Sequence
atgc intronic sequence ATGC exonic sequence...cttttcatcccttaattactgttttcattttactagaactgtcttgtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g42530.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 3
------cttttcatcccttaattactgttttcattttactagaactgtcttgtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
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aggtatgttctgttgctctgcatgatattcttaactt-ttaagcccgtaaatgagcttccagaatctgttgattttg-atcaattttg----tttggtattcccagGACCTGTTATGGCCAAATTTACTATAGCGTTGAGAGAAATCAGTACTTACAAGGAACGGCTCCGGTTTCAA
upper sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 3
-------cttttcatcccttaattactgttttcattttactagaactgtcttgtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
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cccttgtttttttaaccgtcacgcattctttgaatagt--taatacaacattacattcatttttgttattaattttgataaactt--tgag---ttggtattgtcagGACCTGTCATGACCAAATTTTCTATTGCTTTGAGAGAAATCAGTACATACAAGGAACTTCTTCGGTCCCAG
upper sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 3
---cttttcatcccttaattactgttttcattttactagaactgtcttgtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
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ttgggactgacttcataatt--tgattttaagtctgtatgttacctttaactctaa-aagtctaatggtgatgaaatgatttatgattgagtttctattccagGCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAG
upper sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 3
---cttttcatcccttaattactgttttcattttactagaactgtcttgtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
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actaaactgacttcataatt--tgattttaagtctgtatgttacctttaactctaa-aagtctaatggtgatgaaatgatttatgactgagtttctattacagGTCCTGTTATGACCAAATTCACCATAGCCTTACGAGAAATTGGTACATACAAGGAAGTTCTTCGATCACAG
upper sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 3
cttttcatcccttaattac-tgttttcatttta----ctagaactgtcttgtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
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---tttaactggaaattgcatgatatggtactagctcctagaag-gcctgttcataagtgaaatttactggcattgttgatgaaatctctatttgtt-tcttcagGCCCTGTTATGACCAAATTCACTATTGCATTGAGAGAGATTGGGACATACAAGGAAGTTCTTCGCTCCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
ctctaat putative branch site (score: 3)
catttctcctctcc putative PPT
tctaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttcatcccttaattactgttttcattttactagaactgtcttgtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -ttcatcc
- - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - -tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatac