Sequence
atgc intronic sequence ATGC exonic sequencegtaatatatgaagttaactttatctagatttagttattatgacctgttgattgcccgtataacatatataaggtgcacgcaattttaaaatggacttttactgttatcacgtttcttgttttccaatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTGGCTTGTAGATGCTGGAGGATGTGTTTTGCTTGATACTTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g16170.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g16170.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G153434_T03 (Zea mays), 3'ss of exon 11
gtaatatatgaagttaactttatctagatttagttattatgacctgttgattgcccgtataacatatataaggtgcacgcaattttaaaatggacttttactgttatcacgtttcttgttttc-caatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTGGCTTGTAGATGCTGGAGGATGTGTTTTGCTTGATACTTTT---------
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------------------tttgtctcgaatgaataagcatgtcaacttttcttattgtgtgatct--------tgaacctagt---ggcatgca---ttactgttctctcattcctttttttttcaatgcagTATACTTGTAAATAGCTTGGACTGGTCGAAACTTAGACCAAATCTCCCGTGGCTTGTAGAATCGGGAGGATGTGTTTTGCTGGATTCTTGTGTATCCTTT
upper sequence: LOC_Os01g16170.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G153434_T02 (Zea mays), 3'ss of exon 8
gtaatatatgaagttaactttatctagatttagttattatgacctgttgattgcccgtataacatatataaggtgcacgcaattttaaaatggacttttactgttatcacgtttcttgttttc-caatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTGGCTTGTAGATGCTGGAGGATGTGTTTTGCTTGATACTTTT
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------------------tttgtctcgaatgaataagcatgtcaacttttcttattgtgtgatct--------tgaacctagt---ggcatgca---ttactgttctctcattcctttttttttcaatgcagTATACTTGTAAATAGCTTGGACTGGTCGAAACTTAGACCAAATCTCCCGTGGCTTGTAGAATCGGGAGGATGTGTTTTGCTGGATTCTTGT
upper sequence: LOC_Os01g16170.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G024733_T01 (Zea mays), 3'ss of exon 11
gtaatatatgaagttaactttatctagatttagttattatgacctgttgattgcccgtataacatatataaggtgcacgcaattttaaaatggacttttactgttatcacgtttcttgttttc-caatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTGGCTTGTAGATGCTGGAGGATGTGTTTTGCTTGATACTTTT
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--------------------------------gttatcacactgttctcccatgtcatcttctctttttgtgtgatctcgaaacctggtggaatgcattactgttttctcattgcttcttttttcaatgcagCATACTTGTAAATAGCTTGGACTGGTCGAAAGTTGGACCAAATCTCCCGTGGCTCGTAGACGCTGGAGGATGTGTTTTGCTGGATTCTTTT
upper sequence: LOC_Os01g16170.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G27330.1 (Glycine max), 3'ss of exon 13
gtaatatatgaagtta----actttatctagatttagttattatgacctgttgattgc--ccgtataacatatataaggtgcacgcaattttaaaatggacttttactgttatcacgtttcttgttttccaatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTGGCTTGTAGATGCTGGAGGATGTGTTTTGCTTGATACTTTT
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gtatcctaccagtttatattatcttctctattttaagtctcagcaccaaagtgacttttgccaactgaaattagtgacg-gtatgaaattatcaca-gtatattcaatg--aacgtttagttttccttttgatgcagTATACTTGTGATCAGCTTGGATTGGTCAAAAATCAGACCGAATTTGCCATGGCTAGTAGATGCTGGAGGGTGTGTCCTTCTTGATTTTTTT
upper sequence: LOC_Os01g16170.5 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G41050.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatatatgaagttaactttatctagatttagttattatgacctgttgattgcccgtataacatatataaggtgc-acgcaattttaaaatggacttttactgttatcacgtttcttgttttccaatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTGGCTTGTAGATGCTGGAGGATGTGTTTTGCTTGATACTTTT
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-------------------------------------------gtgaagatcaacaata-gttatactcaactctctaaataacctctggtggaaccttcttaactctcttttttgtatgttttggttgcagCATACTCGTGAACAGTGTCGAATGGTTAAAACTTGCACCGAATCTACCATGGCTTGTTGATGCAGGAGGATGTGTTGTGCTTGATTTTCTTMapped 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|29663858|gb|CB660133.1|CB660133EST: CCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATACGTTGGAAG TATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTG
genomic: CCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATACGTTGGAAGgtaatatatg ... tccaatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTG
EST:
gi|33684544|gb|CF312783.1|CF312783EST: CCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATACGTTGGAAG TATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTG
genomic: CCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATACGTTGGAAGgtaatatatg ... tccaatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgcaattttaaaatggacttttactgttatcacgtttcttgttttccaatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTGGCTTGTAGATGCTGGAGGATGTGTTTTGCTTGATACTTTT
cgtttcttgttttcc CT-rich tract
attttaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatatgaagttaactttatctagatttagttattatgacctgttgattgcccgtataacatatataaggtgcacgcaattttaaaatggacttttactgttatcacgtttcttgttttccaatgcagTATACTTGTGAAAAGCATGGATTGGTCAAAACTTAAGCCGAATCTACCGTGGCTTGTAGATGCTGGAGGATGTGTTTTGCTTGATACTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG