Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctagtgtgcagaggatttgctctgtacatattatagattacattttggatgaattacgatctttattactgggtgcttgttggtcttattcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g19850.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G439885_T01 (Zea mays), 3'ss of exon 8
------gtaagtctag--tgtgcagaggatttgctctgtacatattatagattacattt--tggatgaatta-cgatcttta----ttactgggtgcttgttggtcttattcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAG
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gtatgtgcatttatagattatgcagcagaatatatgtcattttattgtacattacatgtgtcagactcattagtgagttacaacatctgctgattgcttgttggacccattctc--------agAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTATAGAG
upper sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 10
------gtaagtctag--tgtgcagaggatttgctc-------tgtacatattatagattacattt-tggatgaattacgatctttattactgggtgcttgttggtcttattcttg--cagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAG
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gtatgtgcatttatagattatgcagcagactatgtcattttattgtacattacatgtgtcagactcatcagtgagttacaacatct---gctgattgcttgttggacccattattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG
upper sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ09242 (Selaginella moellendorffii), 3'ss of exon 11
gtaagtctagtgtgcagaggatttgctctgtacatattatagattacattttggatgaattacgatctttattactgggtgcttgttggtcttattcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAG
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----------------------------------------------------gtaattctaggaaaatccaccgcccgctggtt-ttaacctc-ttgctgcagATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGTTTACTTTTCCAACACAGGGTCCGTTCATATCGAG
upper sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ07136 (Selaginella moellendorffii), 3'ss of exon 11
gtaagtctagtgtgcagaggatttgctctgtacatattatagattacattttggatgaattacgatctttattactgggtgcttgttggtcttattcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAG
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----------------------------------------------------gtaatactaggaaaatccaccgcccgctggtt-ttaacctc-ttgctgcagATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGTTTACTTTTCCAACACAGGGTCCGTTCATATCGAGMapped 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|29626606|gb|CB631617.1|CB631617EST: AAACCTCTGGACATGCTGCAAACTACAAGGAGAATATGTTTGTTTTTGAG ATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGC
genomic: AAACCTCTGGACATGCTGCAAACTACAAGGAGAATATGTTTGTTTTTGAGgtaagtctag ... attcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGC
EST:
gi|88376802|gb|CI639127.1|CI639127EST: ATGCTGCAAACTACAAGGAGAATATGTTTGTTTTTGAG ATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGC
genomic: ATGCTGCAAACTACAAGGAGAATATGTTTGTTTTTGAGgtaagtctag ... attcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGC
EST:
gi|29686166|gb|CB682441.1|CB682441EST: AAACCTCTGGACATGCTGCAAACTACAAGGAGAATATGTTTGTTTTTGAG ATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGC
genomic: AAACCTCTGGACATGCTGCAAACTACAAGGAGAATATGTTTGTTTTTGAGgtaagtctag ... attcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGC
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:
65 (upstream exon),
72 (downstream exon)
Score:
30GTTTTGAGCCCAAATATTTACAATATGCAACTCTGGGAAACCTCTGGACATGCTGCAAACTACAAGGAGAATATGTTTGTTTTTGAGgtaagtctag ... attcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggatgaattacgatctttattactgggtgcttgttggtcttattcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAG
tcttattctt CT-rich tract
atctttatta TA-rich tract