Sequence
atgc intronic sequence ATGC exonic sequence...aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g23990.2 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 19
-aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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gtattgattaacacagtgtaaagataggttttgaaatattgattagttcattttaatttttcttctgatttagcgttttattacttggatctacaa-tcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 19
-aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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tgatgaacacagatagtgtaaagataggttttgaaatattgattacttcattttaatttttcttctgatttagccttttattacttggatctacaa-tcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 19
---aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaacct---tttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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gtaagtttagcactcttgattttaaaagaatcgcgaggttagatgg--tttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 19
---aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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ttaagcgatgtaagacacagaattctatactagcctgtttatccatggcctttttgcttccatttgatttttaccc--ctggccacatttttcattga-tcagATATGTAAAACGCGCGCTGTATCTTCTGCATCTCACTTGTGGCCCATCTCATCCAAACACTGCTGCGACATATATCAATGTGGCTATGATGGAGGAAGGC
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 4
---aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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ttaagcgatgtaaaacacagaattctatactatcctgtttatccatggcctttttgcttccatttgatttttaccc--ctggccacatttttcattga-tcagATATGTAAAACGCGCTCTGTATCTTCTGCATCTCACTTGTGGCCCATCTCATCCAAACACTGCTGCGACATATATCAATGTGGCTATGATGGAGGAAGGC
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------------------aatgaattgttcctgt--tctttgttaactgtctacttc---ctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaat-tagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
| | ||| || || || | | | | | | | | | || ||||| | || | ||| | | || ||| | | || ||| || ||||| || | || || || | || ||| | | |||||| || ||||| ||||| || ||||||||||||||||| ||||| |||||||| || ||
gtaagttctaatacccaagcacaggtttctttttggagaatggtctaagatcagagtgtctttgagatcgttaatgattagttgttccgatttttgaactggaattatacggga-aggactgcc---gctcaatttttattttgttggaatgcagATATGTTAATAGAGCTCTCTACTTGCTACATTTAATATGCGGTCCTTCTCACCCAAATACTGCTGCGACATATATCAATGTAGCCATGATGGAAGAGGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
gattaac putative branch site (score: 2)
ccttttctattttt CT-rich tract
attaaccttttctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA