Sequence
atgc intronic sequence ATGC exonic sequencegttataatgcacaatgaggaggatatttacatattcattcattgttattgaagtgcacagaaatcatggtattgttgtcatttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCTCGCAGAATTGATAATCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g21820.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G880102_T01 (Zea mays), 3'ss of exon 2
gttataatgcacaatgaggaggatatttacatattcattcattgttattgaagtgcacagaaatcatggtattgttgtcatttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCTCGCAGAATTGATAATCAG
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gttatatggcattataaaagaaacattgatagctctatctgttgctgttca-gtgtagcgtagtgttcacgtgatcaat-tttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG
upper sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 14
gttataatgcacaatgaggaggatatttacatattcattcattgttattgaagtgcacagaaatcatggtattgttgtcatttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCTCGCAGAATTGATAATCAG
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gtcaatttgtttcttgactagtacttcccc----tcatacattgctgttga----tacattattaatg--atcattatgactg---cagGTTGTGGAAGCTGGCGGACTACATGTAGTAGGCACAGAGCGTCATGAATCACGTCGAATTGATAATCAG
upper sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA02G01060.2 (Glycine max), 3'ss of exon 14
gttataatgcacaatgaggaggatatttacatattcattcattgttattgaagtgcacagaaatcatggtattgttgtcatttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCTCGCAGAATTGATAATCAG
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gtcaatttgtttcttgacta--atacttccct--tcatacattgctgttgatgc--------attatta-atgatcattatgactgcagGTTGTGGAAGCTGGTGGACTACATGTAGTAGGCACAGAGCGTCATGAATCACGTCGAATTGATAATCAG
upper sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 14
----gttataatgcacaatgaggaggatatttacatattcattcattgttattgaagtgcacagaaatcatggtattgttgtcatttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCTCGCAGAATTGATAATCAG
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gttagttcaattttccaaacaccagtttgaacggaaggttgtcaatttatat-aaactgta----atttctgttatttcta-cattcctacagGTTGTGTCAGCAGGTGGACTTCATGTGGTGGGGACAGAACGGCATGAATCTCGTCGAATTGACAATCAGMapped 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|29615683|gb|CB620695.1|CB620695EST: TGAAGATAATGGATGAATATAAGGTTTACACAGAGGAGGAAAAGAAG--- -TCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCT
genomic: TGAAGATAATGGATGAATATAAGGTTTACACAGAGGAGGAAAAGAAGCAGgttataatgc ... atttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCT
EST:
gi|66928365|gb|CX115213.1|CX115213EST: TGAAGATAATGGATGAATATAAGG-TTACACAGAGGAGGAAAAGAAGCAG GTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCT
genomic: TGAAGATAATGGATGAATATAAGGTTTACACAGAGGAGGAAAAGAAGCAGgttataatgc ... atttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCT
EST:
gi|58655936|gb|CK044616.1|CK044616EST: GAAGATAATGGATGAATATAAGGTTTCACACAGAGGAGGAAAAGAAGCAG GTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGCAACGTCATGAATC
genomic: GAAGATAATGGATGAATATAAGGTTT-ACACAGAGGAGGAAAAGAAGCAGgttataatgc ... atttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAG-AACGTCATGAATC
EST:
gi|58691936|gb|CK080623.1|CK080623EST: TGAAGATAATGGATGAATATAAGGTTTACACAGAGGAGGAAAAGAAGCAG GTCATTTCAGCAGGTGGACTTCATGTA
genomic: TGAAGATAATGGATGAATATAAGGTTTACACAGAGGAGGAAAAGAAGCAGgttataatgc ... atttgttcagGTCATTTCAGCAGGTGGACTTCATGTA
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:
56 (upstream exon),
45 (downstream exon)
Score:
10GGACCAACTCGTGATGAAGTAATTGCAAATCTGAGAAGTGCATTCATGAAGATAATGGATGAATATAAGGTTTACACAGAGGAGGAAAAGAAGCAGgttataatgc ... atttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCTCGCAGAATTGATAATCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattcattgttattgaagtgcacagaaatcatggtattgttgtcatttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCTCGCAGAATTGATAATCAG
tttgttc CT-rich tract
attgttatt TA-rich tract