Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttttacttgtttcttttgatttagtttctttgaaaatggtactactgagtttttttcccctgaaagtactcatatggagtgttttgaataacctctttacttttgcttgactcctcagGTTTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g46570.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G101181_T02 (Zea mays), 3'ss of exon 6
gtatgcttttacttgtttcttttgatttagt----ttctttgaaaatggtactactgagtttttttcccctgaaagtactcatatggagtgttttgaataacctctttacttttgcttgactcctcagGTTTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTA
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gtaaactctgg-ttgtttatgataattcaatgctgccttttgataattgaagttatga-----ttgaccatgaaagta---aaaaaaaa-----tgaaca------taactgttgtttg-tttatcagGTTTGAACCTGACATGCTTGCATTTTCTGGCTGTTACTACGGTGGCGGTGAAAAAGAAAGAAAGGAATTGGGTGAAATTAGGAAACGATGGGATACATTA
upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 6
gtatgcttttacttgtttcttttgatttagtttctttgaaaatggtactactgagtttttttcccctgaaagtactcatatggagtgttttgaataacctctttacttttgcttgactcct--cagGTTTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTA
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-------------------ttccaacacaatttaat-aatagctgtgtggc--aggtttgcgctatagccattgcttctataaaatgtt---aaggatctcataattcataat-gattcatggcagGTTTGAGTCAGATATGCTGGCATTTTCAGGTTGTTATTTTGGTGGTGGTGAAAAAGAAAGACGCGAGCTTGGTGAAATCAGGAAAAGGTGGACAACGTTG
upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G15170.1 (Glycine max), 3'ss of exon 6
gtatgcttttacttgtttcttttgatttagtttctttgaaaatggtactactgagtttttttcccctgaaagtactcatatggagtgttttgaataacctctttacttttgcttgactcct--cagGTTTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTA
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------------------aacgcaatttaataa-tagcaatgtggcaggtttgagctata---gccagccattgcctctataaaatgtt---aaggatctcataagtcataat-gattcatggcagGTTCGAGCCAGATATGCTGGCATTTTCAGGTTGTTATTTTGGTGGTGGTGAAAAAGAAAGACGCGAGCTAGGTGAAATCAGGAAAAGGTGGACAACACTG
upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 6
-------gtatgcttttacttgtttcttttgatttagtttctttgaaaatggtactactgagtttttttcccctgaaagtactcatatggagtgttttgaataacctctttacttttgcttgact---cctcagGTTTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTA
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gtttattaagtttctttaacaacccatattagattgtgttccctgatttttgc-ttaatagtctcaatcatgttataagca-tgacatcttcatctccatgttatttatgtaaccatacttttacgaactgcagATTTGAGCCTGACATGCTAGCCTTTTCTGGTTGTGACTTTGGTGGGGGTGAAAAAGAGAGAGCTGAGCTAGCAGAAATAAGAAAACGATGGGACACATTG
upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0229g00100.t01 (Vitis vinifera), 3'ss of exon 6
gtatgcttttacttgtttcttttgatttagtttctttgaaaatggtactactgagtttttt----tcccctgaaagtactcatatggagtgtt--ttgaataacctctttacttttgcttgactcct---cagGTTTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTA
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----------gtttgtaccttcca--ccaaaaaaggggagaatggaactgagaacttatttaaaattcacaaaaaaaattgaaataatgctttcattttttgggttcatgatatgaaaccattttcatgacagGTTTGAAGCTGATATGCTAGCATTTTCTGGATGCTACTATGGTGGGGGTGAAAAGGAGAGATATGAGCTTGGTGAAATAAGGAAACGCTGGGCAACATTAMapped 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|33677331|gb|CF305570.1|CF305570EST: GTGCGCAAGCTGAGGAGCATGAGCTCACGATACGTTGCCGTTCACTTGAG GTTTGAGCCTGACATGCTTGCATT
genomic: GTGCGCAAGCTGAGGAGCATGAGCTCACGATACGTTGCCGTTCACTTGAGgtatgctttt ... gactcctcagGTTTGAGCCTGACATGCTTGCATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtactcatatggagtgttttgaataacctctttacttttgcttgactcctcagGTTTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTA
ctcctc CT-rich tract
ttttgaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttttacttgtttcttttgatttagtttctttgaaaatggtactactgagtttttttcccctgaaagtactcatatggagtgttttgaataacctctttacttttgcttgactcctcagGTTTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTA
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