Sequence
atgc intronic sequence ATGC exonic sequence...aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttcttgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40830.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 5
-aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttct-tgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
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gtcaaagtaacttaatgcaca-tcatcaatctcctttttctgaaatggttgtatattttatgaagttttttttaaccctcatttctgattgcccattt-cagCTCATTATTGCTTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------aagaattaaaccattaggtagttaatatgcatgttcccctatttcag---ataggggttcttgactt--cttgctgtagac--taactgatt---ttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
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gtaagtttcctgcttcaaaaaattttctttgatttgcgttatatacaaatttaaattcttataacttctataatgtgtggctccctctttccttcat-tacagtttctttaaatttaaccaataaattttttttatgttgcttattataattcttttcttattatgtttttgcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAG
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 5
-------aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttcttgacttcttgctgtagact---aactgattttcactcattt-tcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
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gtatgctactacgcaaatgatgagct-gctgctattcat-ttccctacttctaggcatgctgttttcataccctgctgtaatatctaaaacgctttcctttcctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAGAAGTTCCCTGACATGATCATCAAG
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 5
aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttcttgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
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gtcctgcccatatttgtgtgttttaccattttatcatgaaattacacttgaaaatatagatctaaatttaagatgtttactcacatattctgctctccagATCATAATTGCATGTAGAAAGGGAGGAACCAGCATCGAAGACCTTGCAGAGAAATTCCCTGACATGATTGTCAAGMapped 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|13420568|gb|AU174658.1|AU174658EST: GAATACTGCTGGTCCG CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: GAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST:
gi|88730444|gb|CI754057.1|CI754057EST: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agataggggttcttgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
ttttcactcattttc CT-rich tract
tgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttcttgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT