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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGAACTTGTTCACCGAGTTGAGAAGGATCTCATTAGTATTATGCATGGGGTATCTATCAgtatccttttggtttttgttgcttgcttatgttccactcacatgttgccttaattacaattgactcaacatcattttcatcatagtttgttccgttgaaa...

Basic information

species Oryza sativa
transcript LOC_Os05g28010.1
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28010.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G147614_T03 (Zea mays), 5'ss of exon 3
GCCGAACTTGTTCACCGAGTTGAGAAGGATCTCATTAGTATTATGCATGGGGTATCTATCAgtatccttttggtttttgttgcttgcttatgttccactcacatgttgccttaattacaattgactcaacatcattttcatcatagtttgttccgttgaaa--
|| || || ||| ||| |||||||||| |||| || ||||| |||||||| |||||| |||||||||||||| ||||  | || |||   |     | |   |   ||  ||   | | |    ||    |  | |   || |||||    |   ||   |  
GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGAGTATCTGTCAgtatccttttg-ttttcttcgcctgccacttgctaaatggtagcatgtgttgtattctagcagctgggaaaaaatggtat-atagtactcttttttactatt
















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|86536687|gb|CI176893.1|CI176893
EST:     AGAAGGATCTCATTAGTATTATGCATGGGGTATCTATCA                         ACCAGAATGCCAGTGCAATTCTAAGGGCAGGAGAAGGTGGCGATCGTAAGA
genomic: AGAAGGATCTCATTAGTATTATGCATGGGGTATCTATCAgtatcctttt ... cggttgatagACCAGAATGCCAGTGCAATTCTAAGGGCAGGAGAAGGTGGCGATCGTAAGA
EST: gi|88223765|gb|CI223614.1|CI223614
EST:     TCACCGAGTTGAGAAGGATCTCATTAGTATTATGCATGGGGTATCTATCA                         ACCAGAATGCCAGTGCAATTCTAAGGGCAGGAGAAGGTGGCGATCGTAAGA
genomic: TCACCGAGTTGAGAAGGATCTCATTAGTATTATGCATGGGGTATCTATCAgtatcctttt ... cggttgatagACCAGAATGCCAGTGCAATTCTAAGGGCAGGAGAAGGTGGCGATCGTAAGA
EST: gi|88977292|gb|CI025029.1|CI025029
EST:     TCACCGAGTTGAGAAGGATCTCATTAGTATTATGCATGGGGTATCTATCA                         ACCAGAATGCCAGTGCAATTCTAAGGGCAGGAGAAGGTGGCGATCGTAAGA
genomic: TCACCGAGTTGAGAAGGATCTCATTAGTATTATGCATGGGGTATCTATCAgtatcctttt ... cggttgatagACCAGAATGCCAGTGCAATTCTAAGGGCAGGAGAAGGTGGCGATCGTAAGA

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: 62 (upstream exon), 62 (downstream exon)
Score: 13

GCCGAACTTGTTCACCGAGTTGAGAAGGATCTCATTAGTATTATGCATGGGGTATCTATCAgtatcctttt ... cggttgatagACCAGAATGCCAGTGCAATTCTAAGGGCAGGAGAAGGTGGCGATCGTAAGAAAGCGGGACCAGCTCCAGCAACCAAACCTAATGTCAAACAACCTGCTGC




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