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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGTTGATAAGCTTGCAAAGTACGGAGGCTGCAAAGAATTGAAGCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatccaacttactcaataaattccttccaggcaagttcatctcgatggtgctaactcaatctttgcatgttgaatag

Basic information

species Oryza sativa
transcript LOC_Os12g06800.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G039505_T01 (Zea mays), 5'ss of exon 11
AAAGTTGATAAGCTTGCAAAGTACGGAGGCTGCAAAGAATTGAAGCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatccaacttactcaataaattccttccaggcaagttcatctcgatggtgctaactcaatctttgcatgttgaatag
||| | ||||||||| | |  || ||||||||||||||  ||||| | ||||| || || ||||||||||| ||||| ||||| |||| ||| || |||||| |  | |||||| |  || |||| | |       ||  | ||    ||  |||| | |   |     ||| || || ||
AAAATGGATAAGCTTTCGAGATATGGAGGCTGCAAAGAGCTGAAGTTAAGTTTCGTAGGTCATTCCATTGGAAACGTCATCATTAGAAGTGCCCTGGCAGgtctctttcaactttcctaacaaatactt---gaagaatctgatagatatattgctgatttttttgccccatctt-aacag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G468799_T01 (Zea mays), 5'ss of exon 11
AAAGTTGATAAGCTTGCAAAGTACGGAGGCTGCAAAGAATTGAAGCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatccaacttactcaataaattccttccaggcaagttcatctcgatggtgctaactcaatctttgcatgttgaatag
||| | ||||||||| | |  || ||||||||||||||  ||||| | |||||||| ||||||||||| |||||| | ||||| |||| ||| || |||||| |  |||||||| |  || |||| | || |||| ||  | ||    ||  |||| | |   |||   | | || || ||
AAAATGGATAAGCTTTCTAGATATGGAGGCTGCAAAGAGCTGAAGTTAAGTTTTGTCGGCCATTCCATCGGGAACATCATCATTAGAAGTGCCCTGGCAGgtctcttccaactttcctaacaaat-cttttcagg-aatctgatagatattttgctgatttt-tctccccgtctt-aacag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G163594_T01 (Zea mays), 5'ss of exon 7
-----------AAAGTTGATAAGCTTGCAAAGTA-CGGAGGCTGCAAAGAATTGAA-GCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatccaacttactcaataaattccttccaggcaagttcatctcgatggtgctaactcaatctttgcatgttgaatag------------
           |   | ||   | ||||  | |  | ||||||    |  ||  ||    |||     |     |    || || | |    |   | |    | | ||||   |  |    ||   | |  ||||| |  ||| ||  | |       | | |     || | ||  ||||   |                    
GCTTCTATTGGACCCTGGAGCTGATTGCCTAATGTCTGAGGCTAATGAAGATAAAACATCTAGAGACTTCAAAGAA---ATGGGTAGCAGGTTGGCCGGGGAGgtaattgcct-tcctgaagaagaaaatggataaact--ttctagatatggaggctgcaaagagctgaagttaagttttgtcggccattccatcgggaacatca

