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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTTATGTTCCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttctgtcattgtttaaatttctacctaagaaagtgcaaaagtctctaatcagataccattatttgattctgcag

Basic information

species Oryza sativa
transcript LOC_Os10g25130.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25130.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G088064_T02 (Zea mays), 5'ss of exon 4
TGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTTATGTTCCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttctgtcattgtttaaatttctaccta---------agaaagtgcaaaagtctctaatcagataccattatttgattctgcag
||||||||| |||||||||||||||||  | || ||||||||| |||| |||||||||||||| || |||||||| |||||||||||||||||||||||||||     | ||  ||| |||||||| |  |||          || || ||| |||   || | | | | | ||||  || ||||| |||
TGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCTATGCTCCAATATCACTGGTCAAATCCTTGCGAGCCTCGTCATGAATCCACCAAAGgtctgccatatggaattctttaaattacgccctggttggaattaggaaatgccaaatcgtccagttaaaaatcattgctttattctccag
















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|2796858|gb|AA750152.1|AA750152
EST:     CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAG                         GCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
genomic: CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttc ... gattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
EST: gi|29668876|gb|CB665151.1|CB665151
EST:     CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAG                         GCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
genomic: CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttc ... gattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
EST: gi|218502337|gb|FG952302.1|FG952302
EST:     CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAG                         GCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
genomic: CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttc ... gattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
EST: gi|38481162|gb|CF965251.1|CF965251
EST:     CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAG                         GCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
genomic: CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttc ... gattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
EST: gi|29666343|gb|CB662618.1|CB662618
EST:     CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAG                         GCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
genomic: CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttc ... gattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
EST: gi|163926601|gb|EG713617.1|EG713617
EST:     CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAG                         GCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
genomic: CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttc ... gattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
EST: gi|29666342|gb|CB662617.1|CB662617
EST:     CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAG                         GCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
genomic: CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttc ... gattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
EST: gi|13165185|gb|AU173982.1|AU173982
EST:     CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAG                         GCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC
genomic: CCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttc ... gattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTC

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: 75 (upstream exon), 72 (downstream exon)
Score: 170

TGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTTATGTTCCAATATCACTGGCCAGATCCTTGCCAGCCTCGTCATGAATCCACCAAAGgtcaatgttc ... gattctgcagGCTGGAGATGCATCATATGCTTCATACAAGGCAGAGAAAGATGGAATCCTCCAATCATTAGCTCGCCGTGCAAAG




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