || ||| |   ||  |    |   | | 
ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTGCCCTTTCTAACCTTCAGCAGAGAGAAATAAGCAgtaagctactgtcactt-taatagaagggcaggcctggtgaaatggtgagagctatctcaccgagtcactagg--tcgtggattcgaagcaccctctccgctt

upper sequence: LOC_Os08g39420.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA09G00500.2 (Glycine max), 5'ss of exon 12
ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttctctca--tcaataataatagtaaaatcc-taattctg-taattatctctacaactaaatactt-aggcatcctggttcataaagatttgcaaggtt
| ||||| ||||| ||||| |||||||||||||| |||||| ||||||| |||||| || |   | |  ||| | |    ||  || || || |  ||  |||  |  |   |  | ||   | |   || |  |||||| |  | ||  | | || |   | | |  | |  | |   || |      
ACATTGCTCTTGTGAAGAATAATGCTCTTGTTGGAGCTAAAGTTGCTGTAGCCCTTGCTCA--ATTAAGAGAAAATTGTCAAAGgtgagcttataccagttcagcatgagcgggtatatgtatgacattgattcttatctttgtagctgcaaattttacttaacataatcctgagaaggtttct-----
















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|88846577|gb|CI373345.1|CI373345
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|88224122|gb|CI223971.1|CI223971
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|88835296|gb|CI370599.1|CI370599
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|88296760|gb|CI540112.1|CI540112
EST:     TNCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|86853962|gb|CI329408.1|CI329408
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|15858529|gb|BI811341.1|BI811341
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAAC-AACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|86879940|gb|CI340002.1|CI340002
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|89174503|gb|CI110701.1|CI110701
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|88846107|gb|CI372875.1|CI372875
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACTAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|66916970|gb|CX103818.1|CX103818
EST:     AGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: AGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT

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: 55 (upstream exon), 69 (downstream exon)
Score: 4

ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCTGAAACATGGGGCATCCTATTCATCCTCACAATGTATGCTTGTACAACTA




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