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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacaaccaccacgacaacaacaaacacctctgcatctgcacaacgcatcatgtctaacacggatccgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATCGGGGACGACGAGACGGCGGTCGGGGTGGGCACGGTGGGGTCGTCGGAGGCCATCA

Basic information

species Oryza sativa
transcript LOC_Os04g37460.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g37460.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G101069_T01 (Zea mays), 3'ss of exon 2
-------------------gtaaacaaccaccacgacaacaacaaac-acctctgcatctgcacaacgcat-catgtcta---acacggatccgat--gaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATCGGGGACGACGAGACGGCGGTCGGGGTGGGCACGGTGGGGTCGTCGGAGGCCATCA
                   |    || | |||  |   | | | | | | |  |   ||     ||  |     |||||    ||  ||||   |   |||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||||||||| || || || || |||||||||||||
gtacgcttctgtctctgctggcggcagctacctggctcagatcgatcgatcggtcggtcgatctaatacgcatgtgtctctgtacttggattgaaacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGACGACGAGACGGCGGTCGGGGTGGGGACCGTCGGCTCCTCGGAGGCCATCA
















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|88399109|gb|CI603776.1|CI603776
EST:     ACAAGAACTAAGTCGACATGGATGAGTACCC-GTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCATTTGTTCAACGCGCCGATCGGG
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATCGGG
EST: gi|88407609|gb|CI586450.1|CI586450
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGC
EST: gi|88390990|gb|CI592898.1|CI592898
EST:     ACAAGAACTACGTCGAAATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGC
EST: gi|88407570|gb|CI586411.1|CI586411
EST:     ACAAGAACTACGTTGACATGGATGAGTACCC-GTCACCACCGAGCTCCAC                         AACCGGTGCGTGACCCTGATCGCGTATCTGTTCAACGCG
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCG
EST: gi|88370815|gb|CI592581.1|CI592581
EST:     ACAAGAACTACGTCGACATGGATGAGTACCC-GTCACCACCGAGCTCCAG                         AAC-GGTGCGTGAAC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAAC
EST: gi|88433402|gb|CI594216.1|CI594216
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGTGTGAACATGATCGCGCATCTG
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTG
EST: gi|88397154|gb|CI593366.1|CI593366
EST:     CAAGAACTATGTCGACATTGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCTGGTGCGTGAACATG
genomic: CAAGAACTACGTCGACAT-GGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACC-GGTGCGTGAACATG
EST: gi|88294554|gb|CI597137.1|CI597137
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATTGGGGAC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATCGGGGAC
EST: gi|88377254|gb|CI600409.1|CI600409
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATCGGGG
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATCGGGG
EST: gi|88405268|gb|CI586089.1|CI586089
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCAC-GAGCTCCAG                         AAC-GGTGCGTGAA-ATGATCGCGCATCTGTTGAACGCG
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCG
EST: gi|88398046|gb|CI585549.1|CI585549
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGA
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGA
EST: gi|88445535|gb|CI587148.1|CI587148
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACTGGTGCGTGAACATGATGGCGCATCT
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCT
EST: gi|88427051|gb|CI602012.1|CI602012
EST:     AATGAACTACTGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGA
genomic: AA-GAACTAC-GTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGA
EST: gi|88395943|gb|CI593145.1|CI593145
EST:     CAAGAACTAAGTCGACATGGATGAGTACCCCGTCACCCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCATGTGTTCAACG
genomic: CAAGAACTACGTCGACATGGATGAGTACCCCGTCACC-ACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACG

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: 66 (upstream exon), 53 (downstream exon)
Score: 18

CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATGATGGCCGCCATCAACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtaaacaacc ... cgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATCGGGGACGACGAGACGGCGGTCGGGGTGGGCACGGTGGGGTCGTCGGAGGCCATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaacacctctgcatctgcacaacgcatcatgtctaacacggatccgatgaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATCGGGGACGACGAGACGGCGGTCGGGGTGGGCACGGTGGGGTCGTCGGAGGCCATCA
                               gtctaac  putative branch site (score: 18)