Sequence
atgc intronic sequence ATGC exonic sequenceGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA09G37610.1 (Glycine max), 5'ss of exon 9
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacag-actgtctatggaccttaattagttctgaaagat--ttgcgtaagtttttctatcattcag---------------------------------------------------------------------
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GTTTGTGGATTTGATCTCTTGAGATGCGAGGGACGCTCCTATGTTTGTGACGTGAATGGATGGAGCTTTGTTAAAAACTCACACAAgtaatattttgtgatttattgttttggcattgttgcatggttcaaaatacatcaatagttattcactctgcttgtatctataattggaaaatcttatttacaactctttttgcatgatatctttttggtgaaatttttatcatttcttgtttgctacttctgaag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA18G49000.1 (Glycine max), 5'ss of exon 11
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaattt------attta--atcctagtgttcttttct--tacagactg--tctatggaccttaattagttctgaa---agatttgcgtaagtttttctatcattcag---------------------------------------------------------
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GTTTGTGGGTTTGATCTCTTGAGATGCGAGGGACGATCCTATGTTTGTGACGTGAATGGATGGAGCTTTGTTAAAAATTCACACAAgtaatattttgtgatttattgttttggcactgttatatggttcaaaatgcatcaatagttattcactctgcttgtatctataattggaaaagcttatttacaactctttttgcataatatctttatggtgaaattttcatcatttctcgtttgctacttctgaag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA13G05060.1 (Glycine max), 5'ss of exon 12
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaaga---tttg----cgtaagtttttctatcattcag
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GTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAAgtaaattttgtaattagatttttttggcattgctgttttaatagagtttgatattgagagagagagagagtttgaaaatgaagaagatattattattcaa
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA19G02260.1 (Glycine max), 5'ss of exon 9
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcag----------
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GTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAAgtaaattttgtaattagatttttttgtcagttctgttttgatatcggcagca--tggttc-aaaatactttaatagttattcattttctttatataaacagaa
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 12
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaattta----tttaatcctagtgttcttttcttacagactgtctatggaccttaattag--ttctgaaagatttgcgtaagtttttctatcattcag----------------------------------------------------------------------------
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GTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAAgtaagctagcatctgcatttttattttctttcttaaaatcatagttgtatttataggttaagtttctagaataaatgctgagatggtttttagactggcatgtttcgcctctttcttaactctctaaaagttgagtttcaattttaaagtattcacaaatctcttgcactgtaag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 5'ss of exon 12
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatc---ctagtgttcttttcttacagactgtctatggaccttaattagttctg---aaagatttgcgtaagtttttctatcattcag---
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GTTTGCGGTTTTGATCTCCTACGATCTGAGGGAAGTTCATATGTTTGTGACGTAAATGGATGGAGTTTTGTGAAGAACTCCTATAAgtgagacactaatctggacttctatttttcttctcagttctgcttattg-tttcagttatatcttcgcaaggaaaatcacaaatcattgtat-atttgctgc
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 11
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacagac-----------tgtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcag
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GTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAAgtaat--atttgttttttgtttctccattttaaatacccctgttactgtatttatgcatttgcattcactttgctgcatatg-gtttgcttttgcattgtagt-
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 5'ss of exon 11
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcag------------------------------------------------------
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GTGTGCGGGTTTGATTTACTCCGATCACAAGGCCGGTCATATGTTTGTGATGTTAATGGGTGGAGTTTCGTTAAGAACTCTTACAAgtgagtt-ttcattatttttactgcttttcta---agtatttatgtctttgtggtagtggaccaagtaatcttcttgctcttctagcactacatgatgctctggtcttgtgatactgagagactaaatttctctaccgcgatcccag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S70_284V6.1 (Physcomitrella patens), 5'ss of exon 11
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacagactgtctatggacct-taat--tagttctgaaagatttgcgt-----aagtttttctatcattcag-----------------------------------
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GTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAAgtaagtaaac-aatct--gtgcgattttttcacctaatattcatccctctgtaataccagattgaggaatttttctttcccaatgttctacgaggatctagtctattgatactgattatattagtgttgattccag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ07403 (Selaginella moellendorffii), 5'ss of exon 11
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcag
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GTGTGTGGTTTTGACCTCTTGCGATCTCAAGGGAGGTCTTATGTTTGCGATGTCAATGGATGGAGTTTTGTAAAAAACTCGTACAAgtaggcaatgttgtccatgt-taaacttgctgcaacttgctttcctag---------------------------------------------
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ19878 (Selaginella moellendorffii), 5'ss of exon 11
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcag
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GTGTGTGGTTTTGACCTCTTGCGATCTCAAGGGAGGTCTTATGTTTGCGATGTCAATGGATGGAGTTTTGTAAAAAACTCGTACAAgtaggcaatgttgtccatgt-taaacttgctgcaacttgctt-----tcttag----------------------------------------Mapped 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|29674285|gb|CB670560.1|CB670560EST: TCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA GTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAA
genomic: TCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatt ... tatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAA
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 |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC