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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcacactaataccttgtgacacaatagaggaaagaagggttcaagaatcttatgttcttcctcctctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCATTTTTCAACAAAACGAAGACAAGCTCCAGTTCTTCTATGATGGACAAGGG

Basic information

species Oryza sativa
transcript LOC_Os10g02750.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g02750.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AC202435.3_FGT003 (Zea mays), 3'ss of exon 11
--gtgagcacactaataccttgtgacacaatagaggaa-----agaagggttcaag-------aatcttatgttcttcctcctctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCATTTTTCAACAAAACGAAGACAAGCTCCAGTTCTTCTATGATGGACAAGGG
     |||||  ||  |    | ||   | |  || ||     ||   | ||| ||       || ||| ||   || || ||   |||| |||||| | ||||| ||||| || |||||||| || ||||||||||||||  | || || | |||| | |||||||||| ||||||||| || || ||||||
gtacaagcaccatacgatacagagatgaattcaagtaactttcagtccgtttccagcctactgaaccttgtgaaattgcttcttcttttttagTCCACTCCAGTATTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGTCTTCCATCCAAACAAGGACAAGCTCCGGTTCTTCTACGACGGGCAAGGG

upper sequence: LOC_Os10g02750.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G351232_T02 (Zea mays), 3'ss of exon 4
--gtgagcacactaataccttgtgacacaatagaggaa-----agaagggttcaa-------gaatcttatgttcttcctcctctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCATTTTTCAACAAAACGAAGACAAGCTCCAGTTCTTCTATGATGGACAAGGG
     |||||  ||  |    | ||   | |  || ||     ||   | ||| |       ||| ||| ||   || || ||    |||||| ||| | ||||| ||||| || |||||||| || ||||||||||||||  | || || | |||| | |||||||||| ||||||||| || || ||||||
gtacaagcaccatatgatacagagattaattcaagtaacttttagtccgtttccaacctactgaaccttgtgaaattgcttcttctgtttcagCCCACTCCAGTATTTCACGAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGTCTTCCATCCAAACAAGGACAAGCTCCGGTTCTTCTACGACGGGCAAGGG

upper sequence: LOC_Os10g02750.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G01880.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------gtgagcacactaataccttgtgacacaatagaggaaagaagggttcaagaatcttatgttcttcctcctctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCATTTTTCAACAAAACGA---AGACAAGCTCCAGTTCTTCTATGATGGACAAGGG
                                      |     | ||| ||  |||| | |   |   | ||  |||      | ||  | |  |   |  |        |  |||  ||  || |   | || |||||||| ||||||||||||||||||||   | |||| | |   ||   | |  | ||| |  | |  || |||||||||   
gtaaaattataagtacttatttgttgagtttaaaatgtttctttctctattaagttgttatattttgttgaaagaaag------aaaacttaacatatattttggaaatggtgaagTAAAACCCAATTTCTTACAAGTGGAGGAGGATCAAAGGCATGGAGAGGACATGTTCAGCCATGGGATCCAAAAGAACTCAAACTGTATTACGATGGACAA---

Mapped 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|88503456|gb|CI430962.1|CI430962
EST:     ACATCAATGGGGCATGATCACTGCCTGGAGCACATCAGCAGCAGAAACAG                         TCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
genomic: ACATCAAT-GGGCATGATCACTGCCTGGAGCACATCAGCAGCAGAAACAGgtgagcacac ... ctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
EST: gi|88505369|gb|CI432875.1|CI432875
EST:     TACATCAATGGGCATGATCACTGCCTGGAGCACATCAGCAGCAGAAACAG                         TCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
genomic: TACATCAATGGGCATGATCACTGCCTGGAGCACATCAGCAGCAGAAACAGgtgagcacac ... ctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
EST: gi|88222938|gb|CI220684.1|CI220684
EST:     TACATCAATGGGCATGATCACTGCCTGGAGCACATCAGCAGCAGAAACAG                         TCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
genomic: TACATCAATGGGCATGATCACTGCCTGGAGCACATCAGCAGCAGAAACAGgtgagcacac ... ctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
EST: gi|88512849|gb|CI440355.1|CI440355
EST:     CAATGGGCATGATCACTGCCTGGAGCACATCAGCAGCAGAAACAG                         TCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
genomic: CAATGGGCATGATCACTGCCTGGAGCACATCAGCAGCAGAAACAGgtgagcacac ... ctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
EST: gi|88486772|gb|CI424043.1|CI424043
EST:     CTGGAGCACATCAGCAGCAGAAACAG                         TCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
genomic: CTGGAGCACATCAGCAGCAGAAACAGgtgagcacac ... ctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
EST: gi|88481764|gb|CI419035.1|CI419035
EST:     GCAGCAGAAACAG                         TCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT
genomic: GCAGCAGAAACAGgtgagcacac ... ctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatagaggaaagaagggttcaagaatcttatgttcttcctcctctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCATTTTTCAACAAAACGAAGACAAGCTCCAGTTCTTCTATGATGGACAAGGG
                           tcttatgttcttcctc  CT-rich tract
                         aatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcacactaataccttgtgacacaatagaggaaagaagggttcaagaatcttatgttcttcctcctctcttttcagTCCAATTCAGTACTTCACTAGTGGAGGCGGATCAAAGGCATGGAGAGGCATTTTTCAACAAAACGAAGACAAGCTCCAGTTCTTCTATGATGGACAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA