Sequence
atgc intronic sequence ATGC exonic sequence...tatacaattttaactaaatttgcctgaacaaagaaacatctttgtgatatgttctgttatcgtttttttcttaattagcacctcattttcttctattcagATACAGACAATACAACGCTTGAAAGATGAAAGAGATAACATGCTGCAGCAAAATCAGCAAATGCAACGTGAATTGGTCAGCCTTATTTTTTTGCAATTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g43594.3 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g43594.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 6
-tatac-aattttaactaaatttgcctgaacaaagaaacatctttgtgatatgttctgttatcgtttttttcttaattagc-acctcattttcttctattcagATACAGACAATACAACGCTTGAAAGATGAAAGAGATAACATGCTGCAGCAAAATCAGCAAATGCAACGTGAATTGGTCAGCCTTATTTTTTTGCAATTCA
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gtgcattagcactgatcaagactgtatgaacgagtaaacatcctt-tgggacaacttg--gtcatttttttctcacgaagttgtccccttttatcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG-------------------------
upper sequence: LOC_Os02g43594.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G074173_T01 (Zea mays), 3'ss of exon 7
tatacaattttaactaaatttgcctgaacaaagaaacatc-tttgtgatatgttctgttatcgtttttttcttaattagc-acctcattttcttctattcagATACAGACAATACAACGCTTGAAAGATGAAAGAGATAACATGCTGCAGCAAAATCAGCAAATGCAACGTGAATTGGTCAGCCTTATTTTTTTGCAATTCA
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actggaaactcatagatgactgcatgaatgagcaaacatcctttgggacaacttgggtcat--tttttttctcagtaagctgtccccttctgttttactcagATCCAGACAATTCAGCGGGTGAAGGAAGAAAGAGATAACATGCTTCAGCAAAACCAGCAAATGCAACGTGAATTG-------------------------Mapped 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|88460736|gb|CI534608.1|CI534608EST: ATGCTGAAGAATGCAAGCATTGAAGAG ATACAGACAATACAACGCTTGAAAGATGAAAGAGATAACATGCTGCAGCAA
genomic: ATGCTGAAGAATGCAAGCATTGAAGAGgtaatgcaac ... ttctattcagATACAGACAATACAACGCTTGAAAGATGAAAGAGATAACATGCTGCAGCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatgttctgttatcgtttttttcttaattagcacctcattttcttctattcagATACAGACAATACAACGCTTGAAAGATGAAAGAGATAACATGCTGCAGCAAAATCAGCAAATGCAACGTGAATTGGTCAGCCTTATTTTTTTGCAATTCA
tcttaat putative branch site (score: 3)
cctcattttcttctat putative PPT
ttatcgtttttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatacaattttaactaaatttgcctgaacaaagaaacatctttgtgatatgttctgttatcgtttttttcttaattagcacctcattttcttctattcagATACAGACAATACAACGCTTGAAAGATGAAAGAGATAACATGCTGCAGCAAAATCAGCAAATGCAACGTGAATTGGTCAGCCTTATTTTTTTGCAATTCA
- - - - - -aactaaa
- - - - - - - - - -ttgcctg
- - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - -ttgtgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacctc