Sequence
atgc intronic sequence ATGC exonic sequenceTTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g47080.1 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggct--gattttttttattttttattcagtcatact-
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TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcacatgttttgctttttgctcaaaagaaattgatgttattag---ttgttagctaagggtggctccaagagttagcaagccagctcataacttgcca
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA20G30430.1 (Glycine max), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata-tccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttatt-cagtcatact
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TTCACCCGACACCAACCAGAGCCGAGGTATCCGATATTGCAATTGCTGTTCGAGAAGGTTCTGATGCAATAATGCTTTCTGGGGAAACTGCTCATGGAAAgtaagtaataattccatgcctcaaagtgtccaattaccttggcaggtgatgttctcctatttgagtt--cttacaaaggacaggaaatatcacaatcaaatt
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA16G28980.2 (Glycine max), 5'ss of exon 8
--------------------------------------------------------------------------TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact
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AGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAGAGgtatcagatatagcaattgcagttcgtgaaggttctgatggaataatgttgtctggagaaacagctcatggaaagtaagtaa-atagttttcctgcgccta-------------------------------------------------------------------------
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA09G23150.1 (Glycine max), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact-
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TTCACCCAACTCCAACCAGAGCAGAGGTATCGGATATAGCAATTGCTGTTCGAGAAGGTTCTGATGGAATAATGTTGTCTGGAGAAACAGCTCATGGAAAgtaagtaaatagttttccttcccctatagtgtccaattattcagtcactttatattactagtagcatgtatatgactttt-tggcaaatctgggctttgaa
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA10G37210.1 (Glycine max), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata-tccttttcttatgcatagatgatcactcacatgatcaaaatt-taataactaaagtag-gctgattttttttattttttattcagtcatact
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TTCACCCAACACCAACCAGAGCCGAGGTATCCGATATTGCAATTGCTGTTCGAGAAGGTTCTGATGCAATAATGCTTTCTGGGGAAACTGCTCACGGAAAgtaagtaataattccatgccttgaagtgtcctattaccttggcaggcgatattctcatatttgagttcttacaaaggacaggaaaatcacaatcaaatgc---
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA16G28980.1 (Glycine max), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcataga-----tgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact
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TTCACCCAACTCCAACCAGAGCAGAGGTATCAGATATAGCAATTGCAGTTCGTGAAGGTTCTGATGGAATAATGTTGTCTGGAGAAACAGCTCATGGAAAgtaagtaa-atagttttcctgcgcctaaagcatccaattactttgaaaggctggtcttagaagtttgtgactggtaaggggaccattttaccactaagtcc----
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcata--gatgatcactcacatgatcaaaatttaataactaaagtaggc-tgattttt---tttattttttattcagtcatact
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TTCATCCAACTCCAACCCGGGCAGAGGTCTCAGACATTGCTATCGCTGTTAGAGAAGGTGCTGATGCGGTAATGCTTTCAGGAGAAACTGCTCACGGAAAgtaagtggcagtatcttttcatgtactctattgatttagcttataat-ggcattgaatgtttattatatgcatgaatctcaactttacttgatat-cag-------
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtca-tact-----
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TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagc----tctttctcttggagtttctagttccttaagatg--tagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 5'ss of exon 7
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtg-----atatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact
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CTCACCCTACGCCCACACGAGCAGAAGTCTCAGACATAGCCATCGCTGTCCGTGAAGGTGCGGATGCAATTATGCTTTCAGGGGAAACCGCTCATGGAAAgtaagcgcgattaaaccagtgcactatctctcgacagtttttttttctgcttgaagtaaatttttgtgtttcgaatatcgtattactgttgaggacgatc-----
upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 5'ss of exon 7
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcat-act-
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CTCACCCCACTCCCACACGAGCAGAGGTTTCAGACATAGCTATTGCCGTCCGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagt-acctttggaatttgttgatag-tcttctttaatatcatctaagctcatagcccagtaactgccaaaattttggggcatcaggcttatcgtcagtgMapped 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|58599601|gb|CK010129.1|CK010129EST: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAA GTTTCCTTTGAAAGCTGTTAAGGTCATGCATACT
genomic: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTTAAGGTCATGCATACT
EST:
gi|2309639|gb|C25794.1|C25794EST: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGGAACTGNACACGGAA- GTTTCCTTTGNAAGCTGTT
genomic: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTT
EST:
gi|58683676|gb|CK072363.1|CK072363EST: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAA GTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGAGAACTGA
genomic: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGAGAACTGA
EST:
gi|58668249|gb|CK056935.1|CK056935EST: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAA GTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGA
genomic: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGA
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:
52 (upstream exon),
67 (downstream exon)
Score:
34TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGAGAACTGAAGCCACTATGTCTGGTGGGGAAACACCGGCTAACCTTGGTCAGGTGTTC
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