Sequence
atgc intronic sequence ATGC exonic sequencegtatggtgaggaacttttgtacaagcatttggatagttattcgtggctgccaatgattacatgggctggttgtaacatatacttattttgttttactagtgactatgcctgttgattgccttatgtacttgtcaatttaatgtaaaccacaaaatttctttgttctttgcagTATATGATATGTGAAGCATCAAATAAGTCATCGCAACTTGTTGATTTCCTTGTGCAGAACAATGGAAAGAAAATAATGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g07080.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G367714_T01 (Zea mays), 3'ss of exon 5
gtatggtgaggaacttttgtacaagcatttggatagttattcgtggctgccaatgattacatgggctggttgtaacatatacttattttgttttactagtgactatgcctgttgattgccttatgtacttgtcaatttaatgtaaaccacaaaatttctttgttctttgcagTATATGATATGTGAAGCATCAAATAAGTCATCGCAACTTGTTGATTTCCTTGTGCAGAACAATGGAAAGAAAATAATGGT
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--------------------------------------------------------------------gtt-caatcaatatacttcttgtttttattatgattgtgttc--tgattttcttgaattctagctgttccctacaaaatcataaccttgttttggt----gcagTATATGGTATGTGAAGCATCAAAGAAGTCATCTCAGCTTGCTGATTTCCTTGTGCAGAATAGTGGGAAGAAAATAATGGT
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G125947_T01 (Zea mays), 3'ss of exon 3
gtatggtgaggaacttttgtacaagcatttggatagttattcgtggctgccaatgattacatgggctggttgtaacatatacttattttgttttactagtgactatgcctgttgattgccttatgtacttgtcaatttaatgtaaaccacaaaatttctttgttctttgcagTATATGATATGTGAAGCATCAAATAAGTCATCGCAACTTGTTGATTTCCTTGTGCAGAACAATGGAAAGAAAATAATGGT
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--------------------------------------------------------------------gtt-caatcaatatacttcttgtttttattatgattgtgtta--tgattttcttgaattctagctgttctctacaaaatcataaccttgttttggt----gtagTATATGATATGCGAAGCATCAAATAAGTCATCTCAGCTTGTTGATTTCCTTGTGCAGAATAGTGGGAAGAAAATAATGGT
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G303752_T03 (Zea mays), 3'ss of exon 3
gtatggtgaggaacttttgtacaagcatttggatagttattcgtggctgccaatgattacatgggctggttgtaacatatacttattttgttttactagtgactatgcctgttgattgccttatgtacttgtcaatttaatgtaaaccacaaaatttctttgttctttgcagTATATGATATGTGAAGCATCAAATAAGTCATCGCAACTTGTTGATTTCCTTGTGCAGAACAATGGAAAGAAAATAATGGT
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--------------------------------------------------------------------gtt-caatcaatatacttcttgttttatta-tgattgtgatc--tgattttcttgaattctagctgttccctacaaaatcataaccttgttttggt----gcagTATATGATATGTGAAGCATCAAAGAAGTCATCTCAGCTTGTTGATTTCCTTGTGCAGAATAGTGGGAAGAAAATAATGGTMapped 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|29639070|gb|CB644079.1|CB644079EST: CTCAACAAGAGCTTGGTCCATCCAAAACACCGTTGGGTCTTCGATTGGAG TATATGATATGTGAAGCATCANATAAGTCATCGCA
genomic: CTCAACAAGAGCTTGGTCCATCCAAAACACCGTTGGGTCTTCGATTGGAGgtatggtgag ... ttctttgcagTATATGATATGTGAAGCATCAAATAAGTCATCGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccttatgtacttgtcaatttaatgtaaaccacaaaatttctttgttctttgcagTATATGATATGTGAAGCATCAAATAAGTCATCGCAACTTGTTGATTTCCTTGTGCAGAACAATGGAAAGAAAATAATGGT
atttaat putative branch site (score: 4)
tttctttgttctttgc putative PPT
tcaatttaatgtaaa 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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gtatggtgaggaacttttgtacaagcatttggatagttattcgtggctgccaatgattacatgggctggttgtaacatatacttattttgttttactagtgactatgcctgttgattgccttatgtacttgtcaatttaatgtaaaccacaaaatttctttgttctttgcagTATATGATATGTGAAGCATCAAATAAGTCATCGCAACTTGTTGATTTCCTTGTGCAGAACAATGGAAAGAAAATAATGGT
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