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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGCACATAGATGGACAAAAACGCTGGATTGGTAACAGTACTTTTGCTGATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatcagctttagattcgatctttggaattgaagcataaatgactcagctagtgttgctatctaataattcatttggctccttgtag

Basic information

species Oryza sativa
transcript LOC_Os01g06600.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G862219_T02 (Zea mays), 5'ss of exon 8
GGTGGCACATAGATGGACAAAAACGCTGGATTGGTAACAGTACTTTTGCTGATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatca-gctttagat-----tcgatctttggaattgaagcataaatgactcagctagtgttgct----atctaataattcatttggct-ccttgtag----------------------------------------------------------------
|||||||||||||||| |||||||||||||| |||||||||||||| || ||||||||||| || ||||| |||||||| | ||| |||| ||||||||||||| |||| || || || | | ||| | || || | |||| |||| || || |||| | ||| | | || | |
GGTGGCACATAGATGGTCAAAAACGCTGGATCGGTAACAGTACTTTCGCCGATGTGCTCGTCGTGTTAGCCAGGAATGCAGACACACAACAGCTAAATGGgtaaatcatcttgccttggaccaccattgtacttaagcatccaaccgattatgaacacgctatattttcttccaatctgttgtctcaagcgccaaccctatcttcgtgttataaagtcagtttccactgacgagttctgcgttgccttgttttctcgcttccaccag
















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|29676104|gb|CB672379.1|CB672379
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTNGAA-GCTACAAAGATTGA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTT-GAAAGCTACAAAGATTGA
EST: gi|29666427|gb|CB662702.1|CB662702
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|29666426|gb|CB662701.1|CB662701
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|14713699|gb|AU197670.1|AU197670
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|33683998|gb|CF312237.1|CF312237
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTG-GNAGGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAG
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTG-A-GGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAG
EST: gi|88344179|gb|CI654609.1|CI654609
EST:     TCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: TCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|13165132|gb|AU173929.1|AU173929
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|56157778|gb|C26441.2|C26441
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|29666428|gb|CB662703.1|CB662703
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|29678764|gb|CB675039.1|CB675039
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA

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: 60 (upstream exon), 66 (downstream exon)
Score: 30

GGTGGCACATAGATGGACAAAAACGCTGGATTGGTAACAGTACTTTTGCTGATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAACAAAATTGGTCTCAGAATGGTTCAGAACGGTGATATAGTTTTTAATAAA




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