Sequence
atgc intronic sequence ATGC exonic sequence...caaatggcaaaggagtaatagaagagttttttcatccttttagcatcatgatatgttctttccttcctgttctgcttaacatgtgcagttctcgttgcagGTATTCCATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56670.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 5
---caaatggcaaaggagtaatagaagagttttttcatccttttagcatcatgatatgttctt--tccttcctgttctgcttaacatgtgcagttctcgttgcagGTATTCCATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAG
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ccatgtctggccaacttg-aacaaaata-ccattttacctttttaacatcatgtcatgttcttaatttattgtgtctttcttgactagt---gttgtctttgcagGTATTCCATTTGGATCTGTTAATTTATTGTACGGAGTCGATGAAAATGAAAGCAAG
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 4
caaatggcaaaggagtaatagaagagttt-tttcatccttttagcatcatgatatgttctt-tccttcctgttctgcttaacatgtgcagttctcgttgcagGTATTCCATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAG
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agaattaaatatattttatcctctcccttattttcccccctcatccaaacaaagggtaatagttcatcgtatgttgtctttcatgtgctatgtt--ttgcagGAATTCCATTTGGATCTGTAAACTTGTTACATGGAGTTGATAAACATGAAAGCAAG
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 5
-----caaatggcaaaggagtaatagaagagttttttcatccttttagcatcatgatatgttctttccttcctgttctgcttaacatgtgcagttctcgttgcagGTATTCCATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAG-------------
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tagcacagagatctttactttaatagagaaaaagctttaaatgttctctgttat-agacttctatcatattatgacctctttaagctatgatgt----attgcagGAATTCCCTTTGGATCTGTCAATCTATTGCATGGAGTTGATGAACATGAAAGCAAGGCAAAGCCTCTCTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29678673|gb|CB674948.1|CB674948EST: AGCGGCTGACTTAGCTCAAAGATTGCTACCTGCATTTGACACTCCAACAG GTATTCCATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAA
genomic: AGCGGCTGACTTAGCTCAAAGATTGCTACCTGCATTTGACACTCCAACAGgtttactacg ... ctcgttgcagGTATTCCATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgatatgttctttccttcctgttctgcttaacatgtgcagttctcgttgcagGTATTCCATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAG
gcttaac putative branch site (score: 3)
ttctcgtt putative PPT
atatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaatggcaaaggagtaatagaagagttttttcatccttttagcatcatgatatgttctttccttcctgttctgcttaacatgtgcagttctcgttgcagGTATTCCATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - aatagaag
- - - - - - - - - - - - - - - ttcatcc
- - - - - - - - - - - - - - - - - - - - - - -tcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgc