Sequence
atgc intronic sequence ATGC exonic sequencegtaatgcatcttcaaccaaagaagttctactcgtttggatttctgagagacaaattgatagtcttgttctgctttgatagGTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCTTCAATTTTGGAGTTGCTTTTGCGCCTTCGGCAGTGTTGTGACCACCCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32570.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32570.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G057504_T01 (Zea mays), 3'ss of exon 2
gtaatgcatcttcaaccaaagaagttctactcgtttggatttctgagagacaaattgatagtcttgttctgctttgatagGTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCTTCAATTTTGGAGTTGCTTTTGCGCCTTCGGCAGTGTTGTGACCACCCAT
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gtaatgcg-cttctactgataag--cgtattc-------tttcagggaaacaaattaattgccttgtgttgatt--atagGTAAAATTTGATCAATTTGTTGAGCAAGGAAGGGTTCTGCACAACTATGCTTCAATTTTGGAGTTACTTTTGCGCCTAAGGCAATGCTGTGATCATCCAT
upper sequence: LOC_Os02g32570.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 14
-------------gtaatgcatcttcaaccaaagaagttctactcgtttggattt--ctgagagacaa-----attgat---agtc-ttgttctgctttg-atagGTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCTTCAATTTTGGAGTTGCTTTTGCGCCTTCGGCAGTGTTGTGACCACCCAT
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gtattctgagtttctaatctaaatttaatattttcagtttttcaccttattttttggcaatgaaacaagtcacattgatccaactcattgatgaaatttatgcagGTAAAATTTGACCAGTTTGTTGAGCAAGGGCGTGTTCTTCATAATTATGCTTCAATATTGGAGTTACTTTTACGTCTTCGGCAATGTTGTGATCATCCAT
upper sequence: LOC_Os02g32570.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA17G05390.1 (Glycine max), 3'ss of exon 13
-------------gtaatgcatcttcaaccaaagaagttctactcgtttggattt----ctgagaga---caaattgat---agtc-ttgttctgctttg-atagGTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCTTCAATTTTGGAGTTGCTTTTGCGCCTTCGGCAGTGTTGTGACCACCCAT
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gtattctgagtttctaatctaaatttaatattttcagtttttcaccttattttttggcactgaaacaaaccacattgatccaactcgttgatgaaatttatgcagGTAAAATTTGACCAGTTTGTTGAGCAAGGGCGTGTTCTTCATAATTATGCTTCAATATTGGAGTTACTTTTACGTCTTCGGCAATGTTGTGATCATCCAT
upper sequence: LOC_Os02g32570.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 3'ss of exon 13
gtaatgcatcttc-aaccaaagaagttctactcgtttggatttctgagagacaaat-tgatagtcttgttctgctttgat-------------agGTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCTTCAATTTTGGAGTTGCTTTTGCGCCTTCGGCAGTGTTGTGACCACCCAT
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-----gtattccctgacttaaatgattgta-ttgactgcatttttctgattttagtatgacaccttttctttaatttgattgaaacattcttcagGTGAAGTTTGATCAATTTGTTGAGCAAGGACGGGTTCTTCATAATTATGCTTCTATTTTGGAGTTGCTTTTATGTCTTCGCCAATGTTGTGATCATCCATMapped 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|66917088|gb|CX103936.1|CX103936EST: TGTCAGAGACTGAGAAGGATTTCTATGATGCTCTGTTTCGACGATCTAAG GTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCT
genomic: TGTCAGAGACTGAGAAGGATTTCTATGATGCTCTGTTTCGACGATCTAAGgtaatgcatc ... gctttgatagGTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctactcgtttggatttctgagagacaaattgatagtcttgttctgctttgatagGTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCTTCAATTTTGGAGTTGCTTTTGCGCCTTCGGCAGTGTTGTGACCACCCAT
aattgat putative branch site (score: 4)
tcttgttctgcttt putative PPT
aaattgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgcatcttcaaccaaagaagttctactcgtttggatttctgagagacaaattgatagtcttgttctgctttgatagGTGAAATTTGATCAATTCGTGGAACAAGGAAGGGTCTTGCACAATTATGCTTCAATTTTGGAGTTGCTTTTGCGCCTTCGGCAGTGTTGTGACCACCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG