Sequence
atgc intronic sequence ATGC exonic sequence...ttcaaaaaaaaattctccaagttttttgtgaaattcctatttctgaaaaatttacagtgtttatctgaaaatttacactgttttggtgaagggtttgcagGTACCTGCCGTTGCCGGAGGGGGCGCTGTGCCTGGTGGCGTCGACGGCGTTCATGGCGGAGCTCCTCCTCTTCTACTTCCACTCCACCACCCACCAGGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os11g40570.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g40570.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G089598_T01 (Zea mays), 3'ss of exon 1
-------------------------------------ttcaaaaaaaaattctccaa---gttttttgtgaaattcctatt-tctgaaaaatttacagtgtttatctgaaaatttacactgt----------tttggtgaagggtttgcagGTACCTGCCGTTGCCGGAGGGGGCGCTGTGCCTGGTGGCGTCGACGGCGTTCATGGCGGAGCTCCTCCTCTTCTACTTCCACTCCACCACCCACCAGGGC
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gtcggtcccgtgtaatgctaatgcccgcctccattgtctcaacatgagctcgatcgacgcgatcaaggttcaattttggttctttctaaaacaaaaagagcatactttagtactagtaatatcgcaatggcgtcggacgggatggccgcagGTACCTGCCTTTATCGGACGACGCGCTGAGCCTGGTGTTCGCGAGCGCATTCACGGCGGAGTTCCTGCTCTTCTACTTCCACTCCACCACGCACGCGGGG
upper sequence: LOC_Os11g40570.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G076435_T01 (Zea mays), 3'ss of exon 1
ttcaaaaaaaaattctcca--agttttttgtgaaattcctatt----tctgaaaaatttacagtgtttatctgaaaatttacactgttttggtgaagggtttgcagGTACCTGCCGTTGCCGGAGGGGGCGCTGTGCCTGGTGGCGTCGACGGCGTTCATGGCGGAGCTCCTCCTCTTCTACTTCCACTCCACCACCCACCAGGGC
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-tcatgcagtcgtacaacgccattattatataaagtacgcagcaaagcatgagtagtaaacaatggg-gtgttgaactgaacaacgaat--acgaacggt--gcagGCACTTCCCGCTGACGGACGGAGCGCTGTGCCTGGTGGCGGCGACGGCGTTCACGGCGGAGCTGGTGCTCTTCTACTTCCACTCCACGACGCACATGGGGMapped 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|25798478|gb|CA754439.1|CA754439EST: CTCATGTTCTTCCTCTTCGGCATCCTCGCCCTCCTCTCCCAAAAAACCAG GTACCTGCCGTTGCCGGAGGGGGCGCTGTGCCTGGTGGCGTCGACGGCGTT
genomic: CTCATGTTCTTCCTCTTCGGCATCCTCGCCCTCCTCTCCCAAAAAACCAGgtaacctagc ... gggtttgcagGTACCTGCCGTTGCCGGAGGGGGCGCTGTGCCTGGTGGCGTCGACGGCGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaatttacagtgtttatctgaaaatttacactgttttggtgaagggtttgcagGTACCTGCCGTTGCCGGAGGGGGCGCTGTGCCTGGTGGCGTCGACGGCGTTCATGGCGGAGCTCCTCCTCTTCTACTTCCACTCCACCACCCACCAGGGC
tttatctgaaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaaaaaaaaattctccaagttttttgtgaaattcctatttctgaaaaatttacagtgtttatctgaaaatttacactgttttggtgaagggtttgcagGTACCTGCCGTTGCCGGAGGGGGCGCTGTGCCTGGTGGCGTCGACGGCGTTCATGGCGGAGCTCCTCCTCTTCTACTTCCACTCCACCACCCACCAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- caaaaaa
- - - - - - - ctccaag
- - - - - - - - - - - - - - - - - - - -tttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg