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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaacttcatatataattccactctacaccatcaatataatgcatgcatgatatcttcacgtacgaataatataatgtatgcatgatatctttatgaacgaataatgtatatgtgtggcggtttcag

Basic information

species Oryza sativa
transcript LOC_Os01g37000.1
intron # 2
splice site 5'
intron type U2

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|86901781|gb|CI310543.1|CI310543
EST:     CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG                         ATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
genomic: CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaac ... gcggtttcagATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
EST: gi|58612594|gb|CK040306.1|CK040306
EST:     CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG                         ATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
genomic: CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaac ... gcggtttcagATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
EST: gi|88352833|gb|CI678859.1|CI678859
EST:     CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG                         ATGCGAACTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAANACGTTCC
genomic: CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaac ... gcggtttcagATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGT-CC
EST: gi|58611754|gb|CK039466.1|CK039466
EST:     CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG                         ATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGA
genomic: CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaac ... gcggtttcagATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGA
EST: gi|33654001|gb|CF276615.1|CF276615
EST:     CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG                         ATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
genomic: CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaac ... gcggtttcagATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
EST: gi|88429320|gb|CI690221.1|CI690221
EST:     CAATCANAC-TGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG                         ATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
genomic: CAATCA-ACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaac ... gcggtttcagATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
EST: gi|88738709|gb|CI762217.1|CI762217
EST:     CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG                         ATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
genomic: CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaac ... gcggtttcagATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
EST: gi|88425735|gb|CI689388.1|CI689388
EST:     CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG                         ATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA
genomic: CCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaac ... gcggtttcagATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCA

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: 72 (upstream exon), 40 (downstream exon)
Score: 12

AGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAGgtgaattaac ... gcggtttcagATGCGACCTTCTATCCAGCCAAGTGGCCTATATGGAGAAGCAACACGTCCATTCACCCAAACATGGAATCAGAATGGCGAAAAGTGCCCTGACAATACTA




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