Sequence
atgc intronic sequence ATGC exonic sequencegtaggttttgcagaagaacacccatggaatttctgtgttctctcaagttacatctcttgttgcattgtattagagctgaactaaaaagtttgttaaatctattatctgttcgcagGGCATTGACAGGCATTATGGATGATTATTTTGATGGCTACTTTTCTGAAGAAATGATAGAATGTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g61860.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G096470_T01 (Zea mays), 3'ss of exon 6
gtaggttttgcagaagaacacccatggaatttctgtgttctctcaagttacatctcttg---------ttgcattgtattagagctgaactaaaaagtttgttaaat--ctattatctgttcgcagGGCATTGACAGGCATTATGGATGATTATTTTGATGGCTACTTTTCTGAAGAAATGATAGAATGTCAG
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gtaggttctgtagtgaaac-----ttaaatatgtgtggtattttaagttatttctgctgaaatatcgatttcataattgtactgctgaactaaatacctttttctatgcttatatggtgtccgtagGGCATTGACAGGCATTATGGATGACTATTTTGATGGTTACTTCTCTGAAGAAATGATCGAATCTCAG
upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 6
gtaggttttgcagaagaacacccatggaatttctgtgttctctcaagttacatctcttgttgcatt---gtattagagctgaactaa----aaagtttgttaa-atctattatctgttcgcagGGCATTGACAGGCATTATGGATGATTATTTTGATGGCTACTTTTCTGAAGAAATGATAGAATGTCAG
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--------------------cctgactgattgctttatgctt--atgcagcatcttcagcagcttttacattttaaatttgaactaatttgatattccatcactaactatggttt-ttcccagGACCTTAATGGGCATTTTAGATGATTATTTTGATGGCTATTATTCAGAGGAAATGATAGAGTCTCAG
upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 6
gtaggttttgcagaagaacacccatggaatttctgtgttctctcaagttacatctcttgttgcatt-gtatt--agagctgaactaaaaagtttgttaaatctattatctgttcgcagGGCATTGACAGGCATTATGGATGATTATTTTGATGGCTACTTTTCTGAAGAAATGATAGAATGTCAG
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----------------aatgcctgactgattgctttatgctt--atgcagcatcttcagcagcttttacattgcaaatttgaactaatttaatattcaatcactatggttttccccagGACCTTAATGGGCATTTTAGATGATTATTTTGATGGCTATTATTCAGAGGAAATGATAGAATCTCAG
upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 6
gtaggttttgcagaagaacacccatggaatttctgtgttctctcaagttacatctcttgttgcattgtattagagctgaactaaaaagtttgttaaatctattatctgttcgcagGGCATTGACAGGCATTATGGATGATTATTTTGATGGCTACTTTTCTGAAGAAATGATAGAATGTCAG
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---------atataaatatatatatgtg-tgtgcacacgctttgctcttgtgtatatggtaataatg-attaatat--gattaatatactctggaattatgtaaattactc--agGGCTTTGATGGGCATTATTGATGACTATTTTGATGGCTATTATTCAGAGGAAATGATAGAATCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcattgtattagagctgaactaaaaagtttgttaaatctattatctgttcgcagGGCATTGACAGGCATTATGGATGATTATTTTGATGGCTACTTTTCTGAAGAAATGATAGAATGTCAG
aactaaa putative branch site (score: 2)
tctgttc putative PPT
aactaaaaagtttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggttttgcagaagaacacccatggaatttctgtgttctctcaagttacatctcttgttgcattgtattagagctgaactaaaaagtttgttaaatctattatctgttcgcagGGCATTGACAGGCATTATGGATGATTATTTTGATGGCTACTTTTCTGAAGAAATGATAGAATGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA