Sequence
atgc intronic sequence ATGC exonic sequencegtgagctctaatatgacaagtgacaatataatttgatctcttttcttatctttttccaccattgtttatttttccgcttttcattttaacaagagtaattcaacttaaaagcttgacctaatcaataaattatttgaatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATGGTCGCAGATTGTAATGAGGAAATTACTTCCACGACACATGGAAATTATC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g63270.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 7
gtgagctctaatatgacaagtgacaatataatttgatctcttttcttatctttttccaccattgtttatttttccgcttttcattttaacaagagtaattcaacttaaaagcttgacctaatcaataaattat-ttgaatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATGGTCGCAGATTGTAATGAGGAAATTACTTCCACGACACATGGAAATTATC
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---------------gtgaggttcaattta-tataat-tgatctatagtttttttcgaccagtattttaagctcca----tcaaact--ctagagatgttc-----------ttgaattaattacaaaattatcttccgtggtccagGACAATTTCCTACACCAATCATACAGTTCTCCCCGAAGCTCTTGAAAAATGGTCACAAATTGTGATGAGGAAATTACTTCCCCGACACATGGAAATTATT
upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 7
gtgagctctaatatgacaagtgacaatataatttgatctcttttcttatctttttccaccattgtttatttttccgcttttcattttaacaag--agtaattcaacttaaaagcttgacctaatcaataaattatttgaatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATGGTCGCAGATTGTAATGAGGAAATTACTTCCACGACACATGGAAATTATC
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--------------gtcagtaaattgtagataatgtttttaggaatggttattttccatt-ttctttgttccaccacccctcacagttgtagtgtattattacacctcattaacttgccactaaaacatgatgctacatcttaaccagGACTATTGCTTACACTAATCATACTGTCCTCCCTGAAGCACTAGAGAAATGGTCTCAACCTGTAATGTGGAAACTGCTTCCACGCCATATGGAAATCATA
upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 8
gtgagctctaatatgacaagtgacaatataatttgatctcttttcttatctttttccaccattgtttatttttccgcttttcattttaacaagagtaattcaacttaaaagcttgacctaatcaataaattatttgaatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATGGTCGCAGATTGTAATGAGGAAATTACTTCCACGACACATGGAAATTATC
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--------------gtcagttaattgtagaaaatgttgttagcaatgattattttccatt-ttctttattccaccacccctcac---aattgtagtg-tattactcattacctcatcactaaaacatgatgctatatcttaaccagGACTATTGCGTACACTAATCATACTGTCCTCCCTGAAGCACTGGAGAAATGGTCTCAACCTGTAATGTGGAAACTACTTCCACGCCATATGGAAATCATA
upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgagctctaatatgacaagtgacaatataatttgatctcttttcttatctttttccaccattgtttatttttccgcttttcattttaacaagagtaattcaacttaaaagcttgacctaatcaataaattatttgaatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATGGTCGCAGATTGTAATGAGGAAATTACTTCCACGACACATGGAAATTATC
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--------------------------------------------------------gtaaaatatttatgcatgaacctttcaatatttcccaacaaagt---tttcacacttttctgttgggacttatttatatggtt--tacagGACCGTTGCTTACACCAATCACACTGTCCTTCCTGAAGCGTTGGAGAAATGGTCACAATCTTTGATGTGGAAGCTTCTTCCTCGTCATATGGAAATAATA
upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 7
gtgagctctaatatgacaagtgacaatataatttgatctcttttcttatctttttccaccattgtttatttttccgcttttcattttaacaagagtaattcaacttaaaagcttgacctaatcaataaattatttgaatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATGGTCGCAGATTGTAATGAGGAAATTACTTCCACGACACATGGAAATTATC
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-----gttcactatgttttttg----tttgatagaacactcgctcatgggttttccagcatgaccttctttgtctgttgctttttcttatgt---taatacaactttatggc--------aaaaata------ttgaat----cagAACAATTGCCTATACAAATCACACTGTCCTTCCTGAAGCACTTGAGAAATGGTCACAAGTTGTAATGTGGAAGCTTCTTCCACGCCATATGGAAATCATAMapped 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|29635801|gb|CB640810.1|CB640810EST: ATGGATGTGGAGGGACTTGGTTGGGATGAAGCATGGGATATCACAAATAA AACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATG
genomic: ATGGATGTGGAGGGACTTGGTTGGGATGAAGCATGGGATATCACAAATAAgtgagctcta ... aatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATG
EST:
gi|58688682|gb|CK077369.1|CK077369EST: ATGGATGTGGAGGGACTTGGTTGGGATGAAGCATGGGATATCACAAATAA AACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATG
genomic: ATGGATGTGGAGGGACTTGGTTGGGATGAAGCATGGGATATCACAAATAAgtgagctcta ... aatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATG
EST:
gi|29635744|gb|CB640753.1|CB640753EST: ATGGATGTGGAGGGACTTGGNTGGGATGAAGCATGGGATATNACAAATAA AACAATTGCCTACACCAATCACACT
genomic: ATGGATGTGGAGGGACTTGGTTGGGATGAAGCATGGGATATCACAAATAAgtgagctcta ... aatggtccagAACAATTGCCTACACCAATCACACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagtaattcaacttaaaagcttgacctaatcaataaattatttgaatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATGGTCGCAGATTGTAATGAGGAAATTACTTCCACGACACATGGAAATTATC
acctaat putative branch site (score: 3)
taatcaataaattatt 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 |
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gtgagctctaatatgacaagtgacaatataatttgatctcttttcttatctttttccaccattgtttatttttccgcttttcattttaacaagagtaattcaacttaaaagcttgacctaatcaataaattatttgaatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATGGTCGCAGATTGTAATGAGGAAATTACTTCCACGACACATGGAAATTATC
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