Sequence
atgc intronic sequence ATGC exonic sequenceTGATGTTTACAGCTTTGGCGTTGTCTTCCTTGAACTCATTACAGGACGTAAAGCCATTGATCACACCCAACCTGCAGGGGAGCAAAATCTTGTTGCATGGgtaggttcatccttttatttttaagaatgtgtgggctcaactgtactaaattatctcccttcctttgggtgtagaggggatgttctgtttcaatttcatcatgatgtgaagtgtcttatccttataatttgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os07g47270.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g47270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G177061_T01 (Zea mays), 5'ss of exon 4
TGATGTTTACAGCTTTGGCGTTGTCTTCCTTGAACTCATTACAGGACGTAAAGCCATTGATCACACCCAACCTGCAGGGGAGCAAAATCTTGTTGCATGGgtaggttcatccttttatttttaagaatgtgtgggctcaactgtactaaattatctcccttcctttgggtgtagaggggatgttctgtttcaatttcatcatg-atgtgaagtgtct--tatccttataatttgcag
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TGACGTTTACAGCTTTGGTGTTGTGTTCCTTGAACTTATTACAGGCCGCAAAGCAATCGATCACACCCAGCCTTCAGGGGAGCAAAACCTTGTCGCATGGgtaggttta------------------------------actgcactgagttat-tctattcatttggtttagggaggcaaaggccatgtta-cttcttcacacgtgttaagtgtctgttctccacaaaatttgcag
upper sequence: LOC_Os07g47270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G048210_T02 (Zea mays), 5'ss of exon 4
TGATGTTTACAGCTTTGGCGTTGTCTTCCTTGAACTCATTACAGGACGTAAAGCCATTGATCACACCCAACCTGCAGGGGAGCAAAATCTTGTTGCATGGgtaggttcatccttttatttttaagaatgtgtgggctcaactgtactaaattatctcccttcctttgggtgtagaggg--gatgttctgtttcaatttcatcatgatgtgaagtgtct--tatccttataatttgcag
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TGACGTTTACAGCTTTGGTGTTGTGTTCCTTGAACTTATTACAGGCCGCAAAGCAATCGATCACACCCAGCCTTCAGGGGAGCAAAACCTTGTCGCATGGgtaggttta------------------------------actgcactgagttat-tctattcatttggtttagggaggcaaaggccctgttacttcttca-cacg-tgttaagtgtctgttctccacaaaatttgcag
upper sequence: LOC_Os07g47270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA15G10360.1 (Glycine max), 5'ss of exon 4
TGATGTTTACAGCTTTGGCGTTGTCTTCCTTGAACTCATTACAGGACGTAAAGCCATTGATCACACCCAACCTGCAGGGGAGCAAAATCTTGTTGCATGGgtaggt-tcatccttttatttttaagaatgtgtgggctcaactgtactaaattatctcccttcctttgggtgtagaggggatgttctgtttcaatttcatcatgatgtgaagtgtcttatccttataatttgcag
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TGATGTCTATAGTTTTGGTGTTGTCTTCCTTGAACTCATTACTGGGCGCAAGGCTATTGATAACACCCGTGCACATGGAGAGCATAATCTTGTTGCATGGgtaagtatctctcacttgatcatccttgtgttatgtcatgtttgtataaacttctccataattcgaagaaaatactcggcaaatgaaaaaaaaacttttc-----------------------------------
upper sequence: LOC_Os07g47270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv05s0020g01770.t01 (Vitis vinifera), 5'ss of exon 4
TGATGTTTACAGCTTTGGCGTTGTCTTCCTTGAACTCATTACAGGACGTAAAGCCATTGATCACACCCAACCTGCAGGGGAGCAAAATCTTGTTGCATGGgtaggttcatcctttt---atttttaagaatgtgtgggctcaactgtactaaattatctcccttcctttgggtgtagaggggatgttc---tgtttcaatttcatcatgatgtgaagtgtct------tatccttataatttgcag---------------
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TGATGTTTATAGTTTTGGTGTCGTTTTCCTTGAACTTATCACAGGGCGTAAAGCTATTGATAACAATCGGGCTGCTGGTGAGCATAACCTTGTTGCATGGgtaagtgtttcttttctgcattttcccaatttattggcttttattgtact---ttttctttttaacaatttccatgaaggtgatgcttgcatatactcaatttattattatacaagatttctcttctttttccctttattttgtgggatatgaatctgtagMapped 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|27920800|gb|CB096608.1|CB096608EST: AAGCCATTGATCACACCCAGCCTGCAGGGGAGCAAAATCTTGTTGCATGG GCTCGTCCACTGTTTAGAGACCGAAGGAAGTTCTGCCAAATGGCCGATCCA
genomic: AAGCCATTGATCACACCCAACCTGCAGGGGAGCAAAATCTTGTTGCATGGgtaggttcat ... taatttgcagGCTCGTCCACTGTTTAGAGACCGAAGGAAGTTCTGCCAAATGGCCGATCCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGATGTTTACAGCTTTGGCGTTGTCTTCCTTGAACTCATTACAGGACGTAAAGCCATTGATCACACCCAACCTGCAGGGGAGCAAAATCTTGTTGCATGGgtaggttcatccttttatttttaagaatgtgtgggctcaactgtactaaattatctcccttcctttgggtgtagaggggatgttctgtttcaatttcatcatgatgtgaagtgtcttatccttataatttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA