Sequence
atgc intronic sequence ATGC exonic sequenceCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaattaccatgtttgaatttataaatctgattcagcatacttggtcagatatgttgctgttgcaaaattttgatcagttcatcaaaaaatggcttgtgctcttatcag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g08400.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G017845_T02 (Zea mays), 5'ss of exon 6
CCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaattaccatgtttgaatttataaatctgattcagcatactt---ggtcagatatg--ttgctgt-tgcaaaattttgatcagttcatcaaaaaatggcttgtgctcttatcag
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CCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCTGTAGTTGTGAAAGAATGGAGgtaggc-cagttagcatgtttttcttaatttggtcttgtgggcatatttcatggttagaagagagcctctgtgtgtgaaatttggatcatttcattccaacatggtttgttcacttaccag
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G06650.2 (Glycine max), 5'ss of exon 3
CCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaattaccatgtttgaatttataaatctgattcagcatacttggtcagatatgttgctgttgcaaaattttgatcagttcatcaaaaaatggcttgtgctcttatcag--------------
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CCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTTGTAGTTGCGAAAGAATGGAGgttagttatattg--actcccaaatcttttcatcctatt----attatcaattaga-agctaactgttggatccttcctctcctccccccattccctgtcccgttttcttgccttttcaatcaatgcag
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA02G06720.2 (Glycine max), 5'ss of exon 7
CCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaattaccatgtttgaatttataaatctgattcagcatacttggtcagatatgttgctgttgcaaaattttgatcagttcatcaaaaaatggcttgtgctcttatcag----------------------
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TCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTTGTAGCTGTCAAAGATTGGAGgtcagctatatcagatcacaaaattttttcgtaattttttgttaccaacaagcagatac--tgatgtatcccatctctcactcctttctttgtttttgtctttttcctttccgtatgaaactttccgatcagttcag
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA12G19010.1 (Glycine max), 5'ss of exon 6
CCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaatta--ccatgt-ttgaatttataaatctgatt--cagcatacttggtcagatatgttgctgttgcaaaattttgatcagttcat--------------caaaaaatggcttgtgctcttatcag
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TCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTTGTAGCTGTCAAAGATTGGAGgtcagttatatcagatcacaaatttttttcataaattttgttaccaacaagcagatactgatgtatcccatctctcactcctttctttgtttttgtctttttcctttccgtatgaaactttccgatcatttcag
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA01G38640.1 (Glycine max), 5'ss of exon 6
CCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaattaccatgtttgaatttataaatctgattcagcatacttgg----tcagatatgttgctgttgcaaaattttgatcagttcatcaaaaaatggcttgtgctctta-tcag-----
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TCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTCCTCGTTGTTGTAGCTGCGAAAGAATGGAGgtcagttatattagct--cccaaatcttttcatcctattattaacaattagaagctaactgatggatcccttcccctcctccctccattccctgtcccgttttcttgccttttcaatcagtgcag
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA16G25750.1 (Glycine max), 5'ss of exon 7
CCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaattaccatgtttga-atttataaatctgattcagcatacttggtcagatatgttgctgttgcaaaattttgatcagttcatcaaaaaatggcttgtgctcttatcag
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CCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTTGTAGCTGTCAAAGAATGGAGgtcagttatatcagctagcaaaacatttcatcgtttgttgttaccaacaatatctcactcctttct-ttgtttttgtttgtttccttt-tcatatgaaactttccaatcagtgcag
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 5'ss of exon 11
CCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttc-----aattaccatgtttgaatttataaatctgattcagcatactt-----ggtcagatatgttg-ctgttgcaaaattttgatc----------agttcatcaaaaaatggcttgtgctcttatcag
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AGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTTGTAGTTGTGAACGAACAGAGgttagttggaagaaaatacaacctcccatcccacatactcactgaagaaatcttctcgtagcttgacagattaacaactacagatttctatttttcgttttgtatttctttatagaaaatctgccaacccatgcag
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 5'ss of exon 8
CCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaat-----taccatgtttgaatttataaat-ctgattcagcatacttg--gtcagat----------atgttgctgttgcaaaattttgatcagttcatcaaaaaatggcttgtgctcttatcag
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ACTTATTGAGTATAGAGCACATCCGTTCTGGATGCAAAAGTACTGTCCCTCACACGAGCATGATGGAACTCCTCGGTGTTGTAGTTGTGAAAGAATGGAGgttagttggaagaagatacaaccccccatcccacacacactgaagaaatcttcttgtagcttgatgataaacaacagatctctaatttttcttttttggtatttctttatggaaaatctgccaacccatgcagMapped 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|56158549|gb|AU095148.2|AU095148EST: CACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAG CCAAGGGAATCAAGATATGTATTGCTGGACGATGGTCGCAAACTCTGCCTG
genomic: CACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaa ... ctcttatcagCCAAGGGAATCAAGATATGTATTGCTGGACGATGGTCGCAAACTCTGCCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCTGTAGTTGTGAAAGAATGGAGgtacgttcaattaccatgtttgaatttataaatctgattcagcatacttggtcagatatgttgctgttgcaaaattttgatcagttcatcaaaaaatggcttgtgctcttatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA