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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcatatgccagcctgaaaacaaccaatctcgcctgcttaatttttgtgtgaacgggtttgagctaaccgatcgcgtttctcgtgttggtacatcacttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGGTATCACTGATCATCATTCATCAACGGGCGATGCCTGCTCAGTTCATCAC

Basic information

species Oryza sativa
transcript LOC_Os04g51160.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074761_T01 (Zea mays), 3'ss of exon 2
gtacgcatatgccagcctgaaaacaaccaatctcgcctgcttaatttttgtgtgaacgggtttgagctaaccgatcgcgtttctcgtgttggtacatcacttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGGTATCACTGATCATCATTCATCAACGGGCGATGCCTGCTCAGTT-CATCAC-----
|||||     ||  || |     |   |||      | || || ||||||| |   |   | ||| ||||  ||||| ||||||    ||||   ||      |||||||||||||  | ||||| |||||||||| ||| |||||||||||| |||| || |||| || |       |||||| |   |||  | | ||     || |     
gtacg---gcgcgggcttagtggcttgcaaga--atccgcctactttttgt-tcggccaatctgaactaattgatcg-gtttct----ttgg---at------tgcagGACATCCATTACCAGGGCATGAAGCTGAGGGACACGCCTGCGCCTCTCGGCTACCACTAATTA------GTCAACGTGGCCTGCTAGTTTAGCAATGTCGCCTGTA
















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|15856344|gb|BI809156.1|BI809156
EST:     TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCG                         GACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
genomic: TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcatat ... acttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
EST: gi|86495711|gb|CI138344.1|CI138344
EST:     TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCG                         GACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
genomic: TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcatat ... acttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
EST: gi|8527374|gb|AU092189.1|AU092189
EST:     TCATCCGCGCCGACGAGGCGCACCACCGCGACNTCAACCATTTCGCATCG                         GACATCCAGCNACAGGGGATGAAGCTGAAGGATNCGCCTGCGCCTATCGGG
genomic: TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcatat ... acttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
EST: gi|88228270|gb|CI227750.1|CI227750
EST:     TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCG                         GACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
genomic: TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcatat ... acttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
EST: gi|9864900|gb|AU100650.1|AU100650
EST:     TCATCCGCGCCGNCGAGGCGCACCACCGCGACCTCAACCATTTCGCATCG                         GACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
genomic: TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcatat ... acttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
EST: gi|89182691|gb|CI114060.1|CI114060
EST:     TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCG                         GACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
genomic: TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcatat ... acttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
EST: gi|86539820|gb|CI180026.1|CI180026
EST:     TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCG                         GACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
genomic: TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcatat ... acttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
EST: gi|86493549|gb|CI136182.1|CI136182
EST:     TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCG                         GACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG
genomic: TCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcatat ... acttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGG

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: 70 (upstream exon), 26 (downstream exon)
Score: 2

CGACTACTGGCGCCTCCCCGCCGACGCCACGCTCAAGGACGTCGTCACCGTCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcatat ... acttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGGTATCACTGATCATCATTCATCAACGGGCGATGCCTGCTCAGTTCATCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacgggtttgagctaaccgatcgcgtttctcgtgttggtacatcacttgtgcagGACATCCAGCAACAGGGGATGAAGCTGAAGGATACGCCTGCGCCTATCGGGTATCACTGATCATCATTCATCAACGGGCGATGCCTGCTCAGTTCATCAC
           agctaac  putative branch site (score: 2)