Sequence
atgc intronic sequence ATGC exonic sequencegtttgttgagcatacaactggctaaattaatttgatggttatgggctaaggcacttcaatttctgacatttggtatggaatgttatttgtactgatatgccagGTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGAGGACCAAACCTATGATCTTAACTTCAAGGAAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g14450.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 10
gtttgttgagcatacaactggctaaattaatttgatggttatgggctaaggcacttcaatttctgacatttggtatggaatgttatttgtactgatatgccagGTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGA---GGACCAAACCTATGATCTTAACTTCAAGGAAGAG
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-------------------------gttgagttttcgtctactgagtctaatttatca--tcttaatatattatattgctgattaatt--tctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTATGATAACAAGGACAAAACCTATGACTTGAATTTTAAGGAAGAG
upper sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 10
gtttgttgagcatacaactggctaaattaatttgatggttatgggctaaggc-acttcaatttctgacatttggtatggaatgttatttgtactgatatgccagGTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGA---GGACCAAACCTATGATCTTAACTTCAAGGAAGAG
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-----------------------------gttgaatctttgtctactgaatctaatttagtatcttataac--atatggctgattagtt--tctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAG
upper sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 10
----gtttgttgagcatacaa--ctggctaaattaatttgatggttatgggctaaggcacttcaatttctgacatttggtatggaatgttatttgtactgatatgccagGTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGA---GGACCAAACCTATGATCTTAACTTCAAGGAAGAG
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gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttattatttttggttttacattcactgattattg-acttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGMapped 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|29678594|gb|CB674869.1|CB674869EST: TGAGCTTTTGAAGACTGCAATTGAAAAGGCTGGATACACTGGCAAG GTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGAGGACCAA
genomic: TGAGCTTTTGAAGACTGCAATTGAAAAGGCTGGATACACTGGCAAGgtttgttgag ... gatatgccagGTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGAGGACCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggcacttcaatttctgacatttggtatggaatgttatttgtactgatatgccagGTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGAGGACCAAACCTATGATCTTAACTTCAAGGAAGAG
tactgat putative branch site (score: 2)
aatgttattt 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 |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttgagcatacaactggctaaattaatttgatggttatgggctaaggcacttcaatttctgacatttggtatggaatgttatttgtactgatatgccagGTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGAGGACCAAACCTATGATCTTAACTTCAAGGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA