Sequence
atgc intronic sequence ATGC exonic sequencegtagagaggcctgaattaattttccactctatttgtttaatattgtcctgttaccttcctaggtcatggattaagattagtataatgttagtttctttcttttccttcttttgctaacagtctgaattttgcagATATATGTGCACAGTAAGTTGATGATCATTGATGACCGGATGACACTGATTGGATCAGCTAACATAAATGACAGAAGTTTGCTTGGATCAAGGGATTCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g20860.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G158008_T01 (Zea mays), 3'ss of exon 5
gtagagaggcctgaattaattttccactctatttgtttaatattgtcctgttaccttcc-taggtcatggattaagattagtataatgttagtttctttcttttccttcttttgctaacagtctgaattttgcagATATATGTGCACAGTAAGTTGATGATCATTGATGACCGGATGACACTGATTGGATCAGCTAACATAAATGACAGAAGTTTGCTTGGATCAAGGGATTCTG
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--gtacttttttttgttggtggtggtagggtgggggtcaaaatgcttctgttacactcaataggtcatgcctttaggcaaggttagtttctgtgcttctttta---tttttttcctaacaatttgcatgttgcagATATATGTGCACAGTAAATTGATGATTATTGATGATCGCATGGCATTGATTGGCTCAGCCAACATAAATGATAGAAGCTTGCTTGGATCTAGGGATTCTG
upper sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA20G38200.1 (Glycine max), 3'ss of exon 16
----------------------------------------gtagagaggcctgaattaattttccactctat------ttgtttaatattgtcctgttaccttcctaggtcatgga------ttaagattagtataatgtt-----agtttctttcttttccttcttttgctaacagtctgaattttg---cagATATATGTGCACAGTAAGTTGATGATCATTGATGACCGGATGACACTGATTGGATCAGCTAACATAAATGACAGAAGTTTGCTTGGATCAAGGGATTCTG
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gtatcttaccatatatattgaaacatcttttgattttgcttttaaaacatcaaatatttttctctgagccaaaagagatcttggaaaagtgcaatttggatctcctagatcttgtgcacaacttttaacttttataatgatttaacagctcaaatatttgtcttatttggtgtataattcccatattgatacagGTATATGTGCACAGTAAATTGATGATAATTGATGACCGTATAGCTTTTATTGGATCATCTAATATAAATGACCGTAGTTTGCTTGGATTAAGAGACTCTG
upper sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 16
---------------------------------------------gtagagaggcctgaattaattttccactctatttgt----------ttaatattgtcctgtt---accttccta--ggtcatggattaag--att-agtataatgttagtttctttcttttccttcttttgctaacagtctgaattttgcagATATATGTGCACAGTAAGTTGATGATCATTGATGACCGGATGACACTGATTGGATCAGCTAACATAAATGACAGAAGTTTGCTTGGATCAAGGGATTCTG
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gtattgtgttttgctgatgcacataatcacatatgtacatttattttcaatgttccctaatcaattacaaaatctatttgtatgcatctttttcatgtttttttttttaaatttttataatggacatgggaaaaacaattgagcttggaactcagtggtatatcatttttcacattatattcctattgtttctgtagGTGTATGTGCATAGCAAAATCATGATAGTTGATGACTGCACAACCTTGATTGGATCCGCTAACATTAATGATAGGAGTTTGCTTGGATCAAGAGATTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtataatgttagtttctttcttttccttcttttgctaacagtctgaattttgcagATATATGTGCACAGTAAGTTGATGATCATTGATGACCGGATGACACTGATTGGATCAGCTAACATAAATGACAGAAGTTTGCTTGGATCAAGGGATTCTG
tgctaac putative branch site (score: 1)
tttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagagaggcctgaattaattttccactctatttgtttaatattgtcctgttaccttcctaggtcatggattaagattagtataatgttagtttctttcttttccttcttttgctaacagtctgaattttgcagATATATGTGCACAGTAAGTTGATGATCATTGATGACCGGATGACACTGATTGGATCAGCTAACATAAATGACAGAAGTTTGCTTGGATCAAGGGATTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT