Sequence
atgc intronic sequence ATGC exonic sequencegtataattctaccatctgagttttttagtttgttaaatggcagattattctattttagtacgtgtaatcaaacttattattgctaaggaagaggttgttcacgttatggcacaatcatgaggataaccagactatctttgcttcagATTGTAAGGTTCAAAGACAAAGAGTCCCATCAGGTATTTCTTGAACCAGAGGGCAGAGATGTTCCTGAGCTTTATCTGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g72980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g72980.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 6
gtataattctaccatctgagttttttagtttgttaaatggcaga-ttattctattttagtacgtg------taatcaaacttat-tattgctaaggaagaggttgttcacgttatggcacaatcatgaggataaccagactatctttgcttcagATTGTAAGGTTCAAAGACAAAGAGTCCCATCAGGTATTTCTTGAACCAGAGGGCAGAGATGTTCCTGAGCTTTATCTGCAG
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--gtaatg-tataatg-gaccttgttggtttgttacatggcaaacttcttttattttgattattggattgccaacagaacttgtattttttcttgcaaaaaattaagtactatacc-tacaacgactgatgtacccac-taacccttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG
upper sequence: LOC_Os01g72980.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G32720.1 (Glycine max), 3'ss of exon 3
gtataattctaccatctgagttttttagtttgttaaatggcagattattctattttagtacgtgtaatcaaacttattattgctaaggaagaggttgttcacgttatggcacaatcatgaggataaccagactatctttgcttcagATTGTAAGGTTCAAAGACAAAGAGTCCCATCAGGTATTTCTTGAACCAGAGGGCAGAGATGTTCCTGAGCTTTATCTGCAG
|| |||| | || | | |||| || | ||||| |||| | | ||| |||| || |||| | | || || |||||||||| ||| |||| |||||||| ||||| ||||||||||||| ||||| || ||| |||||||| ||| |||||
---------------------------gtgtgtttcaaaaaagctaccttggttttgaaacatcagatcaactatatt------------ggaatcgtttttattattttctgat----gtgatatattgttcacttt---tttagATTGTAAGATTCCAAGATAAAGAGTCTCATCAAATATTTCTTGAACCTGAGGGTCGAAGTGTGCCTGAGCTCTATGTGCAG
upper sequence: LOC_Os01g72980.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 5
---------------------------------gtataattctaccatctgagttt-tttagtttgttaaa--tggcagattattctattttagtacgtgtaatcaaacttattattgctaagga----agaggttgttcacgttatggcacaatcatgaggataaccagactatct------ttgct-----tcagATTGTAAGGTTCAAAGACAAAGAGTCCCATCAGGTATTTCTTGAACCAGAGGGCAGAGATGTTCCTGAGCTTTATCTGCAG
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gtgtgtttcaaaaaagctaccttggttttcttcatatcagtttaatatgtgtatgtacctgattaactatagttaccatttcattccatactcagat-tgaacctgaaccatttagaaaaaggggtctgaaacatcagataaactatattggaatcatttgtattattttatgatgtgatatattgttcactttcagATTGTAAGATTCCAAGATAAAGAGTCTCATCAAATATTTCTTGAACCTGAGGGTCGAAATGTGCCTGAGCTCTATGTGCAG
upper sequence: LOC_Os01g72980.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G13440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtataattctaccatctgagttttttagtttgttaaatggcagattattctattttagtacgtgtaatcaaacttattattgctaaggaagaggttgttcacgttatggcacaatc-atgaggataaccagactatctttgcttcagATTGTAAGGTTCAAAGACAAAGAGTCCCATCAGGTATTTCTTGAACCAGAGGGCAGAGATGTTCCTGAGCTTTATCTGCAG
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------------------------------------cttgcatttgctttttctacagttggcacaa--agaataagttgaacca---------tctttctctttaaactgcttttgatgaacttaaaaaatcttgtttggtttcagATTGTTAGGTTCAAAGACAAAGAGTCTCATCAAATATTCCTCGAACCAGAGGGCCGAGATGTTCCTGAGATCTATGTGCAG
upper sequence: LOC_Os01g72980.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 6
gtataattctaccatctgagttttttagtttgttaaatggcagattattctattttagtacgtgtaatcaaacttattattgctaaggaagaggttgttcacgttatggcacaatcatgaggataaccagactatctttgcttcagATTGTAAGGTTCAAAGACAAAGAGTCCCATCAGGTATTTCTTGAACCAGAGGGCAGAGATGTTCCTGAGCTTTATCTGCAG
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----------------------------------------tggtttataatattt--gtcaagagagatgcattttttatt--taactatgattacaagaaaatttctgaactgttcaaacatt--tttttttttggtggtttcagATTGTGAGATTTCAAGATAAAGAGTCTCATCAGATTTTTCTTGAACCAGAAGGTCGAAATGTGCCTGAGCTCTATGTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggttgttcacgttatggcacaatcatgaggataaccagactatctttgcttcagATTGTAAGGTTCAAAGACAAAGAGTCCCATCAGGTATTTCTTGAACCAGAGGGCAGAGATGTTCCTGAGCTTTATCTGCAG
ggataac putative branch site (score: 3)
tctttgcttc putative PPT
tatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataattctaccatctgagttttttagtttgttaaatggcagattattctattttagtacgtgtaatcaaacttattattgctaaggaagaggttgttcacgttatggcacaatcatgaggataaccagactatctttgcttcagATTGTAAGGTTCAAAGACAAAGAGTCCCATCAGGTATTTCTTGAACCAGAGGGCAGAGATGTTCCTGAGCTTTATCTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG