Sequence
atgc intronic sequence ATGC exonic sequencegtataaaaagattcaacctttacctgctcctaccatttggacgccctgtttgcctgatgttcaatgttgcttgctagagctgtaagttttgatggatgttggtttggtgttcgtcagGTGCAAGGATGCTGCAGCACTCCAACAGCGCGAACGAGCTAATGCTGCGGCGGAAGCTCGAGGAGCAGCAACAGGCGGCGGAGCTGCAGCAGGCTATTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g21160.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g21160.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G003424_T01 (Zea mays), 3'ss of exon 4
gtataaaaagattcaacctttacctgctcctaccatttggacgccc-tgtttgcctgatgttcaatgttgcttgctagagctgtaagttttgatggatgttggtttggtgttcgtcagGTGCAAGGATGCTGCAGCACTCCAACAGCGCGAACGAGCTAATGCTGCGGCGGAAGCTCGAGGAGCAGCAACAGGCGGCGGAGCTGCAGCAGGCTATTGA
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gtaaaagaagacccc-caacgatgttctcttcatctttggttggttgtgttctcccg----tcgctgatacctg-----ggtatggtttt-----ggttttgttgtggtgattgtcagGCGCGAGGATGCTGCAACATTCGAACAGCGCCAACGAGCTGCTGTTGCGCCGGAAGCTGGAGGAGCAGCAGCAGGCTGCCGAACTGCAGCACGCCATTGA
upper sequence: LOC_Os03g21160.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 5
gtataaaaagattcaacctttacctgctcctaccatttggacgccc-tgtttgcctgatgttcaatgttgcttgctagagctgtaagttttgatggatgttggtttggtgttcgtcagGTGCAAGGATGCTGCAGCACTCCAACAGCGCGAACGAGCTAATGCTGCGGCGGAAGCTCGAGGAGCAGCAACAGGCGGCGGAGCTGCAGCAGGCTATTGA
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gtaaaagaagacccc-caacgatgttctcttcatccttggttggttgtgttctccag----tcgctgatacctg-----gctatggtttt-----ggttttgttgtggtgattgtcagGCGCGAGGATGCTGCAGCATTCGAACAGCGCCAACGAGCTGCTCTTGCGCCGGAAGCTGGAGGAGCAGCAGCAGGCTGCCGAACTTCAGCACGCCATTGA
upper sequence: LOC_Os03g21160.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G819035_T02 (Zea mays), 3'ss of exon 4
gtataaaaagattcaacctttacctgctcctaccatttggacgccc-tgtttgcctgatgttcaatgttgcttgctagagctgtaagttttgatggatgttggtttggtgttcgtcagGTGCAAGGATGCTGCAGCACTCCAACAGCGCGAACGAGCTAATGCTGCGGCGGAAGCTCGAGGAGCAGCAACAGGCGGCGGAGCTGCAGCAGGCTATTGA-----------------
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---------------------atgttctcttcatccttggttggttgtgttctccag----tcgctgatacctg-----gctatggtttt-----ggttttgttgtggtgattgtcaggcgcgaggatgctgcagCATTCGAACAGCGCCAACGAGCTGCTCTTGCGCCGGAAGCTGGAGGAGCAGCAGCAGGCTGCCGAACTTCAGCACGCCATTGAGCTCCAGAGCCGCCGCC
upper sequence: LOC_Os03g21160.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 4
gtataaaaagattcaacctttacctgctcctaccatttggacgccctgtttgcctgatgttcaatgttgcttgctagagctgtaagttttgatggatgttggtttggtgttcgtcagGTGCAAGGATGCTGCAGCACTCCAACAGCGCGAACGAGCTAATGCTGCGGCGGAAGCTCGAGGAGCAGCAACAGGCGGCGGAGCTGCAGCAGGCTATTGA--
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--gtaaaaggacc---ccccagcgatgtcctctctccttgat-ctttggttggttg-tgttggcgaacttgggccagtcgttgatgcctgtgtggtttttgttgtggtgatcgtcagGCGGCAGGATGCTGCAGCACTCGAGCAGCGCCAACGAGCTGCTCCTACGCCGAAAGCTGGAGGAACAGCAGCAGGCCATTGAGCTCCAG--AGCCGTCGCCTMapped 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|163928946|gb|EG711958.1|EG711958EST: GTCGCCCACGGGGTTAGACGCCAGGGACCCCTTTGATTTTCACCAGCTCG GTGCAAGGATGCTGCAGCACTCCAACAGCGCGAACGAGCTAATG
genomic: GTCGCCCACGGGGTTAGACGCCAGGGACCCCTTTGATTTTCACCAGCTCGgtataaaaag ... tgttcgtcagGTGCAAGGATGCTGCAGCACTCCAACAGCGCGAACGAGCTAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgttgcttgctagagctgtaagttttgatggatgttggtttggtgttcgtcagGTGCAAGGATGCTGCAGCACTCCAACAGCGCGAACGAGCTAATGCTGCGGCGGAAGCTCGAGGAGCAGCAACAGGCGGCGGAGCTGCAGCAGGCTATTGA
ttttgat putative branch site (score: 4)
taagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaaaagattcaacctttacctgctcctaccatttggacgccctgtttgcctgatgttcaatgttgcttgctagagctgtaagttttgatggatgttggtttggtgttcgtcagGTGCAAGGATGCTGCAGCACTCCAACAGCGCGAACGAGCTAATGCTGCGGCGGAAGCTCGAGGAGCAGCAACAGGCGGCGGAGCTGCAGCAGGCTATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG