Sequence
atgc intronic sequence ATGC exonic sequencegtacatgaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttctgcagGTCAGCCCTGAGCTGTATGGAGACAGTAACCCAAGGTTCTTCACATATTGGACA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g28000.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G129947_T01 (Zea mays), 3'ss of exon 5
gtacat--gaacggaggaattaga-----ttctgccatcttaa-------acaaaaagtgatgaataattatatg-tactattttgaacgagc---acttgtaatttatttttcttttgctc-------cttctgcagGTCAGCCCTGAGCTGTATGGAGACAGTAACCCAAGGTTCTTCACATATTGGACA
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gtacatttgaaccaaatgagtaggcatggtcctgctatatgcatgcagacacaaacacccctgcatcactatgtaatactctctccattcttttttatttgtcgcccactagtccaatgatatgtcatgcttttatagGTAAGCCCAGAGCTATACGGAGACAGTAACCCAAGATTCTTCACCTACTGGACA
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G02460.1 (Glycine max), 3'ss of exon 5
gtacatgaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttc-tgcagGTCAGCCCTGAGCTGTATGGAGACAGTAACCCAAGGTTCTTCACATATTGGACA
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----------------------------------------------------------------gtttttagtccatcaatttctagctaaataacaagcatactttccttcagGTAAGCCCTGAGCTATATGGAGACAACTATCCTAGGTTCTTCACTTATTGGACAMapped 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|58654016|gb|CK042696.1|CK042696EST: TCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAG GTCAGCCCCGAGCTGTATGGAGACAGTAACCCAAGGTTCTTCACATTTTGG
genomic: TCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaac ... ccttctgcagGTCAGCCCTGAGCTGTATGGAGACAGTAACCCAAGGTTCTTCACATATTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtactattttgaacgagcacttgtaatttatttttcttttgctccttctgcagGTCAGCCCTGAGCTGTATGGAGACAGTAACCCAAGGTTCTTCACATATTGGACA
tttatttttcttttgc CT-rich tract
acttgtaatttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatgaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttctgcagGTCAGCCCTGAGCTGTATGGAGACAGTAACCCAAGGTTCTTCACATATTGGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA