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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgttttag

Basic information

species Oryza sativa
transcript LOC_Os05g06430.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AC199571.3_FGT004 (Zea mays), 5'ss of exon 3
GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttag
|||||||||||||||||||||||||||||||||||| | || ||| ||| || |||| || |||| | | || | |||| | | ||| ||| || ||||| |||||
GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagagtat-----tagcttgaaaatttccaaattattgca--gcggtcttcattttttttgtggact-gaacatgtacttgaatttag

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G159369_T01 (Zea mays), 5'ss of exon 6
GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttag
|||||||||||||||||||||||||||||||||||| | || ||| ||| || |||| || |||| | | || | |||| | | ||| ||| || |||| |||||
GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagagtat-----tagcttgaaaatttccaaattattgca--gcggtcttcattttttttgtggact-gaacatgtacttaaatttag

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G170845_T01 (Zea mays), 5'ss of exon 2
GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttag
||||||||||| |||||||||||||||||||||||| | || ||| ||| || |||| || |||| | | ||| |||| | | ||| ||| || ||||| |||||
GTGTGGTCACTACAAGCATCTTGCTCCGgttagtagagtat-----tagcttgaaaatttccaaattattgcagcgg---tcttcatttttttgtggact-gaacatgtacttgaatttag

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|58662435|gb|CK051121.1|CK051121
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCT
EST: gi|58675064|gb|CK063751.1|CK063751
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|58684543|gb|CK073230.1|CK073230
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGG
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGG
EST: gi|27577315|gb|CB000010.1|CB000010
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|58653948|gb|CK042628.1|CK042628
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTGAGTGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTAT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTA-TGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTAT
EST: gi|58659841|gb|CK048521.1|CK048521
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|58690891|gb|CK079578.1|CK079578
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|12622813|gb|AU173026.1|AU173026
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT

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: 28 (upstream exon), 69 (downstream exon)
Score: 50

GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA




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