Sequence
atgc intronic sequence ATGC exonic sequence...cttatattaagcatagttttcttaagtggaatgtgctactgcaatcaccatatgctggatatgaggttcacttggaatttggaaatgcatttgtttgcagGGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTATATACCAGAAGAAGGTGGGAAAATGCTAGTTATACTCGAAAAGGATAACA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g39640.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G153928_T02 (Zea mays), 3'ss of exon 6
cttatattaagcatagttttc-ttaagtggaatgtgctactgcaatcaccatatgctggatatgaggttcacttggaat--ttggaaatgcatttgtttgcagGGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTATATACCAGAAGAAGGTGGGAAAATGCTAGTTATACTCGAAAAGGATAACA
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--tattcccttggcagtcatcattatgtggtgctgtgtatttctgtcattttttcatagattggcttatatcttgagacacttggacac-catttttttgcagGGACATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGCATCTTTTGGCTATATTCCAGAAGAAGGTGGGAAAATGCTTGTGATTCTTGAAAAGAATTTCA
upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 12
--cttatattaagcatagttttcttaagtggaatgtgctactgcaatcaccatatgctggatatgaggttcacttggaatttggaa-atgcatttgttt--------gcagGGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTATATACCAGAAGAAGGTGGGAAAATGCTAGTTATACTCGAAAAGGATAACA
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gtaatatactctgtagccgtgtctttagtgtgtccctctagaaggaagaaccgatctttaagattgcttgttggcagagtataaactatccttttgtttcccttttcgcagGGCCATCAGTATGAGACAGTCTCAGGTTTTGTCTGTGAGGCCTTTGGGTATATCCCAAAGACAGGTGAGAGTGTGACGGTAGTTCTTGAAAAGGAAAACTMapped 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|58603218|gb|CK013746.1|CK013746EST: ACTTGGTGTTAAAATACCAGAG GGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTAT
genomic: ACTTGGTGTTAAAATACCAGAGgtgttatttc ... ttgtttgcagGGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccatatgctggatatgaggttcacttggaatttggaaatgcatttgtttgcagGGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTATATACCAGAAGAAGGTGGGAAAATGCTAGTTATACTCGAAAAGGATAACA
tttgttt CT-rich tract
atttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttatattaagcatagttttcttaagtggaatgtgctactgcaatcaccatatgctggatatgaggttcacttggaatttggaaatgcatttgtttgcagGGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTATATACCAGAAGAAGGTGGGAAAATGCTAGTTATACTCGAAAAGGATAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG