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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgttatagtgtaattcatttctcgtcatgtactttcaattgtcaaatgtcttgtaccgaactttcacgaaagtagaagcatgcatgttaagcactcc...

Basic information

species Oryza sativa
transcript LOC_Os06g39640.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 5
AAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgtt-atagtgtaattcatttctcgtcatgtactttcaattgtcaaatgtcttgtaccgaactttcacgaaagtagaagcatgcatgttaagcactcc----
| || || |||||||| |||||||| ||||| |||||||| ||||| ||||| ||||||||||| || ||||| |||||||| |||||||||||||||||||||||| | | | | | | |||| |  |  |         | ||| |  |||| | |  |    ||  |   | |  | |||  | || | | | ||       
AGGCATTACGGGGCGTAAAAGTTGAGGTCACGCACCGGGGGAATGTAAGGCGCAAGTATCGCATATCTGGGCTCACAACACAGCCAACTCATGAACTGATgtatgtttagattctgaatgatttttactagttcctaaagtactgttac-tgtcatctctc---tttcgatacatggtgtagcccg-atttgacgaacataaaaa

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G079080_T01 (Zea mays), 5'ss of exon 6
AAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgtt-atagtgtaattcattt---ctcgtcatgtactttcaattgtcaa-atgtcttgtaccgaactttcacgaaagtagaagcatgcatgttaagcactcc
| || |||||||| || |||||||| |||||||||||||| |||||  |||| ||||||||||||||||| || |||||||| |||||||||||| ||||||||||| | | | | | | ||||   || ||     |  | |  ||||    || |||  | ||      |   | |  ||||    |   || |  |      
AGGCATTGCGGGGTGTAAAAGTTGAGGTCACTCACCGGGGGAATGTACGGCGCAAGTATCGCATTTCAGGCCTCACAACACAGCCAACTCATGAATTGATgtatgtttagattctgaatgatttttactagttcctgaagtgctgttgttgtcatctctcttcccag----tggtggatctagatttttttttggtgtgggggg-
















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|29667767|gb|CB664042.1|CB664042
EST:     CAACACAACCACCTCATGAACTGAT                         TTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCCA
genomic: CAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA
EST: gi|58664728|gb|CK053414.1|CK053414
EST:     CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGAT                         TTTCCCAATCGATGACCAAATGAACATGAAATCTGCCGTAGAGTATTTCAA
genomic: CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA
EST: gi|29636940|gb|CB641949.1|CB641949
EST:     CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGAT                         TTTCCCA-TCGATGACCAAATGAACATG
genomic: CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATG
EST: gi|58662235|gb|CK050915.1|CK050915
EST:     TGACAACACAACCAACTCATGAACTGAT                         TTTGCGAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA
genomic: TGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA
EST: gi|29636971|gb|CB641980.1|CB641980
EST:     CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGAT                         TTTCC-AATCGATGACCAA-TGAACATGAAATCTGTCGTAGAGTATTTCAA
genomic: CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA

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: 71 (upstream exon), 70 (downstream exon)
Score: 10

AAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG




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