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G176042_T01 (Zea mays), 5'ss of exon 6
AAAGTTGATAAGCTTGCAAAGTACGGAGGCTGCAAAGAATTGAAGCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatccaacttactcaataaattccttccaggcaagttcatctcgatggtgctaactcaatctttgcatgttgaatag
||| | ||||| ||| | |  || ||||| ||||||||  ||||| | |||||||| ||||||||||| |||||| | ||||| |||| ||| || |||||| |  || ||||| |  || |||| | || |||| ||  | ||    ||  |||| | |   |||   | | || || ||
AAAATGGATAAACTTTCTAGATATGGAGGTTGCAAAGAGCTGAAGTTAAGTTTTGTCGGCCATTCCATCGGGAACATCATCATTAGAAGTGCCCTAGCAGgtctcttctaactttcctaacaaat-cttttcagg-aatctgatagatattttgctgatttt-tctccccgtctt-aacag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G127810_T02 (Zea mays), 5'ss of exon 2
AAAGTTGATAAGCTTGCAAAGTACGGAGGCTGCAAAGAATTGAAGCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatccaacttactcaataaattccttccaggcaagttcatctcgatggtgctaactcaatctttgcatgttgaatag
||| | ||||| ||| | |  || ||||||||||||||  ||||  | |||||||||||||||||||| |||||| | ||||| |||| ||| || |||||| |  || ||||| |  || |||| | || |||| ||  | ||    ||  |||| | |   |||   | | || || ||
AAAATGGATAAACTTTCTAGATATGGAGGCTGCAAAGAGCTGAAATTAAGTTTTGTTGGCCATTCCATCGGGAACATCATCATTAGAAGTGCCCTAGCAGgtctcttctaactttcctaacaaat-cttttcagg-aatctgatagatattttgctgatttt-tctccccgtctt-aacag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA08G19570.1 (Glycine max), 5'ss of exon 14
AAAGTTGATAAGCTTGCAAAGTACGGAGGCTGCAAAGAATTGAAGCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatccaacttactcaataaat------tccttccaggcaag--ttcatctcg--atggtgctaactcaatctttgcatgttgaatag---
||  | |||||   | |||     |||  ||  |||||  |||||||||| |||||||||||||| ||||||||  | ||||||||| ||||  | |||||||||  |  ||    |  |  |||      |  | |    |||   || |||| |  |  ||  |    |  | |||  || || |||     
AAGATGGATAAAGCTTCAAGAGTTGGAAACTTAAAAGATATGAAGCTTAGCTTTGTTGGCCATTCTATTGGGAATCTCATCATCAGAGCTGCTTTGGCAGgtatttacacacagttttgaagaatagagaataatactcatcaaaatttaatcttgggacagtaatgtaccttttttttaatttttaatttcag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA15G05480.1 (Glycine max), 5'ss of exon 15
AAAGTTGATAAGCTTGCAAAGTACGGAGGCTGCAAAGAATTGAAGCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtatt---atccaactt-actcaata---aattccttccaggcaagttcatctcgatggtgctaactcaatctttgcatgttgaatag---
||  | |||||   | |||     |||  ||  |||||  | |||||||| |||||||||||||| ||||||||  | ||||||||| ||||  | |||||||||   ||  |  ||    ||||    |||     |||   || |  |       |    |||       |||  || || |||     
AAGATGGATAAAGCTTCAAGAGTTGGAAACTTAAAAGATATCAAGCTTAGCTTTGTTGGCCATTCTATTGGGAATCTCATCATCAGAGCTGCTTTGGCAGgtatttacatatagttttgaacaatggagaataatacccatcaaaatctaatattgggacagtaatgtgccttttttatttttaatttcag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G09980.1 (Arabidopsis thaliana), 5'ss of exon 12
AAAGTTGATAAGCTTGCAAAGTACGGAGGCTGCAAAGAATTGAAGCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatcc--aacttactcaataaattccttccagg-----caagttcatctcgatggtgctaact-----caatctttgcatgttgaatag
|||   ||||| | ||| |  |||||  |||  ||| |  | ||||| ||||||||||| ||||| ||||| ||||| ||||||||| ||||| | || |||||  ||    | |  ||||   |||   |   | |      || |   | | | || |  | | |     | |  | || || |     ||
AAAAAGGATAAACATGCGAGATACGGGCGCTTGAAAAACATCAAGCTGAGTTTTGTTGGACATTCAATTGGTAACGTCATCATCAGAGCTGCAATAGCTGgtatgttcttagaatctctcagacaatgtttaaaacggttcgtaaatcggttttggtgttaatcattattcccgacttatgtatttgttgcag

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|58660828|gb|CK049508.1|CK049508
EST:     TTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAG                         AACCCGCATTACAACCATACTTGA
genomic: TTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatcca ... tgttgaatagAACCCGCATTACAACCATACTTGA
EST: gi|58605583|gb|CK033616.1|CK033616
EST:     TTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAG                         AACCCGCATTACAACCATACTTGA
genomic: TTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatcca ... tgttgaatagAACCCGCATTACAACCATACTTGA
EST: gi|33676097|gb|CF304336.1|CF304336
EST:     TTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAG                         AACCCGCATTACAACCATACTTGAAGACACCTGTACACGTACATGTCAATA
genomic: TTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatcca ... tgttgaatagAACCCGCATTACAACCATACTTGAAGA-ACCTGTACACGTACATGTCAATA
EST: gi|33381178|gb|CF196521.1|CF196521
EST:     TTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAG                         AACCCGCATTACAACCATACTTGAAGAACCTGTACACGTACATGTCAATAT
genomic: TTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatcca ... tgttgaatagAACCCGCATTACAACCATACTTGAAGAACCTGTACACGTACATGTCAATAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 44 (upstream exon), 70 (downstream exon)
Score: 9

AAAGTTGATAAGCTTGCAAAGTACGGAGGCTGCAAAGAATTGAAGCTTAGTTTTGTTGGCCATTCCATTGGGAACGTTATCATCAGAACTGCACTTGCAGgtattatcca ... tgttgaatagAACCCGCATTACAACCATACTTGAAGAACCTGTACACGTACATGTCAATATCAGGCCCACACTTGGGCTACTGGTACAGCTCAAACTCTTTATTCAACTC




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