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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgctaatctatagcttccctagaggtgcagaaattcatttgtttgcattatatacatgaaatatactttattgggcttcaaagattggatttg...

Basic information

species Oryza sativa
transcript LOC_Os05g50970.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G412937_T01 (Zea mays), 5'ss of exon 8
GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgcta-atctatagcttccctaga-ggtgcagaaattcatttgtttgcattatatacatgaaatatactttattgggcttcaaagattggatttg-
|||||||||||| |||| || ||||||||||| ||| ||||||||||||||||||||||||||||| |||||||||||||||||  | ||  ||| ||  ||||   ||||  | | | |   ||  |  || |  |   |      | ||| ||  |  ||     | |||| |   
GAACAAGAAATAAATGAGGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTTCGAATGAGgttagtttgtgatatacatatctgacctatttggtggtgcagtcc---tgcatatatcacgtcttttgcgctttcttcatgagcatttttgtagtggagtaat

upper sequence: LOC_Os05g50970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G158818_T01 (Zea mays), 5'ss of exon 6
GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgcta-----atctatagcttccctagaggtgcagaaat-------tcatttgtttgcattatatacatgaaatatactttattgggcttcaaagattggatttg
|||||||||||| ||||||| ||||||||||| ||| |||||||||||||||||||||||||||||||||||||||||||||||  |     |||| |  | |   ||||||||||   ||       ||| ||  ||||  | | | ||||||  ||    |   |   ||| ||           
GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgtgatatacatctttgacctatttagaggtgcaatcatgcagatatcaatttattgcgctttcttcatgaa-catctgctggagtaattctaa-----------
















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|89163537|gb|CI100427.1|CI100427
EST:     AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
genomic: AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
EST: gi|88846730|gb|CI373498.1|CI373498
EST:     AGTTTCTTA-TTTAGCTAGTGATGGCCTGTGGGATCTGGTTCCGAATGAG                         GATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
genomic: AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
EST: gi|88969110|gb|CI099061.1|CI099061
EST:     AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
genomic: AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
EST: gi|88956076|gb|CI092364.1|CI092364
EST:     AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
genomic: AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
EST: gi|89181946|gb|CI113452.1|CI113452
EST:     AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
genomic: AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
EST: gi|25807722|gb|CA763683.1|CA763683
EST:     AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
genomic: AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
EST: gi|86259723|gb|CI065596.1|CI065596
EST:     AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
genomic: AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
EST: gi|58687048|gb|CK075735.1|CK075735
EST:     AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
genomic: AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
EST: gi|12623064|gb|AU173277.1|AU173277
EST:     AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG
genomic: AGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGG

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: 73 (upstream exon), 29 (downstream exon)
Score: 7

GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgc ... gttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGGAAGCTGACAGAGACTGCATTTTCCCGAGGGAGTGGTGACAATATCACAT




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