Sequence
atgc intronic sequence ATGC exonic sequence...tttttattcaataaccaattaaccataacacatagacatatttgatctgactaagaatataacagcaagaacctgtgtctcatttcctttttggatttagGCACAAACAAGTTATGCTTGAGGCATACGAACAGCAATGCGATGAAGCATGCAAGATATTTGCTGAATACCAACGACGACTACATCAATTTGTTAATCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g21780.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G055917_T02 (Zea mays), 3'ss of exon 1
----tttttattcaataaccaattaaccataacacatagacatatttgatctgactaagaatataacagcaagaacctgtgtctcatttccttt---ttggatttagGCACAAACAAGTTATGCTTGAGGCATACGAACAGCAATGCGATGAAGCATGCAAGATATTTGCTGAATACCAACGACGACTACATCAATTTGTTAATCAA
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ttcatttttatttatttat--ataaattgtggcaagtggtgat----ggtgtg-cttgtagcatatctagaataattgacaaggaatttctaaaaaataaaaaatagGCACAAGCAAGTTATGCTCGAAGCATATGAACAGCAATGCGACGAAGCATGCAAAATATTTGCTGAATACCAGCGTCGGCTACATCAGTTTGTCAACCAA
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G116196_T01 (Zea mays), 3'ss of exon 1
--tttttattcaataaccaatt--aaccataacacatagacatatttgatctgactaagaatataacagcaagaacctgtgtctcatttccttt-ttggatttagGCACAAACAAGTTATGCTTGAGGCATACGAACAGCAATGCGATGAAGCATGCAAGATATTTGCTGAATACCAACGACGACTACATCAATTTGTTAATCAA
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caatttcacttatttctttatataaattgtgccaagtggtgat----ggtgtg-cttgtagcagatctacaacaattgacattttttttaaaaaattaaaaatagGCACAAGCAAGTTATGCTCCAAGCATATGAACAGCAATGCGATGAAGCGCACAAAATATTTGCTGAATACCAGCGCCGGCTACATCAGTTCGTTAACCAAMapped 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|29687679|gb|CB683954.1|CB683954EST: CGCGAGGAGGCCGAGCGGAAGCGCGTCCTCGGGGAGCGCTCCAATGCCAG GCACAAACAAGTTATGCTTGAGGCATACGAACAGCAATGCGATGAAGCATG
genomic: CGCGAGGAGGCCGAGCGGAAGCGCGTCCTCGGGGAGCGCTCCAATGCCAGgtacgcgaaa ... ttggatttagGCACAAACAAGTTATGCTTGAGGCATACGAACAGCAATGCGATGAAGCATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgactaagaatataacagcaagaacctgtgtctcatttcctttttggatttagGCACAAACAAGTTATGCTTGAGGCATACGAACAGCAATGCGATGAAGCATGCAAGATATTTGCTGAATACCAACGACGACTACATCAATTTGTTAATCAA
atataac putative branch site (score: 3)
cctgtgtctcatttcc putative PPT
taagaatataa 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
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tttttattcaataaccaattaaccataacacatagacatatttgatctgactaagaatataacagcaagaacctgtgtctcatttcctttttggatttagGCACAAACAAGTTATGCTTGAGGCATACGAACAGCAATGCGATGAAGCATGCAAGATATTTGCTGAATACCAACGACGACTACATCAATTTGTTAATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA