Sequence
atgc intronic sequence ATGC exonic sequencegtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g01630.6 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g01630.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 7
gtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAG
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--gtatggttcttgaaccagagttaacatggcatg-taaaataccactattgagattcttatgtgaacattgtcatctaaat-gtatttcatatttcatatga--agGATAAAGCCACTGTTGAAATGGAATGTATGGAGGAAGGTTTTCTGGCCAAGATAATCCGTGGGGATGGGGCAAAAGAAATTAAAGTTGGTGAG
upper sequence: LOC_Os06g01630.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 7
gtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAG
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--gtatggttcttgaaccagagttaacatggcatg-taaaataccactattaagattcttatgtgaacattgtcatctaaat-gtatttcatatttcatatga--agGATAAAGCCACTGTTGAAATGGAATGTATGGAGGAAGGTTATCTGGCCAAGATAATCCGCGGGGATGGGGCAAAAGAAATTAAAGTTGGTGAG
upper sequence: LOC_Os06g01630.6 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 7
gtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatt--taattaaggagcaacagcagcttaaccatcaatcacatttatggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAG
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gtagggt-ccttgtagctgtcc---------cctttttcaaatttactagttgatcaatgatccaggtttatgtaaagtcatcctgtcaaatttttaatcattttatagGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG
upper sequence: LOC_Os06g01630.6 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 8
-----------gtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactt--tatttaattaaggagcaacagcagc-ttaaccatcaatcacatttatggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAG
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gtagggcccttgtactctgagtctgttggttaaattctctcaattaatggagcactccggttaggtgctttactcatctggaaaactgacgtttacctttcattgaattgatatttgt-agGATAAAGCAACAGTTGAGATGGAATGCATGGAAGAAGGATACCTTGCTAAGATAATTCAAGGAGATGGGGCAAAAGAAATTAAAGTTGGTGAGMapped 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|58669994|gb|CK058680.1|CK058680EST: AAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT GATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAA
genomic: AAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACTgtaagttact ... tggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAG
gcttaac putative branch site (score: 3)
acatttat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAG
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