Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaaataaaagacacatttggtcacataggaggaccgatattaggtgggcttgtgggactgaagaagccgaacaaccatggcgtaccttattctttgactgaagagtttaccagtgtttacagAATGCACTCCCTAATACCAAGCACTCTCAAGCTCAGGGATCCGACAGGGCAACCCGATGCAAATAATTCCCCACCATGCCTGGAAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g26290.6 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 8
lower sequence: AC205471.4_FGT004 (Zea mays), 3'ss of exon 4
gtaagaaaataaaagacacatttggtcacataggaggaccgatattaggtgg-gcttgtgggactgaagaagccgaacaaccatggcgtacct-tattctttgactgaagagtttaccag--tgtttacagAATGCACTCCCTAATACCAAGCACTCT-CAAGCTCAGGGATCCGACAGGGCAACCCGATGCAAATAATTCCCCACCATGCCTGGAAGA------------------------------------------------
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gtgaggatatattat-ctcattttctcatatttgttgaaagaaaacaattaacgctggtattacttttccaagtggaaattttatttacatctgcatattcaaattaattaattagtgagattgtgtacaaatt----tacctcattctaattcttttgtgaagGTATGGTTT--ATTGGGTAAGAAAATAAAAGATACATTTGGTCACATA-GGAGGACCGACATTAGGTGGGCTCGTGGGGTTGAAGAAGCCGATCAACCATGGC
upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G818450_T01 (Zea mays), 3'ss of exon 2
gtaagaaaataaaagacacatttggtcacataggaggaccgatattaggtgg-gcttgtgggactgaagaagccgaacaaccatggcgtaccttattctttgactgaagagtttaccag--tgtttacagAATGCACTCCCTAATACCAAGCACTCTCAAGCTCAGGGATCCGACAGGGCAACCCGATGCAAATAATTCCCCACCATGCCTGGAAGA------------------------------------------------
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gtgaggatatattat-ctcattttctcatatttgttgaaagaaaacaattaacgctgatattacttttccaagtggaaattttatttacatgtcatattcaaattaattaattagtgagattgtgtacaaatt----tacctcattctaattcttttgtgaagGTATGATTT-ATTGGGTAAGAAAATAAAAGATACATTTGGTCACATA-GGAGGACCGACATTAGGTGGGCTTGTGGGATTGAAGAAGCCGATCAACCATGGC
upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G100724_T01 (Zea mays), 3'ss of exon 4
gtaagaaaataaaaga---------cacatttggtcacataggaggaccgatattaggtgggcttgtgggactgaagaagccgaacaaccatggcgtaccttattctttgactgaagagtttaccagtg--tttacagAATGCACTCCCTAATACCAAGC----ACTCTCAAGCTCAGGGATCCGACAGGGCAACCCGAT-GCAAATAATTCCCCACCATGCCTGGAAGA-----------------------------
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gtgaggatatattatctcgttttctcatatttgttgaaagaaaacaattaacactggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaattagtgagattgtgtacaaatttacctcgttctaattcttttgtgaagGTATGGTTTATTGGGTAAGAAAATAAAAAGATACATTTGGTCACATAGGAGGACCGACGTTAGGTGGGCTTGTGGGATTGAAGAAGCCGATCAACCATGG
upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G312997_T01 (Zea mays), 3'ss of exon 6
gtaagaaaataaaagacacatttggtcacataggaggaccgatattaggtgg-gcttgtgggactgaagaagccgaacaaccatggcgtaccttattctttgactgaagagtttaccag---tgtttacagAATGCACTCCCTAATACCAAGCACTCTCAAGCTCAGGG---ATCCGACAGGGCAACCC--GATGCAAATAATTCCCCACCATGCCTGGAAGA----------------------------------------
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gtgaggatatattat-ctcattttctcatatttgttgaaagaaaacaattaacgctggtattacttttccaagtggaaattttatttacatctgcaaattcaaataaattaattagtgagattgtgtaca-aatttacctcatattctaattcttttgtgaagGTATGGTTTATTGGGTAAGAAAATAAAAGATACATTTGGTCACATAGGAGGACCGGCATTAGGTGGGCTTGTGGGATTGAAGAAGCCGATCAACCATGGCMapped 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|29673790|gb|CB670065.1|CB670065EST: CGCGCAAATTGGTATGGATTATTGG AATGCACTCCCTAATACCAAGCACTCTCAAGCTCAGGGATCCGACAGGGCA
genomic: CGCGCAAATTGGTATGGATTATTGGgtaagaaaat ... gtgtttacagAATGCACTCCCTAATACCAAGCACTCTCAAGCTCAGGGATCCGACAGGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaacaaccatggcgtaccttattctttgactgaagagtttaccagtgtttacagAATGCACTCCCTAATACCAAGCACTCTCAAGCTCAGGGATCCGACAGGGCAACCCGATGCAAATAATTCCCCACCATGCCTGGAAGA
ctttgac putative branch site (score: 4)
ttattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaaataaaagacacatttggtcacataggaggaccgatattaggtgggcttgtgggactgaagaagccgaacaaccatggcgtaccttattctttgactgaagagtttaccagtgtttacagAATGCACTCCCTAATACCAAGCACTCTCAAGCTCAGGGATCCGACAGGGCAACCCGATGCAAATAATTCCCCACCATGCCTGGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA