Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgcttgaaatcttgcatctgatttttgtgtaaccatgtgtccattaatcaaataaaaatatctgtctcctgttcccagtctttccatttacattttttaaatatataatcttgttcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATCTACCACACATACTTTGGAGTTGCAGGTGTTTATATTTCTAACCGCAGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g40140.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g40140.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G124557_T02 (Zea mays), 3'ss of exon 8
gtaaatgcttga--aatcttgcatctgatttttgtgtaacc-atgtgtccattaatcaaataaaaatatctgtctcctgttcccagtctttccatttacattttttaaatatataatcttgttcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATCTACCACACATACTTTGGAGTTGCAGGTGTTTATATTTCTAACCGCAGTT
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gtaactgttctattattcccaccactgccatttgcgtaacccgtatgtcccttgacttataacaagta-------ctggttccaactcttctcattca---------------------tgttgatcggcagGACAAAGAGAACGGCGGCATTTCAGATAGACCAGATAATGCAGTCGATATCTATCACACGTACTTTGGAATTGCAG------------------------
upper sequence: LOC_Os08g40140.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv15s0024g00080.t01 (Vitis vinifera), 3'ss of exon 8
gtaaatgcttgaaatcttgcatctgatttttgtgtaaccatgtgtccattaa-tcaaataaaaatatctgtctcctgttcccagtct-ttccatttacat---tttttaaatatataatcttgttcattg-gtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATCTACCACACATACTTTGGAGTTGCAGGTGTTTATATTTCTAACCGCAGTT
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----------gtcagttctaaactaagtgagctgttatttagattcagataacttacacagaaat-cctagcccttatttagatttagtttaacttaaaaaggtggttaaaattctcagtttgtggaaaatgcagGATAAGGAAAATGGAGGAATTTCAGATAGGCCTGACGATGCTGTTGATGTCTTCCATACATACTTTGGAGTCGCTG------------------------
upper sequence: LOC_Os08g40140.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 8
gtaaatgcttgaaatcttgcatctgatttttgtgtaaccatgtgtccattaatcaaataaaaatatc---tgtctcctgttcccagtctttccatttacattttttaaat-atataatcttgttcattg-------gtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATCTACCACACATACTTTGGAGTTGCAGGTGTTTATATTTCTAACCGCAGTT
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gtcagttctaaactaaatgaactgttacttagtttcagtttaatttcatagaaaaacctagaattttgcaccttacctctctgctgctttttcatttacaaggtaaatatgatcctcagttattggctgaaaaattgcagGATAGGGAAAATGGAGGAATTTCTGATAGACCTGATGATGCCGTGGATGTCTTCCATACATACTTTGGAGTCGCAG------------------------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|58681560|gb|CK070247.1|CK070247EST: TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG GACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
genomic: TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgctt ... tcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
EST:
gi|33381466|gb|CF196809.1|CF196809EST: TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG GACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
genomic: TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgctt ... tcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcccagtctttccatttacattttttaaatatataatcttgttcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATCTACCACACATACTTTGGAGTTGCAGGTGTTTATATTTCTAACCGCAGTT
tcttgttc CT-rich tract
atttacattttttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgcttgaaatcttgcatctgatttttgtgtaaccatgtgtccattaatcaaataaaaatatctgtctcctgttcccagtctttccatttacattttttaaatatataatcttgttcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATCTACCACACATACTTTGGAGTTGCAGGTGTTTATATTTCTAACCGCAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG