Sequence
atgc intronic sequence ATGC exonic sequence...aacattcttcgctctgaatgttccaaaatattataataggtttagcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g20340.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g20340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G174170_T02 (Zea mays), 3'ss of exon 2
---aacattcttcgctctgaatgttccaaaatatt-ataataggtttagcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
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gtatgcacactattttcttcttctgtgtacctgttgattgtaagttaaccatttccctggtaagttctc-------ctaattaaat-gctcctttgaacttcagAGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG
upper sequence: LOC_Os06g20340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G174170_T01 (Zea mays), 3'ss of exon 2
---aacattcttcgctctgaatgttccaaaatatt-ataataggtttagcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
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gtatgcacactattttcttcttctgtgtacctgttgattgtaagttaaccatttccctggtaagttctc-------ctaattaaat-gctcctttgaacttcagAGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA----
upper sequence: LOC_Os06g20340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G04550.1 (Arabidopsis thaliana), 3'ss of exon 2
aacattcttcgctctgaatgttccaaaatattataataggttta-gcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
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---------------gtatgtt----gattctatctcaagtttctagatttcatctttatgattttt-----tcttgacggtct--tgctttg---tgtagACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAGMapped 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|24468882|gb|CA305831.1|CA305831EST: TCAAGACGAGAAGACTTTGCAGTTTGATGATGCAATCCAATTTTTAG AACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGA
genomic: TCAAGACGAGAAGACTTTGCAGTTTGATGATGCAATCCAATTTTTAGgtattgatgc ... tcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGA
EST:
gi|33675778|gb|CF304017.1|CF304017EST: CCTTCAAGACGAGAAGACTTTGCAGTTTGATGATGCAATCCAATTTTTAG AACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGA
genomic: CCTTCAAGACGAGAAGACTTTGCAGTTTGATGATGCAATCCAATTTTTAGgtattgatgc ... tcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
atctaat putative branch site (score: 3)
ttattttc putative PPT
tttctatatctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacattcttcgctctgaatgttccaaaatattataataggtttagcattcagtcagtatgacctttctatatctaatcagtttgttattttcaacttcagAACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA