Sequence
atgc intronic sequence ATGC exonic sequenceATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATGgtattgctgatctaattagtaattaccatttccttcaactatgcactgatatcttattttgtatcattggcttttggtggttctctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23590.3 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA17G03570.1 (Glycine max), 5'ss of exon 4
ATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATGgt-attgctgat--ctaattagtaattaccatttccttcaactatgcactgatatcttattttgtatcattggcttttggtggttctctgcag-------------
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ATACAATCATCTCATGGAGAGATCCAGAATATGCTACTGAACTGGCACTTAGCTTTCAAGAGCCTAGCGGCTGCTCTTACATATGgttataacttacaactagctaatgattgtcaattgagttatgcttcttctgggttttgtttctgctgctgtagattgagcttaattaccatgcttgttttgttcag
upper sequence: LOC_Os01g23590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA07G37040.1 (Glycine max), 5'ss of exon 2
ATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATGgt-attgctgat--ctaattagtaattacca---------tttccttcaactatgca-ctgatatcttattttgta-tcattggcttttggtggttctctgcag
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ATACAATCATCTCATGGAGAGATCCAGAATATGCTACAGAACTGGCACTTAGCTTTCAAGAGCCTAGTGGCTGCTCTTACATATGgttataacttacaactagctaatgattgccagagttatgttttttctgggttttgtttctgctgctgtagattgagcttaattacctttgcttgttttggtcag
upper sequence: LOC_Os01g23590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S60_97V6.1 (Physcomitrella patens), 5'ss of exon 4
ATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATGgtattgctgatctaattagtaattaccatt--tccttcaactatgcactgatat---cttattttgtatcattggcttttggtggttctctgcag-----
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ATACAATCATATCATGGACGGATCCAGAAGTGGCAACAGATCTAGCCCTCAGTTTCCAAGAAACTATGGGTTGTACTTTCATATGgtaaattcattttactgaaaattcattattactcctttatagacgggtccccctaggctttgtatgtgaaatttgcaagatgaagcctgtttctgttctc
upper sequence: LOC_Os01g23590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S112_103V6.1 (Physcomitrella patens), 5'ss of exon 3
ATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATGgta---ttgctgatctaattagtaattaccat-ttccttcaactatgcactgatatcttattt--tgtatcattggcttttgg-----tggttctctgcag
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ACACTATCATCTCATGGACGGATCCAGAAGTGGCAACAGATTTGGCTCTCAGTTTTCAAGAGACAATGGGTTGTTCCTTCATATGgtaagttagcagtgttacatggatactatcacctttctgtggtgttttggtcatgtcctatttcttgcattcttgagtgtagaggaaatgtttatttgtg-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|29681402|gb|CB677677.1|CB677677EST: ACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATG GGACAACATATGTGACATTCAGAGAAACATTCAGTTTAATAACCTTGGTG
genomic: ACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATGgtattgctga ... ttctctgcagGGACAACATATGTGACATTCAGAGAAACATTCAGTTTAATAACCTTGGTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATGgtattgctgatctaattagtaattaccatttccttcaactatgcactgatatcttattttgtatcattggcttttggtggttctctgcag
- - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT