Sequence
atgc intronic sequence ATGC exonic sequenceGGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATTGTATTATTTGAATCTGAAGAAAGGCATGTCAAGTTGCTTCTGCGCAATTCATTTCAAGAGgtaaaacactgttgaatcttaaaaatctcttcttccctcagttcaataggtatacgcatttatttagtagcctgtttataaatatatgatgttttagtaa...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g39810.1 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g39810.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G103473_T01 (Zea mays), 5'ss of exon 3
GGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATTGTATTATTTGAATCTGAAGAAAGGCATGT---CAAGTTGCTTCTGCGCAATTCATTTCAAGAGgtaaaacactgttgaatcttaaaaat--ctcttcttccctcagttcaataggtatacgcatttatttagtagcc--tgtttataaatatatgatgttttagtaa
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---CGATGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTATTATTCGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatcattgtgccttagatataacttgttttcttttaatctttttcacttaagagttcaatagacacgcattagctaccgctttctagcattctt----
upper sequence: LOC_Os01g39810.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G000937_T02 (Zea mays), 5'ss of exon 10
GGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATTGTATTATTTGAATCTGAAGAAAGGCATGT---CAAGTTGCTTCTGCGCAATTCATTTCAAGAGgtaaaacactgttgaatcttaaaaat--ctcttcttccctcagttcaataggtatacgcatttatttagtagcc--tgtttataaatatatgatgttttagtaa
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---CGATGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTATTATTCGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatcattgtgccttagatataacttgttttcttttaatttttttcacttaagagttcaatagacacacattagctaccgctttctagcattctt----
upper sequence: LOC_Os01g39810.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G164175_T01 (Zea mays), 5'ss of exon 9
GGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATTGTATTATTTGAATCTGAAGAAAGGCATGT---CAAGTTGCTTCTGCGCAATTCATTTCAAGAGgtaaaacactgttgaatcttaaaaatctcttcttccctcagttcaataggtatacgcatttatttagtagcctgtttataaatatatgatgttttagtaa-
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---CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacaccgttgtgccttggatatcacgtgttttcttt-ttcacttagggctagtttgggaactccattttcccatggaatttctatttttccaagggaMapped 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|86427881|gb|CI072978.1|CI072978EST: AATCTGAAGAAAGGCATGTCAAGTTGCTTCTGCGCAATTCATTTCAAGAG GTTAGGAGATTTTTTCACTCCCACTTCAAGGTTGATAGAGACCTTCAATCG
genomic: AATCTGAAGAAAGGCATGTCAAGTTGCTTCTGCGCAATTCATTTCAAGAGgtaaaacact ... tgtttggcagGTTAGGAGATTTTTTCACTCCCACTTCAAGGTTGATAGAGACCTTCAATCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATTGTATTATTTGAATCTGAAGAAAGGCATGTCAAGTTGCTTCTGCGCAATTCATTTCAAGAGgtaaaacactgttgaatcttaaaaatctcttcttccctcagttcaataggtatacgcatttatttagtagcctgtttataaatatatgatgttttagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA