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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgtttagactttagttagtttcaatcaagctgccttgtgttattttcagtgctggctgataatgttgactataacctcatttttgttcttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATGGCAGTGAATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGA

Basic information

species Oryza sativa
transcript LOC_Os08g06480.1
intron # 16
splice site 3'
intron type U2

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|58606002|gb|CK034035.1|CK034035
EST:     GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGGTTCCAATGTGTCTAGTCCTATG
genomic: GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|58664660|gb|CK053346.1|CK053346
EST:     GGGCCACCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
genomic: GGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|66913224|gb|CX100072.1|CX100072
EST:     GCAGAGCATATGAGGGCTCTCGAGGGCCGCCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
genomic: GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|33675906|gb|CF304145.1|CF304145
EST:     GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
genomic: GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|29616634|gb|CB621646.1|CB621646
EST:     GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
genomic: GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|163929084|gb|EG710965.1|EG710965
EST:     GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
genomic: GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|29624933|gb|CB629944.1|CB629944
EST:     GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
genomic: GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|300216043|gb|HO088669.1|HO088669
EST:     AATT-ATACCAAG                         -CCCCAATTGTCAACACCCTTGGTTCTGTTTCC-ATGTGTCTAGTCCTATG
genomic: AATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|33675039|gb|CF303278.1|CF303278
EST:     GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
genomic: GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|33678958|gb|CF307197.1|CF307197
EST:     GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
genomic: GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
EST: gi|58610535|gb|CK038247.1|CK038247
EST:     GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAG                         CCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG
genomic: GCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATG

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: 74 (upstream exon), 75 (downstream exon)
Score: 68

AAAAATATTAGCCAACACTGATGGACAGCGTTTGCTAAGGATGCTAGAGAGCAGAGCATATGAGGGCTCTCGAGGGCCACCTCAACAAATTAATACCAAGgtattgatgc ... cttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATGGCAGTGAATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcagtgctggctgataatgttgactataacctcatttttgttcttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATGGCAGTGAATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGA
                          ctataac  putative branch site (score: 68)
                                cctcatttttgttctt  CT-rich tract
                                    atttttgttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgtttagactttagttagtttcaatcaagctgccttgtgttattttcagtgctggctgataatgttgactataacctcatttttgttcttattgtagCCCCCAATTGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATGGCAGTGAATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGA

- - - - - - - - - - - - - - - agctgcc
- - - - - - - - - - - - - - - - - - -ttgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - tgctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttga