Sequence
atgc intronic sequence ATGC exonic sequenceAAGGCAGAAAAATCTGCCATGGATTATGGATTTCATATGGCCATTACAAAGTGGAATGATGATGTTTCGAGGGAAATGGAAACGATGGTTAAGGAACATGgtcagtacttctttttgtgctgtcagttattttcatcagaaataagaaattccattctggttcatgaagcaactcctatgtttcaacctgaaatcaactt...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g59340.3 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g59340.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G020002_T03 (Zea mays), 5'ss of exon 4
AAGGCAGAAAAATCTGCCATGGATTATGGATTTCATATGGCCATTACAAAGTGGAATGATGATGTTTCGAGGGAAATGGAAACGATGGTTAAGGAACATGgtcagtacttctttttgtgctgtcagttattttcatcagaaat---aagaaattccattctggttcatgaagcaactcctatgtttcaacctgaaatcaactt
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AAAGCCGCAAAAGCTGCCATGGATTATGGCTTTCACATGGCCATTACAAAGTGGAATGATGAGGTTGCAAGGGAAATGGAAGTGATGGTTAAAGAACATGgtcagtgtatacattttgattttcctctactgttgtttattttcttaaggaattaaaccaaacttcgctacataactcatgataatcagttttttttata---
upper sequence: LOC_Os01g59340.3 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 5'ss of exon 4
AAGGCAGAAAAATCTGCCATGGATTATGGATTTCATATGGCCATTACAAAGTGGAATGATGATGTTTCGAGGGAAATGGAAACGATGGTTAAGGAACATGgtcagtacttctttttgtgctgtcagttattttcatcagaaataagaaattccattctggttcatgaagcaactcctatgtttcaacctgaaatcaactt------------
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AAATCTAGAGAATCTTGTATGGATTACGGTTTTCATATGGCAATCACAAAGTGGGATGAAGGTGTTTCCAGGGACATGGAGATGTTGGTCAAGGAAAAGGgtaaatgtcttgtcttgtgacac--attgatgcc-tcacagttttggtgtttctatccctttagtttccctgctaagatgaaactgagtgcatatatctctaaattttgtag
upper sequence: LOC_Os01g59340.3 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 5'ss of exon 4
AAGGCAGAAAAATCTGCCATGGATTATGGATTTCATATGGCCATTACAAAGTGGAATGATGATGTTTCGAGGGAAATGGAAACGATGGTTAAGGAACATGgtcagtacttctttttgtgctgtcagttatt-ttcatcagaaataagaaatt---ccattctggttcatgaagcaactcctatgtttcaacctgaaatcaactt---------------------------------
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AAAGCGAAAAAATCTTGTATGGATTATGGTTTTCATATGGCAATCACAAAATGGGATGAAAATGTTTCAAGGGAGATGGAAATCATGGTTAAGGAGAAAGgttagctgtttttttcaagtttattataataactctacatagattatgacttgatctacattggcaaatgtaaaccccatttggattcttctctaaatctgtatgaaatccttacttgtcttcttttcaacttacag
upper sequence: LOC_Os01g59340.3 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S101_168V6.1 (Physcomitrella patens), 5'ss of exon 4
AAGGCAGAAAAATCTGCCATGGATTATGGATTTCATATGGCCATTACAAAGTGGAATGATGATGTTTCGAGGGAAATGGAAACGATGGTTAAGGAACATGgt-cagtacttctttttgtg-ctgtcagttattttcatcagaaataagaaattcc--attctggttcatgaagcaactcctatgtttcaacctgaaatcaactt
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AAAGCTGAAGAGTCGTGCATGGATTATGGGTTTCATATGGCAATCTCCAAATGGAATGATGATGTTGCTAAGGATATGGATTGGCTTGTCAAAGAGAAAGgtacaccacccatttaaatctctgtgtatcacccgattctagcctttgattgttaggatttttgttcgtgatgcagatggaaaag--cagcctgttgaaagc--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|33794483|gb|CF323129.1|CF323129EST: GTGGAATGATGATGTTTCGAGGGAAATGGAAACGATGGTTAAGGAACATG GGATCAATTCTTTCAAGTTCTTCATGGCGTATAAAGGTTCATTGATGGTCA
genomic: GTGGAATGATGATGTTTCGAGGGAAATGGAAACGATGGTTAAGGAACATGgtcagtactt ... aatatttcagGGATCAATTCTTTCAAGTTCTTCATGGCGTATAAAGGTTCATTGATGGTCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGGCAGAAAAATCTGCCATGGATTATGGATTTCATATGGCCATTACAAAGTGGAATGATGATGTTTCGAGGGAAATGGAAACGATGGTTAAGGAACATGgtcagtacttctttttgtgctgtcagttattttcatcagaaataagaaattccattctggttcatgaagcaactcctatgtttcaacctgaaatcaactt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA