Sequence
atgc intronic sequence ATGC exonic sequenceCACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtggactgtttcctagttctcattgtttgctattcaagtgctctctacgaaagaaacaact...
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.2 |
intron # | 8 |
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 8
lower sequence: GRMZM2G000645_T02 (Zea mays), 5'ss of exon 8
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtggactgtttcctagttc-tcattgtttgctattcaagtgctctctacgaaagaaacaact
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CACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTACTGGATCTGAAGATGGTACAGTTCGTATATGGCATTCGACAACTTACAGgtaacatgtttttatttatctctatgtttgcttgtttatgtaagcagaggtccgttcaatttttctttacaatttggccattatcaattctccatcctga-
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 7
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgt----tgctttcacagt-ttcacttgtgtttttgcttgttgatgtggactg---tttcctagttctcattgtttgctattcaagtgctctctacgaaagaaacaact
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CACATAACATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTACTGGATCCGAAGATGGTACAGTTCGTATATGGCATTCAACAACTTACAGgtaacatgctttttttttgtttatctctatgtttgcttgtttatgtaagtagaagtctgtcagttttcatcgtt-acaatttg---gccatttatcaattctct----
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G419984_T01 (Zea mays), 5'ss of exon 7
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtggactgtttcctagttc-tcattgtttgctattcaagtgctctctacgaaagaaacaact
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-----------------------------------CTCCCTATAATCATTACTGGATCTGAAGATGGTACAGTTCGTATATGGCATTCGACAACTTACAGgtaacatgtttttatttatctctatgtttgcttgtttatgtaagcagaggtctattcaatttttctttacaatttggccattatcaattctccatcctga-
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 8
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtggactgtttcctagttctcattgtttgctattcaagtgctctc-tacgaaagaaacaact-
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CACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGAACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttat--gttgctcacagattattgagttgagagttttattttttcatatttaatttggtgcattgctcttgtctttttgtctcaatgtcatcactc
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 8
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtggactgtttcctagttctcattgtttgctattcaagtgctctc-tacgaaagaaacaact-
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CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTACTGGCTCTGAGGATGGCACAGTGCGCATTTGGCATTCAACAACTTATAGgtaattttat--gttgttcacagattactgagttgagagctttattttttcttatctaatttggtgcattgctcttgcctttttgtctcaatgtcatcactc
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 8
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgt--gtttttgcttgttgatgtggactgtttcctagttctcattgtttgctattcaagtgctctctacgaaagaaacaact-
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CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTACTGGTTCTGAGGATGGCACAGTACGCATATGGCACTCCACAACTTATAGgtaatgtgaaatgcacagattgctgagttatgagggttaacattatgcctattctatttggcat---atgccgctagcttttcttctcccatcatcatcactc
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 8
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgt--gtttttgcttgttgatgtggactgtttcctagttctcattgtttgctattcaagtgctctctacgaaagaaacaact-
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CACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTACTGGTTCTGAGGATGGCACAGTACGCATATGGCACTCCACAACTTATAGgtaatgtgaagtgcacagattactgagttatgaggtttaacattacgcttattctatttggcatatgcctctacct---tttcttctcccatcatcatcactc
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 12
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcaca--gtttcacttg----tgtttttg--cttgttgatgtggactgtttcctagttctcattgtttgctattcaagtgctctctacgaaagaaacaact-----
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CACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTACAGGATCCGAGGATGGAACTGTTCGCATATGGCACGCCACCACTTACAGgtaactcgtatgctgtctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctag
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 8
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtggactgtttcctagttctcattgtttgctat--tcaagtgctctctacgaaagaaacaact-------------------------------------------------------------------------------------
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CACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCACAGGTTCTGAAGATGGCACCGTTCGCATTTGGCATGCAACCACATACAGgt----attataatattaaaca-gtttttttttgttgg-acatattatagta-aacgcttcttgtatgccttggctaaaccatctccactttggcttcattcttgtgcactttttcaccattaccaatttcttttattgtccttccatttgtaatcccaatttcctaatgtctgttttttcttgcag
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 8
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtgg-actgtttcctagttctca--ttgtttgctattcaagtgctctcta--cgaaagaaacaact----------------------------------------------------------------------------------
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CACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCACAGGTTCTGAGGATGGCACTGTTCGCATTTGGCACGCCACTACCTACAGgt-atttttac---ctaac--gttttcctgtcaaaagacataacaatgcttacattttttggggttttttaacacttgaatacactttgttcacatgcggttatttcttgtattcattttcaccataggttcgctttctctattttgtcgtttgatttgttatcttcgattctctttctcttttcag
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 8
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtgg-actgtttcctagttctcattgtttgctattcaagtgctctctacgaaagaaacaact-------
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CACACAATGTTTCTTCAGTCTGTTTCCATCCAGAGCTTCCTATTATTTTTACTGGTTCAGAAGATGGGACTGTTAGAATATGGCATGCAACCACTTATAGgtaagttctatg--tccagatgcagtgatatatattgaagttatgcgatatggaagttcttgg-atttgaagctc-----ctgaccagcaaaggtttttttttttcct
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 8
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtggac-tgtttc-ctagttctcattgtttgctattcaagtgctctctacgaaagaaacaact-
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CACACAATGTTTCTGCAGTCTGCTTCCATCCTGAACTTCCCATAATAATAACAGGTTCTGAGGATGGGACTGTTCGAATATGGCATGCTACCACTTATAGgtaagctccata---tcatatgcaattttctaatatgaagttcacatgttaaactaaccttgacatcctgctgtttcttttttatttatttttgggctttcaaMapped 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|58609972|gb|CK038005.1|CK038005EST: ACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAG ACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATA
genomic: ACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttca ... tattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttcacagtttcacttgtgtttttgcttgttgatgtggactgtttcctagttctcattgtttgctattcaagtgctctctacgaaagaaacaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa