Sequence
atgc intronic sequence ATGC exonic sequenceGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGAAGTTGCAAAGgtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctgaaaggtcttccatgctgtgaagttcattgctaataaacagaatggattctggacattttctgtgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.4 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 17
GGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGAAGTTGCAAAGgtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctgaaaggtcttccatgctgtgaagttcattgctaataaacagaatggattctggacattttctgtgcag
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GGAATCTAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACGGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAATTAGATGTTGCAAAGgtactgattatattgtcactgattttctttctccaaatatcatagactattttg--aggtattgtatactgcattgctacaaaattacaaa-gtaacatactc------------------
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G086015_T01 (Zea mays), 5'ss of exon 3
GGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGAAGTTGCAAAGgtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctga---aaggtcttccatgctgtgaagttcattgctaataaacaga------atggattct---ggacattttctgtgcag
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GGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAATTAGATGTCGCGAAGgtactggttatattgtcattaattttcttctaataccgtgga--ctatattttgagttattgtatactgcattactggaaaaaatactaagtaacatatattatatgacctctcatgactatttactgtacag
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G448913_T01 (Zea mays), 5'ss of exon 7
GGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGAAGTTGCAAAGgtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctga---aaggtcttccatgctgtgaagttcattgctaataaacaga------atggattct---ggacattttctgtgcag
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GGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAATTAGAAGTCGCGAAGgtactggttatattgtcattaattttcttctaataccgtgga--ctatattttgagttattgtatactgcattactggaaaaaatactaagtaacatatattatatgacctctcatgactatttactgtacag
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 18
GGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGAAGTTGCAAAGgtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctga---aaggtcttccatgctgtgaagttcattgctaataaacaga------atggattct---ggacattttctgtgcag
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GGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAATTAGAAGTCGCGAAGgtactggttatattgtcattaattttcttctaatgctgtgga--ctatattttgagttattgtatactgcattactgaaaaaattactaagtaacatatattatatgacctctcatgactatttactgtacagMapped 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|2443004|gb|C74775.1|C74775EST: ATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGATGTTGCAAAG GCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTNGGTGAA
genomic: ATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGAAGTTGCAAAGgtacagaaca ... ttctgtgcagGCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGAAGTTGCAAAGgtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctgaaaggtcttccatgctgtgaagttcattgctaataaacagaatggattctggacattttctgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG