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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTCTCCGCTCGACGAGGCGCGCCTCCGCTTGGCCCGCCTCGCCGACAAGTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgatagatggatgggtaccactctaggtttcggtggatgcgtttgatttgatctgacaaggatggattgcgtgtgcgtgtgtgtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g61710.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G458549_T02 (Zea mays), 5'ss of exon 1
GGCTCTCCGCTCGACGAGGCGCGCCTCCGCTTGGCCCGCCTCGCCGACAAGTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgatagatggat----gggtaccactctaggtttcggtggatgcgtttgatttgatctgacaaggatgg-attgcgtgtgcgtgtgtgtgtgcag
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GGCGCGCAGCTCGACGAGTCGCGCCTCCGCTTCGCCCGCCTCGGGGACCGCTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgcctccgtcccctggactgcgtgtgtgtgcttgagctgaggc-tgagtctgagtctggccccgccggcgccgcgggc-tggctgttgctgcag
















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|29681135|gb|CB677410.1|CB677410
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|29681133|gb|CB677408.1|CB677408
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|88432228|gb|CI565261.1|CI565261
EST:     GTTCCAAGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACCAGGGGTACTCGGCGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|88427193|gb|CI586741.1|CI586741
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|58611982|gb|CK039694.1|CK039694
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|88452999|gb|CI574546.1|CI574546
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|13896515|gb|AU182851.1|AU182851
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|88362762|gb|CI608911.1|CI608911
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|58695416|gb|CK084103.1|CK084103
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|88580201|gb|CI692202.1|CI692202
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
EST: gi|40493179|gb|BX900637.1|BX900637
EST:     GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGG                         GGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT
genomic: GTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGT

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: 45 (upstream exon), 68 (downstream exon)
Score: 5

GGCTCTCCGCTCGACGAGGCGCGCCTCCGCTTGGCCCGCCTCGCCGACAAGTTCCACGCCGTCTACGCCGCGCGCCCCGCGCTCTTCGCCCGCTCTCCGGgtaggttgat ... gtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGTTGCCCATGGCCATCCGGCAGGACATGATCGTCGCCATCAGGAGGGCAGA




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