Sequence
atgc intronic sequence ATGC exonic sequencegttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56580.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 9
gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
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gtttctttttgccaaatagtgtgtttt--tcat-ttcctttcaa---tacactggccttac--tttgccctttccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
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gtt--tgtatattttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctt--tttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 9
----gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
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gtattttgattggtgtatgttatctttcctactattgttggtatatatattttgctcacatctttgttacgcttcatat---gcagAGGAACAATAAGGTATGCAAGTTGCCATGCACATCTTGGTCGTACAGGAAGTCGGAGGGATGATCTGGAGTCATTGGCTTATACATTAATATTTCTGATG
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 9
----gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
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gtttgtggatttctggatgttcataaaaaaaaaaaaaaatgctttgacctttataatatattaatc-----tcctcttttgg-cagGGGAACAATACGGTATGCAAGTGTGCATGCACATTTAGGACGGACAGGAAGTAGAAGGGATGATCTCGAGTCACTAGCTTACACATTAATATTTCTCATTMapped 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|29629024|gb|CB634035.1|CB634035EST: ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG GGGTACAATAAGATATGCT
genomic: ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaattttt ... ttttggacagGGGTACAATAAGATATGCT
EST:
gi|29623307|gb|CB628318.1|CB628318EST: ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG GGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAG
genomic: ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaattttt ... ttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAG
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:
62 (upstream exon),
75 (downstream exon)
Score:
49CATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaattttt ... ttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
tcatctgccttctttt CT-rich tract
atatttatcat TA-rich tract